Starting phenix.real_space_refine on Mon May 4 22:41:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tqd_56135/05_2026/9tqd_56135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tqd_56135/05_2026/9tqd_56135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tqd_56135/05_2026/9tqd_56135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tqd_56135/05_2026/9tqd_56135.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tqd_56135/05_2026/9tqd_56135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tqd_56135/05_2026/9tqd_56135.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 16 9.91 5 Fe 4 7.16 5 S 225 5.16 5 C 14867 2.51 5 N 4284 2.21 5 O 4627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 24023 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 6444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6444 Classifications: {'peptide': 851} Link IDs: {'PTRANS': 24, 'TRANS': 826} Chain breaks: 1 Chain: "B" Number of atoms: 7214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7214 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 26, 'TRANS': 926} Chain breaks: 1 Chain: "C" Number of atoms: 5591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5591 Classifications: {'peptide': 737} Link IDs: {'PTRANS': 23, 'TRANS': 713} Chain breaks: 1 Chain: "D" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1057 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "E" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1112 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 7, 'TRANS': 137} Chain: "F" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1045 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "G" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1112 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 7, 'TRANS': 137} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 62 Unusual residues: {' CA': 6, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 47 Unusual residues: {' CA': 5, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 19 Unusual residues: {' CA': 5, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 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: "G" 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: 5.45, per 1000 atoms: 0.23 Number of scatterers: 24023 At special positions: 0 Unit cell: (133.12, 152.256, 175.552, 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 4 26.01 Ca 16 19.99 S 225 16.00 O 4627 8.00 N 4284 7.00 C 14867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=93, 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=2.02 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=2.02 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 567 " distance=2.04 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 682 " 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 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 808 " distance=2.03 Simple disulfide: pdb=" SG CYS A 757 " - pdb=" SG CYS A 818 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 869 " distance=2.03 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 60 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 202 " distance=2.03 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=2.02 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 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 547 " - pdb=" SG CYS C 557 " distance=2.02 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 626 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 682 " distance=2.03 Simple disulfide: pdb=" SG CYS C 652 " - pdb=" SG CYS C 662 " distance=2.03 Simple disulfide: pdb=" SG CYS C 728 " - pdb=" SG CYS C 762 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 808 " distance=2.03 Simple disulfide: pdb=" SG CYS C 757 " - pdb=" SG CYS C 818 " distance=2.03 Simple disulfide: pdb=" SG CYS C 788 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 835 " - pdb=" SG CYS C 869 " distance=2.03 Simple disulfide: pdb=" SG CYS C 864 " - pdb=" SG CYS C 925 " distance=2.03 Simple disulfide: pdb=" SG CYS C 895 " - pdb=" SG CYS C 905 " distance=2.03 Simple disulfide: pdb=" SG CYS C 938 " - pdb=" SG CYS C 972 " distance=2.03 Simple disulfide: pdb=" SG CYS C 954 " - pdb=" SG CYS C1018 " distance=2.03 Simple disulfide: pdb=" SG CYS C 967 " - pdb=" SG CYS C1028 " distance=2.02 Simple disulfide: pdb=" SG CYS C 998 " - pdb=" SG CYS C1008 " 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=4, symmetry=0 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1201 " - " ASN A1027 " " NAG B1201 " - " ASN B1027 " " NAG B1203 " - " ASN B 445 " " NAG C1201 " - " ASN C1027 " " NAG H 1 " - " ASN A 767 " " NAG I 1 " - " ASN B 767 " " NAG K 1 " - " ASN B 320 " " NAG L 1 " - " ASN C 767 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.0 seconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 34 sheets defined 29.1% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 189 through 199 Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 403 through 414 removed outlier: 4.210A pdb=" N VAL A 409 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.884A pdb=" N CYS A 452 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 removed outlier: 3.563A pdb=" N ARG A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 508 through 517 removed outlier: 3.680A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 3.934A pdb=" N VAL A 619 " --> pdb=" O GLU A 615 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.724A pdb=" N ASP A 813 " --> pdb=" O HIS A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 868 Processing helix chain 'A' and resid 901 through 905 removed outlier: 3.567A pdb=" N GLN A 904 " --> pdb=" O THR A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 920 Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.236A pdb=" N VAL A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'B' and resid 81 through 92 removed outlier: 3.651A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.567A pdb=" N ASP B 129 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 removed outlier: 3.525A pdb=" N VAL B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 341 through 345 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 403 through 415 removed outlier: 3.884A pdb=" N VAL B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 3.945A 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 508 through 519 Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 568 through 571 Processing helix chain 'B' and resid 613 through 624 removed outlier: 3.694A pdb=" N ALA B 617 " --> pdb=" O ASP B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 removed outlier: 4.157A pdb=" N VAL B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 798 Processing helix chain 'B' and resid 809 through 813 removed outlier: 3.811A pdb=" N ASP B 813 " --> pdb=" O HIS B 810 " (cutoff:3.500A) 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 970 Processing helix chain 'B' and resid 1019 through 1023 removed outlier: 3.910A 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 356 through 360 removed outlier: 3.729A pdb=" N ASP C 360 " --> pdb=" O HIS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 414 removed outlier: 3.579A pdb=" N VAL C 409 " --> pdb=" O LYS C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 452 Processing helix chain 'C' and resid 504 through 507 Processing helix chain 'C' and resid 508 through 519 Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.567A pdb=" N LEU C 556 " --> pdb=" O HIS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 603 Processing helix chain 'C' and resid 613 through 618 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 658 through 662 Processing helix chain 'C' and resid 749 through 757 removed outlier: 3.768A pdb=" N ALA C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 755 " --> pdb=" O SER C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 867 Processing helix chain 'C' and resid 901 through 905 Processing helix chain 'C' and resid 916 through 920 Processing helix chain 'C' and resid 959 through 970 removed outlier: 3.518A pdb=" N VAL C 966 " --> pdb=" O ASP C 962 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 970 " --> pdb=" O VAL C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1023 removed outlier: 3.524A pdb=" N ASP C1023 " --> pdb=" O HIS C1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 20 through 36 Processing helix chain 'D' and resid 37 through 43 Processing helix chain 'D' and resid 52 through 71 Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 80 through 89 removed outlier: 3.983A pdb=" N ASP D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 113 removed outlier: 3.524A pdb=" N PHE D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 138 Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 19 through 35 removed outlier: 3.570A pdb=" N VAL E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY E 25 " --> pdb=" O ASP E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 46 removed outlier: 3.816A pdb=" N GLU E 43 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER E 44 " --> pdb=" O PHE E 41 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY E 46 " --> pdb=" O GLU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 57 Processing helix chain 'E' and resid 57 through 77 Processing helix chain 'E' and resid 80 through 85 Processing helix chain 'E' and resid 85 through 97 removed outlier: 3.704A pdb=" N CYS E 93 " --> pdb=" O SER E 89 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS E 97 " --> pdb=" O CYS E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 119 removed outlier: 4.333A pdb=" N PHE E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG E 104 " --> pdb=" O PRO E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' Processing helix chain 'E' and resid 123 through 142 Processing helix chain 'F' and resid 3 through 18 Processing helix chain 'F' and resid 20 through 36 Processing helix chain 'F' and resid 37 through 43 Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.540A pdb=" N LYS F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 74 No H-bonds generated for 'chain 'F' and resid 72 through 74' Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 80 through 89 removed outlier: 3.530A pdb=" N ASP F 85 " --> pdb=" O SER F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 113 removed outlier: 3.540A pdb=" N PHE F 98 " --> pdb=" O ASP F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 137 Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 19 through 35 removed outlier: 3.597A pdb=" N VAL G 23 " --> pdb=" O ASN G 19 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 43 removed outlier: 3.534A pdb=" N ARG G 40 " --> pdb=" O TRP G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 57 Processing helix chain 'G' and resid 57 through 77 removed outlier: 3.713A pdb=" N LYS G 61 " --> pdb=" O ASN G 57 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 85 Processing helix chain 'G' and resid 85 through 95 Processing helix chain 'G' and resid 99 through 119 removed outlier: 4.121A pdb=" N PHE G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG G 104 " --> pdb=" O PRO G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 143 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 4.043A pdb=" N GLU A 158 " --> pdb=" O LYS A 175 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 179 through 182 current: chain 'A' and resid 255 through 258 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 273 removed outlier: 3.620A pdb=" N SER A 265 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY A 271 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER A 276 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 279 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE A 290 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 371 through 376 removed outlier: 6.743A pdb=" N VAL A 386 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL A 397 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU A 437 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS A 396 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 477 through 481 removed outlier: 3.903A pdb=" N THR A 498 " --> pdb=" O HIS A 495 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 498 through 501 current: chain 'A' and resid 574 through 577 Processing sheet with id=AA5, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA6, first strand: chain 'A' and resid 582 through 586 removed outlier: 4.184A pdb=" N GLU A 582 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 606 through 607 removed outlier: 6.029A pdb=" N SER A 606 " --> pdb=" O TRP A 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 649 through 650 Processing sheet with id=AA9, first strand: chain 'A' and resid 719 through 722 removed outlier: 7.050A pdb=" N VAL A 732 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE A 743 " --> pdb=" O VAL A 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 823 through 828 removed outlier: 3.618A pdb=" N SER A 831 " --> pdb=" O SER A 828 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 831 through 832 current: chain 'A' and resid 846 through 850 Processing sheet with id=AB2, first strand: chain 'A' and resid 929 through 932 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 949 through 951 current: chain 'A' and resid 1025 through 1028 Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 68 Processing sheet with id=AB4, first strand: chain 'B' and resid 158 through 162 removed outlier: 4.212A pdb=" N GLU B 158 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 205 through 209 Processing sheet with id=AB6, first strand: chain 'B' and resid 266 through 269 removed outlier: 6.993A pdb=" N LEU B 279 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 290 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 371 through 377 removed outlier: 6.532A pdb=" N VAL B 386 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 397 " --> pdb=" O VAL B 386 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 393 through 397 current: chain 'B' and resid 455 through 457 Processing sheet with id=AB8, first strand: chain 'B' and resid 477 through 480 removed outlier: 6.623A pdb=" N VAL B 491 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 502 " --> pdb=" O VAL B 491 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 582 through 586 removed outlier: 4.174A pdb=" N GLU B 582 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE B 681 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 606 through 607 removed outlier: 6.275A pdb=" N SER B 606 " --> pdb=" O TRP B 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 649 through 650 Processing sheet with id=AC3, first strand: chain 'B' and resid 719 through 722 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 739 through 740 current: chain 'B' and resid 815 through 818 Processing sheet with id=AC4, first strand: chain 'B' and resid 742 through 743 removed outlier: 6.892A pdb=" N THR B 742 " --> pdb=" O LEU B 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 823 through 826 Processing sheet with id=AC6, first strand: chain 'B' and resid 929 through 932 removed outlier: 15.318A pdb=" N GLY B 940 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 11.647A pdb=" N ASP B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 942 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL B 953 " --> pdb=" O VAL B 942 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 265 through 269 removed outlier: 7.047A pdb=" N LEU C 279 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE C 290 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 371 through 380 removed outlier: 4.536A pdb=" N GLY C 378 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA C 383 " --> pdb=" O GLY C 378 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL C 386 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C 397 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU C 394 " --> pdb=" O THR C 435 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU C 437 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS C 396 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 488 through 489 removed outlier: 3.731A pdb=" N VAL C 575 " --> pdb=" O GLY C 489 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 576 " --> pdb=" O VAL C 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 493 through 495 removed outlier: 4.484A pdb=" N ILE C 540 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 583 through 585 removed outlier: 3.570A pdb=" N ARG C 584 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL C 596 " --> pdb=" O LEU C 607 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 649 through 650 Processing sheet with id=AD4, first strand: chain 'C' and resid 720 through 722 Processing sheet with id=AD5, first strand: chain 'C' and resid 765 through 769 removed outlier: 6.823A pdb=" N ILE C 817 " --> pdb=" O ILE C 766 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA C 768 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY C 815 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 822 through 827 removed outlier: 7.243A pdb=" N LEU C 839 " --> pdb=" O VAL C 850 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL C 850 " --> pdb=" O LEU C 839 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 929 through 932 removed outlier: 6.751A pdb=" N VAL C 942 " --> pdb=" O VAL C 953 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL C 953 " --> pdb=" O VAL C 942 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 949 through 953 current: chain 'C' and resid 1012 through 1013 734 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.57 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 9616 1.38 - 1.56: 14701 1.56 - 1.73: 0 1.73 - 1.91: 258 1.91 - 2.08: 16 Bond restraints: 24591 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 2.42e+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 2.42e+01 bond pdb=" O1 OXY F 202 " pdb=" O2 OXY F 202 " ideal model delta sigma weight residual 1.109 1.207 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" O1 OXY G 202 " pdb=" O2 OXY G 202 " ideal model delta sigma weight residual 1.109 1.207 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" N CYS C 938 " pdb=" CA CYS C 938 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.32e-02 5.74e+03 9.75e+00 ... (remaining 24586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 32713 2.19 - 4.38: 584 4.38 - 6.58: 64 6.58 - 8.77: 19 8.77 - 10.96: 3 Bond angle restraints: 33383 Sorted by residual: angle pdb=" C SER B 152 " pdb=" CA SER B 152 " pdb=" CB SER B 152 " ideal model delta sigma weight residual 117.23 110.94 6.29 1.36e+00 5.41e-01 2.14e+01 angle pdb=" N THR C 471 " pdb=" CA THR C 471 " pdb=" C THR C 471 " ideal model delta sigma weight residual 108.34 101.15 7.19 1.64e+00 3.72e-01 1.92e+01 angle pdb=" C SER A 211 " pdb=" CA SER A 211 " pdb=" CB SER A 211 " ideal model delta sigma weight residual 117.23 111.50 5.73 1.36e+00 5.41e-01 1.77e+01 angle pdb=" N GLN A 969 " pdb=" CA GLN A 969 " pdb=" C GLN A 969 " ideal model delta sigma weight residual 111.07 106.70 4.37 1.07e+00 8.73e-01 1.67e+01 angle pdb=" N GLU B 387 " pdb=" CA GLU B 387 " pdb=" CB GLU B 387 " ideal model delta sigma weight residual 110.63 117.14 -6.51 1.63e+00 3.76e-01 1.59e+01 ... (remaining 33378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 12521 17.90 - 35.81: 1574 35.81 - 53.71: 479 53.71 - 71.62: 89 71.62 - 89.52: 36 Dihedral angle restraints: 14699 sinusoidal: 6056 harmonic: 8643 Sorted by residual: dihedral pdb=" CB CYS A 275 " pdb=" SG CYS A 275 " pdb=" SG CYS A 309 " pdb=" CB CYS A 309 " ideal model delta sinusoidal sigma weight residual 93.00 171.97 -78.97 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS C 398 " pdb=" SG CYS C 398 " pdb=" SG CYS C 462 " pdb=" CB CYS C 462 " ideal model delta sinusoidal sigma weight residual -86.00 -159.77 73.77 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS A 592 " pdb=" SG CYS A 592 " pdb=" SG CYS A 682 " pdb=" CB CYS A 682 " ideal model delta sinusoidal sigma weight residual -86.00 -158.59 72.59 1 1.00e+01 1.00e-02 6.73e+01 ... (remaining 14696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2803 0.053 - 0.105: 630 0.105 - 0.158: 109 0.158 - 0.211: 8 0.211 - 0.263: 4 Chirality restraints: 3554 Sorted by residual: chirality pdb=" CA GLU B 387 " pdb=" N GLU B 387 " pdb=" C GLU B 387 " pdb=" CB GLU B 387 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.25 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CG LEU C 554 " pdb=" CB LEU C 554 " pdb=" CD1 LEU C 554 " pdb=" CD2 LEU C 554 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 3551 not shown) Planarity restraints: 4338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 541 " 0.022 2.00e-02 2.50e+03 2.17e-02 1.17e+01 pdb=" CG TRP A 541 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP A 541 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 541 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 541 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 541 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 541 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 541 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 541 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 541 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 37 " 0.020 2.00e-02 2.50e+03 1.72e-02 7.37e+00 pdb=" CG TRP G 37 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP G 37 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP G 37 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 37 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 37 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 37 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 37 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 37 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP G 37 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 847 " 0.018 2.00e-02 2.50e+03 1.61e-02 6.51e+00 pdb=" CG TRP A 847 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 847 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 847 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 847 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 847 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 847 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 847 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 847 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 847 " 0.002 2.00e-02 2.50e+03 ... (remaining 4335 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 80 2.62 - 3.19: 21367 3.19 - 3.76: 38245 3.76 - 4.33: 51413 4.33 - 4.90: 83978 Nonbonded interactions: 195083 Sorted by model distance: nonbonded pdb="FE HEM D 201 " pdb=" O2 OXY D 202 " model vdw 2.047 3.000 nonbonded pdb="FE HEM G 201 " pdb=" O1 OXY G 202 " model vdw 2.141 3.000 nonbonded pdb=" O MET C 786 " pdb="CA CA C1203 " model vdw 2.251 2.510 nonbonded pdb=" OD2 ASP B 746 " pdb="CA CA B1206 " model vdw 2.256 2.510 nonbonded pdb=" OD1 ASP C 749 " pdb="CA CA C1203 " model vdw 2.271 2.510 ... (remaining 195078 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 686 or resid 719 through 1201 or resid 1205 th \ rough 1206)) selection = (chain 'B' and (resid 263 through 1201 or resid 1205 through 1206)) selection = (chain 'C' and (resid 263 through 686 or resid 719 through 1201 or resid 1205 th \ rough 1206)) } ncs_group { reference = (chain 'D' and (resid 1 through 139 or resid 201 through 202)) selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 11.310 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.110 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.309 24701 Z= 0.183 Angle : 0.702 10.960 33608 Z= 0.372 Chirality : 0.046 0.263 3554 Planarity : 0.005 0.094 4330 Dihedral : 17.271 89.524 8912 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.85 % Allowed : 27.99 % Favored : 69.15 % 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: -1.26 (0.14), residues: 3090 helix: 0.75 (0.20), residues: 698 sheet: -0.94 (0.32), residues: 248 loop : -1.47 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 31 TYR 0.016 0.001 TYR C 354 PHE 0.015 0.001 PHE B 842 TRP 0.056 0.002 TRP A 541 HIS 0.021 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00371 (24591) covalent geometry : angle 0.69387 (33383) SS BOND : bond 0.00379 ( 93) SS BOND : angle 1.26363 ( 186) hydrogen bonds : bond 0.14596 ( 734) hydrogen bonds : angle 6.05251 ( 1935) Misc. bond : bond 0.17675 ( 4) link_BETA1-4 : bond 0.00720 ( 5) link_BETA1-4 : angle 2.60304 ( 15) link_NAG-ASN : bond 0.00386 ( 8) link_NAG-ASN : angle 2.00447 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 311 time to evaluate : 0.877 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: 0.5323 (tmm) cc_final: 0.5012 (tmm) REVERT: A 273 THR cc_start: 0.7902 (m) cc_final: 0.7658 (p) REVERT: A 328 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7348 (mt) REVERT: A 485 ILE cc_start: 0.7129 (pt) cc_final: 0.6876 (mt) REVERT: A 786 MET cc_start: 0.7450 (mmt) cc_final: 0.7139 (mmt) REVERT: A 792 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7038 (mt-10) REVERT: B 69 GLN cc_start: 0.5884 (mp10) cc_final: 0.5078 (mm-40) REVERT: B 128 TRP cc_start: 0.7584 (OUTLIER) cc_final: 0.6840 (m100) REVERT: B 137 LYS cc_start: 0.7113 (ttpp) cc_final: 0.6784 (ttpp) REVERT: B 201 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5675 (tm-30) REVERT: B 393 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.6005 (pt) REVERT: B 477 GLU cc_start: 0.6945 (tm-30) cc_final: 0.6719 (tm-30) REVERT: B 612 TRP cc_start: 0.7314 (t60) cc_final: 0.7069 (t-100) REVERT: B 755 VAL cc_start: 0.6705 (t) cc_final: 0.6391 (p) REVERT: B 823 SER cc_start: 0.7770 (OUTLIER) cc_final: 0.6484 (p) REVERT: B 1017 GLU cc_start: 0.6483 (pp20) cc_final: 0.6050 (pp20) REVERT: C 278 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.5585 (ptm160) REVERT: C 593 GLU cc_start: 0.6712 (mp0) cc_final: 0.6335 (mp0) REVERT: C 659 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6205 (pp-130) REVERT: D 56 LYS cc_start: 0.7923 (mptt) cc_final: 0.7716 (mptt) REVERT: E 37 TRP cc_start: 0.7623 (p90) cc_final: 0.7300 (p90) REVERT: E 55 MET cc_start: 0.6392 (mmm) cc_final: 0.6123 (mmm) outliers start: 72 outliers final: 49 residues processed: 356 average time/residue: 0.5352 time to fit residues: 224.3904 Evaluate side-chains 360 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 304 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 998 CYS Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 823 SER Chi-restraints excluded: chain B residue 847 TRP Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 278 ARG Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain C residue 499 TRP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 735 TYR Chi-restraints excluded: chain C residue 855 MET Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 1030 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 145 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 GLN C 904 GLN C 927 ASN E 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.191492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.171174 restraints weight = 36322.006| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 2.59 r_work: 0.4191 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.474 24701 Z= 0.180 Angle : 0.643 9.754 33608 Z= 0.329 Chirality : 0.045 0.243 3554 Planarity : 0.005 0.064 4330 Dihedral : 8.871 87.040 3775 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 5.67 % Allowed : 24.62 % Favored : 69.71 % 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: -1.20 (0.14), residues: 3090 helix: 0.95 (0.20), residues: 709 sheet: -1.00 (0.33), residues: 232 loop : -1.48 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 400 TYR 0.012 0.002 TYR C 735 PHE 0.018 0.002 PHE B 188 TRP 0.042 0.002 TRP A 541 HIS 0.012 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00417 (24591) covalent geometry : angle 0.63375 (33383) SS BOND : bond 0.00505 ( 93) SS BOND : angle 1.19230 ( 186) hydrogen bonds : bond 0.04336 ( 734) hydrogen bonds : angle 5.06100 ( 1935) Misc. bond : bond 0.37721 ( 4) link_BETA1-4 : bond 0.00727 ( 5) link_BETA1-4 : angle 2.63673 ( 15) link_NAG-ASN : bond 0.00467 ( 8) link_NAG-ASN : angle 2.07470 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 336 time to evaluate : 0.860 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: 0.5260 (tmm) cc_final: 0.4909 (tmm) REVERT: A 163 ARG cc_start: 0.7359 (tpm170) cc_final: 0.6984 (tpm170) REVERT: A 273 THR cc_start: 0.7939 (m) cc_final: 0.7700 (p) REVERT: A 485 ILE cc_start: 0.7152 (pt) cc_final: 0.6888 (mt) REVERT: A 507 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8277 (t80) REVERT: A 792 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7122 (mt-10) REVERT: A 944 ILE cc_start: 0.6127 (pt) cc_final: 0.5818 (mp) REVERT: A 980 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7929 (mmmm) REVERT: B 128 TRP cc_start: 0.7667 (OUTLIER) cc_final: 0.6981 (m100) REVERT: B 424 TYR cc_start: 0.7381 (p90) cc_final: 0.7032 (p90) REVERT: B 434 ASN cc_start: 0.8055 (t0) cc_final: 0.7838 (t0) REVERT: B 735 TYR cc_start: 0.8086 (t80) cc_final: 0.7399 (t80) REVERT: B 823 SER cc_start: 0.7892 (OUTLIER) cc_final: 0.6572 (p) REVERT: B 997 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7827 (mmtp) REVERT: B 1017 GLU cc_start: 0.6593 (pp20) cc_final: 0.6186 (pp20) REVERT: C 278 ARG cc_start: 0.6295 (OUTLIER) cc_final: 0.5830 (ppp80) REVERT: C 279 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7005 (tm) REVERT: C 903 TRP cc_start: 0.7005 (OUTLIER) cc_final: 0.5583 (m100) REVERT: D 128 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6241 (t80) REVERT: E 37 TRP cc_start: 0.7679 (p90) cc_final: 0.7380 (p90) REVERT: E 68 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7458 (tt) REVERT: F 31 ARG cc_start: 0.7775 (mtt-85) cc_final: 0.7550 (mtt-85) outliers start: 143 outliers final: 69 residues processed: 440 average time/residue: 0.4719 time to fit residues: 249.7829 Evaluate side-chains 400 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 321 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 998 CYS Chi-restraints excluded: chain A residue 1020 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 SER Chi-restraints excluded: chain B residue 847 TRP Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 997 LYS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 278 ARG Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 499 TRP Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 735 TYR Chi-restraints excluded: chain C residue 855 MET Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 903 TRP Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain G residue 55 MET Chi-restraints excluded: chain G residue 145 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 66 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 301 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 261 optimal weight: 0.0030 chunk 123 optimal weight: 0.1980 chunk 227 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 208 optimal weight: 0.2980 chunk 7 optimal weight: 0.0060 chunk 253 optimal weight: 0.7980 overall best weight: 0.2206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN A 969 GLN A1020 HIS C 892 ASN C 904 GLN C 927 ASN E 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.193762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.173539 restraints weight = 36475.559| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 2.59 r_work: 0.4222 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.328 24701 Z= 0.118 Angle : 0.597 9.351 33608 Z= 0.303 Chirality : 0.043 0.252 3554 Planarity : 0.004 0.059 4330 Dihedral : 8.190 84.804 3736 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.15 % Allowed : 25.26 % Favored : 69.59 % 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: -1.01 (0.15), residues: 3090 helix: 1.20 (0.20), residues: 706 sheet: -0.75 (0.30), residues: 262 loop : -1.41 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 490 TYR 0.011 0.001 TYR C 354 PHE 0.013 0.001 PHE D 128 TRP 0.027 0.001 TRP A 541 HIS 0.007 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00271 (24591) covalent geometry : angle 0.58781 (33383) SS BOND : bond 0.00410 ( 93) SS BOND : angle 1.17974 ( 186) hydrogen bonds : bond 0.03701 ( 734) hydrogen bonds : angle 4.80933 ( 1935) Misc. bond : bond 0.23879 ( 4) link_BETA1-4 : bond 0.00701 ( 5) link_BETA1-4 : angle 2.51556 ( 15) link_NAG-ASN : bond 0.00415 ( 8) link_NAG-ASN : angle 1.94954 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 334 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.5239 (tmm) cc_final: 0.4985 (tmm) REVERT: A 273 THR cc_start: 0.7911 (OUTLIER) cc_final: 0.7692 (p) REVERT: A 485 ILE cc_start: 0.7173 (pt) cc_final: 0.6878 (mt) REVERT: A 792 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7097 (mt-10) REVERT: A 944 ILE cc_start: 0.6006 (pt) cc_final: 0.5682 (mp) REVERT: A 980 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7845 (mmmm) REVERT: B 128 TRP cc_start: 0.7607 (OUTLIER) cc_final: 0.6780 (m100) REVERT: B 284 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.6228 (mp10) REVERT: B 365 CYS cc_start: 0.6098 (OUTLIER) cc_final: 0.5835 (m) REVERT: B 424 TYR cc_start: 0.7242 (p90) cc_final: 0.6870 (p90) REVERT: B 434 ASN cc_start: 0.8102 (t0) cc_final: 0.7834 (t0) REVERT: B 735 TYR cc_start: 0.8037 (t80) cc_final: 0.7314 (t80) REVERT: B 823 SER cc_start: 0.7831 (OUTLIER) cc_final: 0.6692 (t) REVERT: B 997 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7783 (mmtp) REVERT: B 1017 GLU cc_start: 0.6646 (pp20) cc_final: 0.6220 (pp20) REVERT: C 278 ARG cc_start: 0.6219 (OUTLIER) cc_final: 0.5521 (mtm-85) REVERT: C 279 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7717 (tm) REVERT: C 388 VAL cc_start: 0.7559 (OUTLIER) cc_final: 0.7100 (p) REVERT: C 755 VAL cc_start: 0.5484 (OUTLIER) cc_final: 0.4923 (t) REVERT: C 903 TRP cc_start: 0.6721 (OUTLIER) cc_final: 0.6180 (m100) REVERT: E 37 TRP cc_start: 0.7635 (p90) cc_final: 0.7352 (p90) REVERT: F 31 ARG cc_start: 0.7602 (mtt-85) cc_final: 0.7374 (mtt-85) outliers start: 130 outliers final: 60 residues processed: 422 average time/residue: 0.4667 time to fit residues: 236.9995 Evaluate side-chains 380 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 308 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 998 CYS Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 823 SER Chi-restraints excluded: chain B residue 847 TRP Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 997 LYS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 278 ARG Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 499 TRP Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 735 TYR Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 855 MET Chi-restraints excluded: chain C residue 903 TRP Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain G residue 55 MET Chi-restraints excluded: chain G residue 145 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 222 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN A 611 HIS B 718 GLN C 807 ASN C 892 ASN C 904 GLN C 927 ASN E 117 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.188915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.169075 restraints weight = 36198.336| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 2.48 r_work: 0.4170 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.599 24701 Z= 0.236 Angle : 0.682 9.656 33608 Z= 0.349 Chirality : 0.047 0.278 3554 Planarity : 0.005 0.066 4330 Dihedral : 8.337 88.295 3729 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 6.58 % Allowed : 24.90 % Favored : 68.52 % 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: -1.28 (0.14), residues: 3090 helix: 0.94 (0.20), residues: 712 sheet: -1.11 (0.31), residues: 262 loop : -1.55 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 838 TYR 0.014 0.002 TYR C 427 PHE 0.023 0.002 PHE A 208 TRP 0.042 0.002 TRP A 541 HIS 0.010 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00546 (24591) covalent geometry : angle 0.67100 (33383) SS BOND : bond 0.00643 ( 93) SS BOND : angle 1.45190 ( 186) hydrogen bonds : bond 0.04381 ( 734) hydrogen bonds : angle 5.03114 ( 1935) Misc. bond : bond 0.38182 ( 4) link_BETA1-4 : bond 0.00553 ( 5) link_BETA1-4 : angle 2.48521 ( 15) link_NAG-ASN : bond 0.00510 ( 8) link_NAG-ASN : angle 2.18763 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 331 time to evaluate : 0.748 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 273 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7744 (p) REVERT: A 485 ILE cc_start: 0.7138 (OUTLIER) cc_final: 0.6872 (mt) REVERT: A 631 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8420 (t) REVERT: A 637 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7926 (ttm170) REVERT: A 792 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7203 (mt-10) REVERT: A 944 ILE cc_start: 0.6201 (pt) cc_final: 0.5947 (mp) REVERT: B 128 TRP cc_start: 0.7736 (OUTLIER) cc_final: 0.6826 (m100) REVERT: B 237 ASN cc_start: 0.6861 (OUTLIER) cc_final: 0.6381 (p0) REVERT: B 284 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.6231 (mp10) REVERT: B 393 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6372 (pt) REVERT: B 424 TYR cc_start: 0.7370 (p90) cc_final: 0.6941 (p90) REVERT: B 735 TYR cc_start: 0.8157 (t80) cc_final: 0.7437 (t80) REVERT: B 823 SER cc_start: 0.7902 (OUTLIER) cc_final: 0.6763 (t) REVERT: C 279 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7814 (tm) REVERT: C 755 VAL cc_start: 0.5692 (OUTLIER) cc_final: 0.5201 (t) REVERT: C 820 GLU cc_start: 0.5543 (OUTLIER) cc_final: 0.5312 (mm-30) REVERT: C 903 TRP cc_start: 0.7047 (OUTLIER) cc_final: 0.5586 (m100) REVERT: D 128 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6154 (t80) REVERT: E 37 TRP cc_start: 0.7709 (p90) cc_final: 0.7436 (p90) REVERT: E 55 MET cc_start: 0.6288 (mmm) cc_final: 0.6081 (mmm) outliers start: 166 outliers final: 85 residues processed: 455 average time/residue: 0.4725 time to fit residues: 257.9686 Evaluate side-chains 414 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 315 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 889 TRP Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 998 CYS Chi-restraints excluded: chain A residue 1020 HIS Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 SER Chi-restraints excluded: chain B residue 847 TRP Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 278 ARG Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 499 TRP Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 735 TYR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 855 MET Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 903 TRP Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 55 MET Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 145 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 170 optimal weight: 0.9980 chunk 105 optimal weight: 0.0170 chunk 110 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 288 optimal weight: 0.2980 chunk 197 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN B 539 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN C 904 GLN C 927 ASN E 117 HIS G 143 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.190844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.170672 restraints weight = 35968.407| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.57 r_work: 0.4183 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.569 24701 Z= 0.154 Angle : 0.638 9.548 33608 Z= 0.324 Chirality : 0.045 0.242 3554 Planarity : 0.005 0.064 4330 Dihedral : 8.083 89.512 3723 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.75 % Allowed : 25.97 % Favored : 68.28 % 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: -1.20 (0.14), residues: 3090 helix: 1.08 (0.20), residues: 712 sheet: -1.13 (0.33), residues: 240 loop : -1.52 (0.12), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 381 TYR 0.014 0.001 TYR E 130 PHE 0.017 0.001 PHE D 128 TRP 0.043 0.001 TRP A 541 HIS 0.013 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00357 (24591) covalent geometry : angle 0.62829 (33383) SS BOND : bond 0.00540 ( 93) SS BOND : angle 1.32026 ( 186) hydrogen bonds : bond 0.03869 ( 734) hydrogen bonds : angle 4.87468 ( 1935) Misc. bond : bond 0.33240 ( 4) link_BETA1-4 : bond 0.00713 ( 5) link_BETA1-4 : angle 2.41289 ( 15) link_NAG-ASN : bond 0.00475 ( 8) link_NAG-ASN : angle 2.12864 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 337 time to evaluate : 0.641 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: 0.7385 (OUTLIER) cc_final: 0.7136 (tpm170) REVERT: A 273 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7736 (p) REVERT: A 485 ILE cc_start: 0.7138 (pt) cc_final: 0.6871 (mt) REVERT: A 507 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8285 (t80) REVERT: A 792 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7181 (mt-10) REVERT: A 944 ILE cc_start: 0.6133 (pt) cc_final: 0.5892 (mp) REVERT: B 128 TRP cc_start: 0.7707 (OUTLIER) cc_final: 0.6860 (m100) REVERT: B 237 ASN cc_start: 0.6686 (OUTLIER) cc_final: 0.6275 (p0) REVERT: B 284 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.6222 (mp10) REVERT: B 393 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6144 (pt) REVERT: B 424 TYR cc_start: 0.7390 (p90) cc_final: 0.6939 (p90) REVERT: B 436 TRP cc_start: 0.7646 (m100) cc_final: 0.7434 (m100) REVERT: B 583 ILE cc_start: 0.6426 (OUTLIER) cc_final: 0.5850 (pp) REVERT: B 735 TYR cc_start: 0.8114 (t80) cc_final: 0.7442 (t80) REVERT: B 755 VAL cc_start: 0.6714 (t) cc_final: 0.6405 (p) REVERT: B 823 SER cc_start: 0.7853 (OUTLIER) cc_final: 0.6709 (t) REVERT: B 997 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7856 (mmtp) REVERT: C 279 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7751 (tm) REVERT: C 612 TRP cc_start: 0.5099 (t-100) cc_final: 0.4816 (t-100) REVERT: C 733 GLU cc_start: 0.6400 (tt0) cc_final: 0.6032 (tp30) REVERT: C 755 VAL cc_start: 0.5615 (OUTLIER) cc_final: 0.5120 (t) REVERT: C 903 TRP cc_start: 0.6870 (OUTLIER) cc_final: 0.6089 (m100) REVERT: D 128 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6247 (t80) REVERT: E 37 TRP cc_start: 0.7702 (p90) cc_final: 0.7414 (p90) REVERT: E 55 MET cc_start: 0.6295 (mmm) cc_final: 0.6092 (mmm) outliers start: 145 outliers final: 89 residues processed: 440 average time/residue: 0.4839 time to fit residues: 254.0336 Evaluate side-chains 419 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 316 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 998 CYS Chi-restraints excluded: chain A residue 1020 HIS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 823 SER Chi-restraints excluded: chain B residue 847 TRP Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 997 LYS Chi-restraints excluded: chain B residue 1007 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 278 ARG Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 499 TRP Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 735 TYR Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 855 MET Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 903 TRP Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 55 MET Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 145 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 104 optimal weight: 0.0040 chunk 295 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 0.2980 chunk 248 optimal weight: 0.2980 chunk 148 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 266 optimal weight: 0.0970 chunk 279 optimal weight: 0.2980 overall best weight: 0.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN A1020 HIS B 306 GLN B 718 GLN B 986 GLN ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 HIS C 807 ASN C 892 ASN C 904 GLN C 927 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.192994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.172825 restraints weight = 36203.025| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 2.59 r_work: 0.4215 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.396 24701 Z= 0.115 Angle : 0.608 9.476 33608 Z= 0.306 Chirality : 0.043 0.242 3554 Planarity : 0.004 0.060 4330 Dihedral : 7.828 87.014 3721 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.11 % Allowed : 27.24 % Favored : 67.64 % 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: -0.98 (0.15), residues: 3090 helix: 1.32 (0.20), residues: 705 sheet: -0.87 (0.33), residues: 249 loop : -1.40 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 318 TYR 0.011 0.001 TYR C 354 PHE 0.024 0.001 PHE C 979 TRP 0.051 0.001 TRP A 541 HIS 0.011 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00266 (24591) covalent geometry : angle 0.60000 (33383) SS BOND : bond 0.00367 ( 93) SS BOND : angle 1.05752 ( 186) hydrogen bonds : bond 0.03405 ( 734) hydrogen bonds : angle 4.63546 ( 1935) Misc. bond : bond 0.22572 ( 4) link_BETA1-4 : bond 0.00662 ( 5) link_BETA1-4 : angle 2.42354 ( 15) link_NAG-ASN : bond 0.00390 ( 8) link_NAG-ASN : angle 1.97748 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 332 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7091 (tpm170) REVERT: A 273 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7731 (p) REVERT: A 485 ILE cc_start: 0.7146 (pt) cc_final: 0.6842 (mt) REVERT: A 507 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8257 (t80) REVERT: A 792 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7135 (mt-10) REVERT: A 944 ILE cc_start: 0.6116 (pt) cc_final: 0.5857 (mp) REVERT: B 83 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6314 (tp30) REVERT: B 128 TRP cc_start: 0.7667 (OUTLIER) cc_final: 0.7028 (m100) REVERT: B 237 ASN cc_start: 0.6578 (OUTLIER) cc_final: 0.6181 (OUTLIER) REVERT: B 284 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6205 (mp10) REVERT: B 394 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6493 (mm) REVERT: B 424 TYR cc_start: 0.7246 (p90) cc_final: 0.6724 (p90) REVERT: B 434 ASN cc_start: 0.8093 (t0) cc_final: 0.7890 (t0) REVERT: B 436 TRP cc_start: 0.7606 (m100) cc_final: 0.7400 (m100) REVERT: B 583 ILE cc_start: 0.6298 (OUTLIER) cc_final: 0.5663 (pp) REVERT: B 735 TYR cc_start: 0.8033 (t80) cc_final: 0.7581 (t80) REVERT: B 755 VAL cc_start: 0.6634 (t) cc_final: 0.6310 (p) REVERT: B 823 SER cc_start: 0.7842 (OUTLIER) cc_final: 0.6528 (p) REVERT: B 980 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7611 (mtpt) REVERT: B 997 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7766 (mmtp) REVERT: C 279 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7760 (tm) REVERT: C 436 TRP cc_start: 0.5869 (m100) cc_final: 0.5628 (m100) REVERT: C 612 TRP cc_start: 0.5075 (t-100) cc_final: 0.4622 (t-100) REVERT: C 733 GLU cc_start: 0.6342 (tt0) cc_final: 0.5981 (tp30) REVERT: C 755 VAL cc_start: 0.5592 (OUTLIER) cc_final: 0.5117 (t) REVERT: E 37 TRP cc_start: 0.7657 (p90) cc_final: 0.7382 (p90) REVERT: E 55 MET cc_start: 0.6272 (mmm) cc_final: 0.6054 (mmm) REVERT: F 76 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.6347 (mpm) outliers start: 129 outliers final: 72 residues processed: 422 average time/residue: 0.5104 time to fit residues: 255.2711 Evaluate side-chains 406 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 320 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 998 CYS Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 823 SER Chi-restraints excluded: chain B residue 847 TRP Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 980 LYS Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 997 LYS Chi-restraints excluded: chain B residue 1007 ASP Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 278 ARG Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 735 TYR Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 855 MET Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 55 MET Chi-restraints excluded: chain G residue 145 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 37 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 192 optimal weight: 0.6980 chunk 202 optimal weight: 0.0870 chunk 270 optimal weight: 0.5980 chunk 278 optimal weight: 0.9980 chunk 167 optimal weight: 0.3980 chunk 206 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 269 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN A1020 HIS ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS C 904 GLN E 117 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.191230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.171111 restraints weight = 36077.908| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 2.57 r_work: 0.4189 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.548 24701 Z= 0.155 Angle : 0.624 9.635 33608 Z= 0.317 Chirality : 0.044 0.240 3554 Planarity : 0.005 0.062 4330 Dihedral : 7.849 88.169 3719 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.27 % Allowed : 27.68 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 3090 helix: 1.21 (0.20), residues: 713 sheet: -0.93 (0.34), residues: 232 loop : -1.42 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 318 TYR 0.010 0.001 TYR C 354 PHE 0.019 0.001 PHE A 638 TRP 0.050 0.002 TRP A 541 HIS 0.011 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00364 (24591) covalent geometry : angle 0.61562 (33383) SS BOND : bond 0.00446 ( 93) SS BOND : angle 1.11052 ( 186) hydrogen bonds : bond 0.03694 ( 734) hydrogen bonds : angle 4.68167 ( 1935) Misc. bond : bond 0.31283 ( 4) link_BETA1-4 : bond 0.00638 ( 5) link_BETA1-4 : angle 2.41264 ( 15) link_NAG-ASN : bond 0.00408 ( 8) link_NAG-ASN : angle 2.02532 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 322 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7097 (tpm170) REVERT: A 273 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7737 (p) REVERT: A 485 ILE cc_start: 0.7156 (pt) cc_final: 0.6849 (mt) REVERT: A 792 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7167 (mt-10) REVERT: A 944 ILE cc_start: 0.6132 (pt) cc_final: 0.5888 (mp) REVERT: B 128 TRP cc_start: 0.7691 (OUTLIER) cc_final: 0.7109 (m100) REVERT: B 201 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.5632 (tm-30) REVERT: B 237 ASN cc_start: 0.6714 (OUTLIER) cc_final: 0.6287 (p0) REVERT: B 284 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.6236 (mp10) REVERT: B 424 TYR cc_start: 0.7292 (p90) cc_final: 0.6753 (p90) REVERT: B 434 ASN cc_start: 0.8089 (t0) cc_final: 0.7857 (t0) REVERT: B 583 ILE cc_start: 0.6378 (OUTLIER) cc_final: 0.5795 (pp) REVERT: B 599 LYS cc_start: 0.7084 (tptp) cc_final: 0.6874 (tptp) REVERT: B 735 TYR cc_start: 0.8046 (t80) cc_final: 0.7562 (t80) REVERT: B 823 SER cc_start: 0.7874 (OUTLIER) cc_final: 0.6583 (p) REVERT: B 997 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7798 (mmtp) REVERT: C 279 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7695 (tm) REVERT: C 436 TRP cc_start: 0.5966 (m100) cc_final: 0.5688 (m100) REVERT: C 612 TRP cc_start: 0.5122 (t-100) cc_final: 0.4612 (t-100) REVERT: C 733 GLU cc_start: 0.6359 (tt0) cc_final: 0.6039 (tp30) REVERT: C 755 VAL cc_start: 0.5584 (OUTLIER) cc_final: 0.5127 (t) REVERT: E 37 TRP cc_start: 0.7675 (p90) cc_final: 0.7393 (p90) REVERT: E 55 MET cc_start: 0.6295 (mmm) cc_final: 0.6083 (mmm) outliers start: 133 outliers final: 87 residues processed: 418 average time/residue: 0.4908 time to fit residues: 244.8206 Evaluate side-chains 414 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 316 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 998 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 823 SER Chi-restraints excluded: chain B residue 847 TRP Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 997 LYS Chi-restraints excluded: chain B residue 1007 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 278 ARG Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 735 TYR Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 855 MET Chi-restraints excluded: chain C residue 903 TRP Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 145 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 147 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 413 GLN A 618 HIS B 718 GLN B 759 GLN C 475 HIS C 894 GLN C 904 GLN E 117 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.188235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.168484 restraints weight = 35949.131| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.48 r_work: 0.4164 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 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 : 0.008 0.917 24701 Z= 0.221 Angle : 0.691 9.579 33608 Z= 0.353 Chirality : 0.048 0.268 3554 Planarity : 0.005 0.064 4330 Dihedral : 8.091 88.010 3719 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.43 % Allowed : 28.03 % Favored : 66.53 % 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: -1.23 (0.14), residues: 3090 helix: 0.98 (0.20), residues: 713 sheet: -1.04 (0.35), residues: 221 loop : -1.52 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 318 TYR 0.014 0.002 TYR C 424 PHE 0.021 0.002 PHE D 128 TRP 0.065 0.002 TRP A 541 HIS 0.011 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00506 (24591) covalent geometry : angle 0.68113 (33383) SS BOND : bond 0.00642 ( 93) SS BOND : angle 1.34666 ( 186) hydrogen bonds : bond 0.04305 ( 734) hydrogen bonds : angle 4.96070 ( 1935) Misc. bond : bond 0.50773 ( 4) link_BETA1-4 : bond 0.00685 ( 5) link_BETA1-4 : angle 2.38969 ( 15) link_NAG-ASN : bond 0.00506 ( 8) link_NAG-ASN : angle 2.23016 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 342 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7363 (tpm170) cc_final: 0.7064 (tpm170) REVERT: A 273 THR cc_start: 0.7978 (OUTLIER) cc_final: 0.7778 (p) REVERT: A 485 ILE cc_start: 0.7110 (pt) cc_final: 0.6846 (mt) REVERT: A 792 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 1020 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.7122 (t-90) REVERT: B 69 GLN cc_start: 0.5938 (mp10) cc_final: 0.5445 (mm-40) REVERT: B 116 ASP cc_start: 0.7737 (t0) cc_final: 0.7317 (t0) REVERT: B 128 TRP cc_start: 0.7765 (OUTLIER) cc_final: 0.7170 (m100) REVERT: B 237 ASN cc_start: 0.6967 (OUTLIER) cc_final: 0.6411 (p0) REVERT: B 278 ARG cc_start: 0.6051 (OUTLIER) cc_final: 0.5163 (ttp80) REVERT: B 284 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.6240 (mp10) REVERT: B 393 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6377 (pt) REVERT: B 434 ASN cc_start: 0.8022 (t0) cc_final: 0.7768 (t0) REVERT: B 583 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.5980 (pp) REVERT: B 735 TYR cc_start: 0.8113 (t80) cc_final: 0.7608 (t80) REVERT: B 823 SER cc_start: 0.7889 (OUTLIER) cc_final: 0.6551 (p) REVERT: C 279 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7690 (tm) REVERT: C 659 MET cc_start: 0.7132 (ptp) cc_final: 0.6903 (ptp) REVERT: C 733 GLU cc_start: 0.6366 (tt0) cc_final: 0.6135 (tp30) REVERT: C 903 TRP cc_start: 0.6952 (OUTLIER) cc_final: 0.5740 (m100) REVERT: E 55 MET cc_start: 0.6238 (mmm) cc_final: 0.6003 (mmm) outliers start: 137 outliers final: 85 residues processed: 439 average time/residue: 0.4781 time to fit residues: 251.3188 Evaluate side-chains 426 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 330 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 889 TRP Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 998 CYS Chi-restraints excluded: chain A residue 1020 HIS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 SER Chi-restraints excluded: chain B residue 847 TRP Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 855 MET Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 903 TRP Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 145 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 149 optimal weight: 0.9980 chunk 175 optimal weight: 0.0970 chunk 296 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 289 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN A1020 HIS ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 HIS C 807 ASN C 892 ASN C 904 GLN E 117 HIS G 127 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.190253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.170055 restraints weight = 36112.057| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.58 r_work: 0.4182 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.790 24701 Z= 0.159 Angle : 0.666 10.328 33608 Z= 0.337 Chirality : 0.046 0.239 3554 Planarity : 0.005 0.063 4330 Dihedral : 7.881 89.807 3713 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.32 % Allowed : 29.58 % Favored : 66.10 % 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: -1.16 (0.15), residues: 3090 helix: 1.08 (0.20), residues: 714 sheet: -1.00 (0.34), residues: 219 loop : -1.49 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 318 TYR 0.021 0.001 TYR B 424 PHE 0.017 0.001 PHE A 533 TRP 0.063 0.002 TRP A 541 HIS 0.014 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00373 (24591) covalent geometry : angle 0.65772 (33383) SS BOND : bond 0.00450 ( 93) SS BOND : angle 1.20934 ( 186) hydrogen bonds : bond 0.03847 ( 734) hydrogen bonds : angle 4.82533 ( 1935) Misc. bond : bond 0.42687 ( 4) link_BETA1-4 : bond 0.00630 ( 5) link_BETA1-4 : angle 2.32988 ( 15) link_NAG-ASN : bond 0.00421 ( 8) link_NAG-ASN : angle 2.06955 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 319 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7342 (tpm170) cc_final: 0.7017 (tpm170) REVERT: A 191 ASP cc_start: 0.7137 (m-30) cc_final: 0.6922 (m-30) REVERT: A 229 ASN cc_start: 0.6616 (p0) cc_final: 0.6242 (p0) REVERT: A 259 SER cc_start: 0.8362 (t) cc_final: 0.8040 (p) REVERT: A 273 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7749 (p) REVERT: A 485 ILE cc_start: 0.7144 (pt) cc_final: 0.6885 (mt) REVERT: A 786 MET cc_start: 0.7577 (mmt) cc_final: 0.7303 (mmt) REVERT: A 792 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7251 (mt-10) REVERT: B 128 TRP cc_start: 0.7738 (OUTLIER) cc_final: 0.7144 (m100) REVERT: B 201 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5728 (tm-30) REVERT: B 237 ASN cc_start: 0.6695 (OUTLIER) cc_final: 0.6304 (p0) REVERT: B 284 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.6267 (mp10) REVERT: B 393 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6145 (pt) REVERT: B 394 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6588 (mm) REVERT: B 583 ILE cc_start: 0.6475 (OUTLIER) cc_final: 0.5899 (pp) REVERT: B 662 CYS cc_start: 0.6298 (OUTLIER) cc_final: 0.6074 (t) REVERT: B 735 TYR cc_start: 0.8075 (t80) cc_final: 0.7685 (t80) REVERT: B 823 SER cc_start: 0.7830 (OUTLIER) cc_final: 0.6690 (t) REVERT: B 899 PRO cc_start: 0.5523 (Cg_exo) cc_final: 0.5303 (Cg_endo) REVERT: B 997 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7792 (mmtp) REVERT: C 279 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7554 (tm) REVERT: C 612 TRP cc_start: 0.5104 (t-100) cc_final: 0.4812 (t-100) REVERT: C 659 MET cc_start: 0.7101 (ptp) cc_final: 0.6876 (ptp) REVERT: C 733 GLU cc_start: 0.6462 (tt0) cc_final: 0.6194 (tp30) REVERT: C 903 TRP cc_start: 0.6838 (OUTLIER) cc_final: 0.6001 (m100) REVERT: C 929 ILE cc_start: 0.6190 (pp) cc_final: 0.5396 (pt) REVERT: E 55 MET cc_start: 0.6268 (mmm) cc_final: 0.6021 (mmm) outliers start: 109 outliers final: 76 residues processed: 401 average time/residue: 0.4824 time to fit residues: 231.8476 Evaluate side-chains 402 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 313 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 998 CYS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 823 SER Chi-restraints excluded: chain B residue 847 TRP Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 997 LYS Chi-restraints excluded: chain B residue 1007 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 504 ASP Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 855 MET Chi-restraints excluded: chain C residue 872 LYS Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 903 TRP Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 74 optimal weight: 0.9990 chunk 212 optimal weight: 0.0050 chunk 71 optimal weight: 0.3980 chunk 206 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 155 optimal weight: 0.0470 chunk 64 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 246 optimal weight: 0.0870 chunk 287 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 overall best weight: 0.2270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 413 GLN A1020 HIS ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 GLN C 648 HIS C 904 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.192407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.172157 restraints weight = 36237.061| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 2.60 r_work: 0.4208 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.593 24701 Z= 0.124 Angle : 0.641 9.503 33608 Z= 0.324 Chirality : 0.044 0.238 3554 Planarity : 0.004 0.063 4330 Dihedral : 7.665 86.542 3712 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.69 % Allowed : 30.33 % Favored : 65.98 % 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: -0.98 (0.15), residues: 3090 helix: 1.28 (0.20), residues: 712 sheet: -0.97 (0.33), residues: 242 loop : -1.38 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 318 TYR 0.019 0.001 TYR B 424 PHE 0.015 0.001 PHE A 638 TRP 0.051 0.001 TRP G 37 HIS 0.009 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00292 (24591) covalent geometry : angle 0.63364 (33383) SS BOND : bond 0.00391 ( 93) SS BOND : angle 1.15095 ( 186) hydrogen bonds : bond 0.03457 ( 734) hydrogen bonds : angle 4.69216 ( 1935) Misc. bond : bond 0.31716 ( 4) link_BETA1-4 : bond 0.00638 ( 5) link_BETA1-4 : angle 2.34671 ( 15) link_NAG-ASN : bond 0.00375 ( 8) link_NAG-ASN : angle 1.98522 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 324 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7322 (tpm170) cc_final: 0.7003 (tpm170) REVERT: A 191 ASP cc_start: 0.7053 (m-30) cc_final: 0.6808 (m-30) REVERT: A 229 ASN cc_start: 0.6383 (p0) cc_final: 0.6024 (p0) REVERT: A 259 SER cc_start: 0.8343 (t) cc_final: 0.8062 (p) REVERT: A 485 ILE cc_start: 0.7130 (pt) cc_final: 0.6852 (mt) REVERT: A 792 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7204 (mt-10) REVERT: B 128 TRP cc_start: 0.7681 (OUTLIER) cc_final: 0.7170 (m100) REVERT: B 201 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5673 (tm-30) REVERT: B 284 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.6240 (mp10) REVERT: B 393 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6050 (pt) REVERT: B 436 TRP cc_start: 0.7584 (m100) cc_final: 0.7368 (m100) REVERT: B 583 ILE cc_start: 0.6364 (OUTLIER) cc_final: 0.5739 (pp) REVERT: B 662 CYS cc_start: 0.6308 (OUTLIER) cc_final: 0.6086 (t) REVERT: B 823 SER cc_start: 0.7808 (OUTLIER) cc_final: 0.6559 (p) REVERT: B 899 PRO cc_start: 0.5465 (Cg_exo) cc_final: 0.5251 (Cg_endo) REVERT: B 914 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7393 (tt) REVERT: B 997 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7770 (mmtp) REVERT: C 278 ARG cc_start: 0.6320 (ttt90) cc_final: 0.6027 (tpt-90) REVERT: C 279 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7263 (tm) REVERT: C 436 TRP cc_start: 0.5926 (m100) cc_final: 0.5710 (m100) REVERT: C 612 TRP cc_start: 0.5078 (t-100) cc_final: 0.4682 (t-100) REVERT: C 733 GLU cc_start: 0.6372 (tt0) cc_final: 0.6154 (tp30) REVERT: C 929 ILE cc_start: 0.6097 (pp) cc_final: 0.5298 (pt) REVERT: E 37 TRP cc_start: 0.7674 (p90) cc_final: 0.7402 (p90) outliers start: 93 outliers final: 62 residues processed: 393 average time/residue: 0.5220 time to fit residues: 242.4936 Evaluate side-chains 388 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 316 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 998 CYS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 823 SER Chi-restraints excluded: chain B residue 847 TRP Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 997 LYS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 855 MET Chi-restraints excluded: chain C residue 903 TRP Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 257 optimal weight: 0.4980 chunk 296 optimal weight: 1.9990 chunk 140 optimal weight: 0.2980 chunk 16 optimal weight: 0.4980 chunk 263 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 297 optimal weight: 0.3980 chunk 189 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN A1020 HIS ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 HIS C 904 GLN E 117 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.190773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.170491 restraints weight = 36025.315| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 2.58 r_work: 0.4187 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.855 24701 Z= 0.164 Angle : 0.664 9.656 33608 Z= 0.337 Chirality : 0.045 0.241 3554 Planarity : 0.005 0.063 4330 Dihedral : 7.742 87.639 3712 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.57 % Allowed : 30.73 % Favored : 65.70 % 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: -1.05 (0.15), residues: 3090 helix: 1.19 (0.20), residues: 713 sheet: -1.10 (0.33), residues: 244 loop : -1.40 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 381 TYR 0.022 0.002 TYR B 424 PHE 0.019 0.001 PHE A 638 TRP 0.056 0.002 TRP G 37 HIS 0.011 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00383 (24591) covalent geometry : angle 0.65489 (33383) SS BOND : bond 0.00470 ( 93) SS BOND : angle 1.25751 ( 186) hydrogen bonds : bond 0.03755 ( 734) hydrogen bonds : angle 4.76599 ( 1935) Misc. bond : bond 0.45562 ( 4) link_BETA1-4 : bond 0.00680 ( 5) link_BETA1-4 : angle 2.34681 ( 15) link_NAG-ASN : bond 0.00419 ( 8) link_NAG-ASN : angle 2.07855 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8091.20 seconds wall clock time: 138 minutes 36.60 seconds (8316.60 seconds total)