Starting phenix.real_space_refine on Mon May 4 15:15:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nb8_49221/05_2026/9nb8_49221.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nb8_49221/05_2026/9nb8_49221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nb8_49221/05_2026/9nb8_49221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nb8_49221/05_2026/9nb8_49221.map" model { file = "/net/cci-nas-00/data/ceres_data/9nb8_49221/05_2026/9nb8_49221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nb8_49221/05_2026/9nb8_49221.cif" } resolution = 4.0 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= 0.011 sd= 0.055 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 21 9.91 5 Fe 2 7.16 5 S 215 5.16 5 C 13716 2.51 5 N 3967 2.21 5 O 4250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22171 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6494 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 24, 'TRANS': 833} Chain breaks: 1 Chain: "B" Number of atoms: 5684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5684 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 23, 'TRANS': 727} Chain breaks: 1 Chain: "C" Number of atoms: 5684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5684 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 23, 'TRANS': 727} Chain breaks: 1 Chain: "D" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "E" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "F" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2024 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 13, 'TRANS': 245} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CA': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' CA': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.79, per 1000 atoms: 0.26 Number of scatterers: 22171 At special positions: 0 Unit cell: (137.64, 144.3, 158.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 Ca 21 19.99 S 215 16.00 O 4250 8.00 N 3967 7.00 C 13716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=91, symmetry=0 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 258 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 472 " distance=2.02 Simple disulfide: pdb=" SG CYS A 442 " - pdb=" SG CYS A 452 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 547 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 682 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 693 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 808 " distance=2.03 Simple disulfide: pdb=" SG CYS A 757 " - pdb=" SG CYS A 818 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 869 " distance=2.03 Simple disulfide: pdb=" SG CYS A 864 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS A 905 " distance=2.03 Simple disulfide: pdb=" SG CYS A 938 " - pdb=" SG CYS A 972 " distance=2.03 Simple disulfide: pdb=" SG CYS A 954 " - pdb=" SG CYS A1018 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A1028 " distance=2.03 Simple disulfide: pdb=" SG CYS A 998 " - pdb=" SG CYS A1008 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.04 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 442 " - pdb=" SG CYS B 452 " distance=2.03 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 547 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 693 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 728 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 808 " distance=2.03 Simple disulfide: pdb=" SG CYS B 757 " - pdb=" SG CYS B 818 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B 869 " distance=2.03 Simple disulfide: pdb=" SG CYS B 864 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B 895 " - pdb=" SG CYS B 905 " distance=2.03 Simple disulfide: pdb=" SG CYS B 938 " - pdb=" SG CYS B 972 " distance=2.03 Simple disulfide: pdb=" SG CYS B 954 " - pdb=" SG CYS B1018 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B1028 " distance=2.03 Simple disulfide: pdb=" SG CYS B 998 " - pdb=" SG CYS B1008 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 309 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 355 " distance=2.04 Simple disulfide: pdb=" SG CYS C 304 " - pdb=" SG CYS C 365 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 416 " distance=2.03 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 462 " distance=2.03 Simple disulfide: pdb=" SG CYS C 411 " - pdb=" SG CYS C 472 " distance=2.03 Simple disulfide: pdb=" SG CYS C 442 " - pdb=" SG CYS C 452 " distance=2.03 Simple disulfide: pdb=" SG CYS C 487 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 516 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 547 " - pdb=" SG CYS C 557 " distance=2.03 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 626 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 672 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 693 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 728 " - pdb=" SG CYS C 762 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 808 " distance=2.03 Simple disulfide: pdb=" SG CYS C 757 " - pdb=" SG CYS C 818 " distance=2.03 Simple disulfide: pdb=" SG CYS C 788 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 835 " - pdb=" SG CYS C 869 " distance=2.03 Simple disulfide: pdb=" SG CYS C 864 " - pdb=" SG CYS C 925 " distance=2.03 Simple disulfide: pdb=" SG CYS C 895 " - pdb=" SG CYS C 905 " distance=2.03 Simple disulfide: pdb=" SG CYS C 938 " - pdb=" SG CYS C 972 " distance=2.03 Simple disulfide: pdb=" SG CYS C 954 " - pdb=" SG CYS C1018 " distance=2.03 Simple disulfide: pdb=" SG CYS C 967 " - pdb=" SG CYS C1028 " distance=2.02 Simple disulfide: pdb=" SG CYS C 998 " - pdb=" SG CYS C1008 " distance=2.03 Simple disulfide: pdb=" SG CYS F 90 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 250 " - pdb=" SG CYS F 281 " distance=2.03 Simple disulfide: pdb=" SG CYS F 292 " - pdb=" SG CYS F 322 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 1.3 seconds 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5156 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 49 sheets defined 22.2% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.621A pdb=" N CYS A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 341 through 346 removed outlier: 4.070A pdb=" N LYS A 346 " --> pdb=" O TRP A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 removed outlier: 3.804A pdb=" N VAL A 409 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 613 through 624 Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 749 through 760 removed outlier: 4.457A pdb=" N VAL A 755 " --> pdb=" O SER A 751 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL A 756 " --> pdb=" O ASP A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 856 through 868 Processing helix chain 'A' and resid 901 through 905 Processing helix chain 'A' and resid 959 through 971 Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 403 through 414 removed outlier: 3.778A pdb=" N VAL B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.519A pdb=" N ASP B 572 " --> pdb=" O HIS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 625 removed outlier: 3.983A pdb=" N ALA B 617 " --> pdb=" O ASP B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 removed outlier: 3.555A pdb=" N VAL B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 756 " --> pdb=" O ASP B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 868 removed outlier: 3.509A pdb=" N LEU B 867 " --> pdb=" O VAL B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 905 Processing helix chain 'B' and resid 959 through 971 Processing helix chain 'B' and resid 1004 through 1008 removed outlier: 3.545A pdb=" N ASP B1007 " --> pdb=" O SER B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1023 removed outlier: 3.778A 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: 3.608A pdb=" N GLU C 359 " --> pdb=" O ASN C 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP C 360 " --> pdb=" O HIS C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 356 through 360' Processing helix chain 'C' and resid 403 through 414 removed outlier: 4.327A pdb=" N VAL C 409 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 519 removed outlier: 4.298A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU C 518 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 613 through 624 removed outlier: 3.911A pdb=" N VAL C 619 " --> pdb=" O GLU C 615 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 620 " --> pdb=" O ASP C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 662 Processing helix chain 'C' and resid 749 through 760 removed outlier: 4.149A pdb=" N VAL C 755 " --> pdb=" O SER C 751 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 756 " --> pdb=" O ASP C 752 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 760 " --> pdb=" O VAL C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 868 Processing helix chain 'C' and resid 901 through 905 Processing helix chain 'C' and resid 959 through 971 removed outlier: 4.059A pdb=" N VAL C 965 " --> pdb=" O ASP C 961 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL C 966 " --> pdb=" O ASP C 962 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS C 967 " --> pdb=" O ALA C 963 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 970 " --> pdb=" O VAL C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1023 Processing helix chain 'D' and resid 4 through 19 Processing helix chain 'D' and resid 21 through 37 Processing helix chain 'D' and resid 38 through 44 removed outlier: 3.656A pdb=" N THR D 42 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE D 44 " --> pdb=" O LYS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 73 Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.689A pdb=" N ALA D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 96 through 114 removed outlier: 4.177A pdb=" N LYS D 100 " --> pdb=" O PRO D 96 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 138 Processing helix chain 'E' and resid 5 through 19 removed outlier: 3.650A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E 19 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 36 removed outlier: 3.844A pdb=" N VAL E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 42 Processing helix chain 'E' and resid 43 through 47 removed outlier: 3.699A pdb=" N PHE E 46 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 58 Processing helix chain 'E' and resid 58 through 78 removed outlier: 3.658A pdb=" N PHE E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 97 removed outlier: 3.542A pdb=" N PHE E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS E 96 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 120 Processing helix chain 'E' and resid 124 through 146 removed outlier: 3.771A pdb=" N LYS E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 147 removed outlier: 3.714A pdb=" N LEU F 145 " --> pdb=" O THR F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 162 removed outlier: 3.510A pdb=" N ILE F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) Proline residue: F 160 - end of helix Processing helix chain 'F' and resid 246 through 256 removed outlier: 3.600A pdb=" N CYS F 250 " --> pdb=" O ASP F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 347 removed outlier: 3.954A pdb=" N ASP F 338 " --> pdb=" O THR F 334 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TRP F 339 " --> pdb=" O SER F 335 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN F 347 " --> pdb=" O THR F 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 269 removed outlier: 3.660A pdb=" N VAL A 269 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 278 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 269 removed outlier: 3.660A pdb=" N VAL A 269 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 278 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 277 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 363 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 376 removed outlier: 7.226A pdb=" N THR A 471 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 376 removed outlier: 6.800A pdb=" N VAL A 386 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL A 397 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU A 437 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS A 396 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 477 through 481 removed outlier: 3.973A pdb=" N GLU A 477 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 575 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLY A 574 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE A 527 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 576 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA9, first strand: chain 'A' and resid 583 through 586 removed outlier: 6.488A pdb=" N VAL A 596 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TRP A 646 " --> pdb=" O TRP A 604 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER A 606 " --> pdb=" O TRP A 646 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 586 Processing sheet with id=AB2, first strand: chain 'A' and resid 649 through 650 Processing sheet with id=AB3, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AB4, first strand: chain 'A' and resid 719 through 722 removed outlier: 3.737A pdb=" N GLY A 730 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 816 " --> pdb=" O GLY A 730 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY A 815 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA A 768 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE A 817 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.513A pdb=" N ARG A 838 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP A 922 " --> pdb=" O ASN A 876 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN A 876 " --> pdb=" O TRP A 922 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR A 924 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 874 " --> pdb=" O THR A 924 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.513A pdb=" N ARG A 838 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 839 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL A 850 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP A 889 " --> pdb=" O TRP A 847 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR A 849 " --> pdb=" O TRP A 889 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 929 through 932 Processing sheet with id=AB8, first strand: chain 'A' and resid 975 through 978 removed outlier: 3.502A pdb=" N LEU A 976 " --> pdb=" O ASN A1027 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN A1027 " --> pdb=" O LEU A 976 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 267 through 269 removed outlier: 6.593A pdb=" N LEU B 279 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE B 290 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP B 329 " --> pdb=" O TRP B 287 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR B 289 " --> pdb=" O TRP B 329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AC2, first strand: chain 'B' and resid 372 through 377 removed outlier: 3.608A pdb=" N ILE B 470 " --> pdb=" O GLY B 384 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B 421 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 396 through 397 removed outlier: 6.299A pdb=" N LYS B 396 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N LEU B 439 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 438 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN B 456 " --> pdb=" O PHE B 438 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 480 through 481 removed outlier: 3.636A pdb=" N SER B 526 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 494 through 495 Processing sheet with id=AC6, first strand: chain 'B' and resid 501 through 502 removed outlier: 6.738A pdb=" N SER B 501 " --> pdb=" O TRP B 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 543 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 583 through 586 removed outlier: 3.509A pdb=" N GLY B 605 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 583 through 586 removed outlier: 3.749A pdb=" N GLY B 594 " --> pdb=" O VAL B 680 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 680 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 649 through 650 removed outlier: 3.869A pdb=" N MET B 649 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 665 " --> pdb=" O MET B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 719 through 722 Processing sheet with id=AD3, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.627A pdb=" N VAL B 816 " --> pdb=" O GLY B 730 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE B 817 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 822 through 827 removed outlier: 3.543A pdb=" N SER B 823 " --> pdb=" O PHE B 842 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 825 " --> pdb=" O GLU B 840 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 822 through 827 removed outlier: 3.543A pdb=" N SER B 823 " --> pdb=" O PHE B 842 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 825 " --> pdb=" O GLU B 840 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 837 " --> pdb=" O ILE B 923 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 929 through 932 removed outlier: 6.438A pdb=" N ALA B1025 " --> pdb=" O ALA B 978 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA B 978 " --> pdb=" O ALA B1025 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN B1027 " --> pdb=" O LEU B 976 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 929 through 932 removed outlier: 7.070A pdb=" N VAL B 942 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL B 953 " --> pdb=" O VAL B 942 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TRP B 992 " --> pdb=" O TRP B 950 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR B 952 " --> pdb=" O TRP B 992 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 266 through 268 removed outlier: 4.022A pdb=" N VAL C 281 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY C 288 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 313 through 316 Processing sheet with id=AE1, first strand: chain 'C' and resid 372 through 376 removed outlier: 6.824A pdb=" N VAL C 386 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL C 397 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N LEU C 437 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS C 396 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N LEU C 439 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 372 through 376 removed outlier: 3.559A pdb=" N ILE C 470 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 477 through 481 removed outlier: 3.548A pdb=" N SER C 526 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 477 through 481 removed outlier: 6.679A pdb=" N VAL C 491 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE C 502 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TRP C 541 " --> pdb=" O TRP C 499 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER C 501 " --> pdb=" O TRP C 541 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 583 through 586 Processing sheet with id=AE6, first strand: chain 'C' and resid 720 through 722 removed outlier: 6.969A pdb=" N VAL C 732 " --> pdb=" O ILE C 743 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE C 743 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TRP C 782 " --> pdb=" O TRP C 740 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N THR C 742 " --> pdb=" O TRP C 782 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 765 through 769 removed outlier: 3.735A pdb=" N ASN C 767 " --> pdb=" O ILE C 817 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 824 through 827 Processing sheet with id=AE9, first strand: chain 'C' and resid 824 through 827 removed outlier: 6.787A pdb=" N LEU C 839 " --> pdb=" O VAL C 850 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP C 889 " --> pdb=" O TRP C 847 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR C 849 " --> pdb=" O TRP C 889 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 929 through 932 Processing sheet with id=AF2, first strand: chain 'C' and resid 929 through 932 removed outlier: 3.792A pdb=" N ALA C1025 " --> pdb=" O PHE C 979 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN C1027 " --> pdb=" O LYS C 977 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS C 977 " --> pdb=" O ASN C1027 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 107 through 108 removed outlier: 4.205A pdb=" N LYS F 238 " --> pdb=" O GLY F 224 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL F 219 " --> pdb=" O HIS F 303 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS F 303 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER F 223 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA F 299 " --> pdb=" O SER F 223 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE F 300 " --> pdb=" O THR F 313 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR F 311 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP F 304 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR F 309 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F 315 " --> pdb=" O VAL F 331 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 170 through 171 removed outlier: 3.894A pdb=" N LYS F 192 " --> pdb=" O LYS F 176 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS F 176 " --> pdb=" O LYS F 192 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1839 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: 4.88 Time building geometry restraints manager: 2.76 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: 8419 1.38 - 1.55: 14000 1.55 - 1.72: 7 1.72 - 1.89: 245 1.89 - 2.06: 8 Bond restraints: 22679 Sorted by residual: bond pdb=" O1 OXY D 202 " pdb=" O2 OXY D 202 " ideal model delta sigma weight residual 1.109 1.206 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" O1 OXY E 202 " pdb=" O2 OXY E 202 " ideal model delta sigma weight residual 1.109 1.205 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" CA GLN C 425 " pdb=" C GLN C 425 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.31e-02 5.83e+03 5.55e+00 bond pdb=" CA TYR A 427 " pdb=" C TYR A 427 " ideal model delta sigma weight residual 1.524 1.498 0.025 1.37e-02 5.33e+03 3.37e+00 bond pdb=" CB CYS A 258 " pdb=" SG CYS A 258 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.46e+00 ... (remaining 22674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 30299 2.21 - 4.42: 408 4.42 - 6.62: 47 6.62 - 8.83: 15 8.83 - 11.04: 2 Bond angle restraints: 30771 Sorted by residual: angle pdb=" N VAL B 426 " pdb=" CA VAL B 426 " pdb=" C VAL B 426 " ideal model delta sigma weight residual 108.11 116.08 -7.97 1.40e+00 5.10e-01 3.24e+01 angle pdb=" N VAL C 426 " pdb=" CA VAL C 426 " pdb=" C VAL C 426 " ideal model delta sigma weight residual 108.11 114.91 -6.80 1.40e+00 5.10e-01 2.36e+01 angle pdb=" CA CYS A 258 " pdb=" CB CYS A 258 " pdb=" SG CYS A 258 " ideal model delta sigma weight residual 114.40 125.44 -11.04 2.30e+00 1.89e-01 2.30e+01 angle pdb=" N LYS B 625 " pdb=" CA LYS B 625 " pdb=" C LYS B 625 " ideal model delta sigma weight residual 113.23 107.73 5.50 1.22e+00 6.72e-01 2.03e+01 angle pdb=" C CYS A 592 " pdb=" N GLU A 593 " pdb=" CA GLU A 593 " ideal model delta sigma weight residual 121.54 130.04 -8.50 1.91e+00 2.74e-01 1.98e+01 ... (remaining 30766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11729 17.99 - 35.99: 1298 35.99 - 53.98: 345 53.98 - 71.98: 45 71.98 - 89.97: 20 Dihedral angle restraints: 13437 sinusoidal: 5345 harmonic: 8092 Sorted by residual: dihedral pdb=" CB CYS C 693 " pdb=" SG CYS C 693 " pdb=" SG CYS C 713 " pdb=" CB CYS C 713 " ideal model delta sinusoidal sigma weight residual -86.00 0.31 -86.31 1 1.00e+01 1.00e-02 8.98e+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 93.00 177.72 -84.72 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS C 516 " pdb=" SG CYS C 516 " pdb=" SG CYS C 577 " pdb=" CB CYS C 577 " ideal model delta sinusoidal sigma weight residual 93.00 171.82 -78.82 1 1.00e+01 1.00e-02 7.74e+01 ... (remaining 13434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2497 0.045 - 0.090: 579 0.090 - 0.135: 173 0.135 - 0.180: 6 0.180 - 0.224: 1 Chirality restraints: 3256 Sorted by residual: chirality pdb=" CG LEU E 69 " pdb=" CB LEU E 69 " pdb=" CD1 LEU E 69 " pdb=" CD2 LEU E 69 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA GLN C 686 " pdb=" N GLN C 686 " pdb=" C GLN C 686 " pdb=" CB GLN C 686 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CG LEU A 519 " pdb=" CB LEU A 519 " pdb=" CD1 LEU A 519 " pdb=" CD2 LEU A 519 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 3253 not shown) Planarity restraints: 4018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 847 " 0.016 2.00e-02 2.50e+03 1.63e-02 6.66e+00 pdb=" CG TRP C 847 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 847 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 847 " -0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP C 847 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 847 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 847 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 847 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 847 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP C 847 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 898 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO A 899 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 424 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C TYR A 424 " -0.035 2.00e-02 2.50e+03 pdb=" O TYR A 424 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 425 " 0.012 2.00e-02 2.50e+03 ... (remaining 4015 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 527 2.66 - 3.22: 22254 3.22 - 3.78: 35447 3.78 - 4.34: 46478 4.34 - 4.90: 73033 Nonbonded interactions: 177739 Sorted by model distance: nonbonded pdb=" O ASP B 891 " pdb=" OG SER B 907 " model vdw 2.101 3.040 nonbonded pdb=" NH2 ARG A 198 " pdb=" O ASN A 231 " model vdw 2.104 3.120 nonbonded pdb=" O SER B 423 " pdb=" OG1 THR B 471 " model vdw 2.140 3.040 nonbonded pdb=" OD1 ASP D 7 " pdb=" OG SER D 125 " model vdw 2.140 3.040 nonbonded pdb=" OD1 ASP B 926 " pdb=" N ASN B 927 " model vdw 2.165 3.120 ... (remaining 177734 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 1205) selection = (chain 'B' and resid 263 through 1205) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.410 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: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.430 Find NCS groups from input model: 0.460 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: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 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 0.299 22772 Z= 0.172 Angle : 0.651 11.039 30953 Z= 0.352 Chirality : 0.042 0.224 3256 Planarity : 0.004 0.053 4018 Dihedral : 15.487 89.969 8008 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 2.02 % Allowed : 15.68 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.15), residues: 2886 helix: 0.80 (0.22), residues: 522 sheet: -1.05 (0.34), residues: 233 loop : -0.70 (0.12), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 517 TYR 0.019 0.002 TYR F 287 PHE 0.014 0.002 PHE C 842 TRP 0.039 0.002 TRP C 847 HIS 0.013 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00364 (22679) covalent geometry : angle 0.64896 (30771) SS BOND : bond 0.00267 ( 91) SS BOND : angle 0.92378 ( 182) hydrogen bonds : bond 0.25511 ( 633) hydrogen bonds : angle 8.88325 ( 1839) Misc. bond : bond 0.21176 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 0.817 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: 0.5692 (tmm) cc_final: 0.5400 (tmm) REVERT: A 188 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: A 427 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6950 (m-80) REVERT: A 649 MET cc_start: 0.6208 (ttt) cc_final: 0.5615 (tpp) REVERT: A 754 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7693 (t-90) REVERT: B 649 MET cc_start: 0.8133 (ptt) cc_final: 0.7483 (ptt) REVERT: B 659 MET cc_start: 0.8604 (tmm) cc_final: 0.8183 (tmm) REVERT: B 914 LEU cc_start: 0.9030 (tp) cc_final: 0.8747 (tt) REVERT: C 509 LEU cc_start: 0.8875 (pt) cc_final: 0.8475 (mt) REVERT: C 583 ILE cc_start: 0.8578 (mm) cc_final: 0.8319 (mm) REVERT: E 20 ASN cc_start: 0.8479 (p0) cc_final: 0.8071 (p0) REVERT: E 86 PHE cc_start: 0.7537 (m-80) cc_final: 0.6901 (m-80) REVERT: E 100 ASP cc_start: 0.8888 (t70) cc_final: 0.8645 (t70) REVERT: E 101 PRO cc_start: 0.8933 (Cg_exo) cc_final: 0.8585 (Cg_endo) REVERT: E 102 GLU cc_start: 0.7417 (mp0) cc_final: 0.7176 (mp0) REVERT: E 104 PHE cc_start: 0.8364 (m-80) cc_final: 0.8020 (m-80) REVERT: F 204 MET cc_start: 0.8373 (tmm) cc_final: 0.8069 (tmm) REVERT: F 218 ARG cc_start: 0.8052 (tpp-160) cc_final: 0.7368 (tpp80) REVERT: F 284 MET cc_start: 0.4328 (ppp) cc_final: 0.3963 (ppp) REVERT: F 330 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.6460 (p90) outliers start: 48 outliers final: 35 residues processed: 259 average time/residue: 0.1387 time to fit residues: 58.8519 Evaluate side-chains 250 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 994 ASN Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain C residue 618 HIS Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 647 ARG Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 475 HIS ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 HIS ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS C 754 HIS F 123 HIS ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.095938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.081771 restraints weight = 92910.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.082842 restraints weight = 64208.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.084579 restraints weight = 46938.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.084546 restraints weight = 38530.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.084525 restraints weight = 34104.862| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.259 22772 Z= 0.166 Angle : 0.624 9.599 30953 Z= 0.329 Chirality : 0.043 0.169 3256 Planarity : 0.004 0.050 4018 Dihedral : 7.034 83.585 3152 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 2.91 % Allowed : 16.31 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 2886 helix: 1.22 (0.23), residues: 545 sheet: -0.83 (0.29), residues: 304 loop : -0.78 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 374 TYR 0.023 0.002 TYR F 330 PHE 0.013 0.001 PHE F 280 TRP 0.019 0.001 TRP B 450 HIS 0.010 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00374 (22679) covalent geometry : angle 0.62163 (30771) SS BOND : bond 0.00349 ( 91) SS BOND : angle 0.90749 ( 182) hydrogen bonds : bond 0.04262 ( 633) hydrogen bonds : angle 5.77223 ( 1839) Misc. bond : bond 0.18311 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 247 time to evaluate : 0.880 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 166 ASN cc_start: 0.7481 (t0) cc_final: 0.7084 (p0) REVERT: A 188 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: A 339 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6783 (pm20) REVERT: A 649 MET cc_start: 0.5794 (ttt) cc_final: 0.5172 (tpp) REVERT: A 688 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: A 754 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.7907 (t-90) REVERT: A 813 ASP cc_start: 0.6284 (OUTLIER) cc_final: 0.6076 (m-30) REVERT: B 649 MET cc_start: 0.7797 (ptt) cc_final: 0.7263 (ptt) REVERT: B 914 LEU cc_start: 0.8916 (tp) cc_final: 0.8585 (tt) REVERT: C 318 ARG cc_start: 0.7132 (ppt170) cc_final: 0.6691 (ptt90) REVERT: C 612 TRP cc_start: 0.8082 (OUTLIER) cc_final: 0.7682 (m-10) REVERT: C 876 ASN cc_start: 0.7917 (p0) cc_final: 0.7562 (p0) REVERT: C 970 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8530 (tp) REVERT: D 76 ASP cc_start: 0.7749 (t0) cc_final: 0.6753 (t0) REVERT: E 20 ASN cc_start: 0.8601 (p0) cc_final: 0.8088 (p0) REVERT: E 101 PRO cc_start: 0.8818 (Cg_exo) cc_final: 0.8531 (Cg_endo) REVERT: E 102 GLU cc_start: 0.7628 (mp0) cc_final: 0.7314 (mp0) REVERT: E 118 HIS cc_start: 0.8022 (OUTLIER) cc_final: 0.7699 (m-70) REVERT: F 218 ARG cc_start: 0.8118 (tpp-160) cc_final: 0.7886 (tpp-160) REVERT: F 284 MET cc_start: 0.4611 (ppp) cc_final: 0.4350 (ppp) REVERT: F 319 ASP cc_start: 0.7742 (p0) cc_final: 0.7380 (p0) REVERT: F 330 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6493 (p90) outliers start: 69 outliers final: 30 residues processed: 299 average time/residue: 0.1408 time to fit residues: 69.0154 Evaluate side-chains 253 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 688 GLN Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 612 TRP Chi-restraints excluded: chain C residue 647 ARG Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 336 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 12 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 286 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN B 495 HIS ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS C 754 HIS F 123 HIS ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.095337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.080825 restraints weight = 92805.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.082313 restraints weight = 63492.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.083274 restraints weight = 47251.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.083549 restraints weight = 40837.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.083652 restraints weight = 35086.944| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.258 22772 Z= 0.168 Angle : 0.608 8.761 30953 Z= 0.320 Chirality : 0.042 0.160 3256 Planarity : 0.004 0.053 4018 Dihedral : 6.388 82.613 3103 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.73 % Rotamer: Outliers : 4.13 % Allowed : 17.95 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.15), residues: 2886 helix: 1.28 (0.23), residues: 545 sheet: -0.96 (0.30), residues: 288 loop : -0.83 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 825 TYR 0.024 0.001 TYR F 330 PHE 0.030 0.002 PHE E 104 TRP 0.031 0.002 TRP C 847 HIS 0.010 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00371 (22679) covalent geometry : angle 0.60609 (30771) SS BOND : bond 0.00340 ( 91) SS BOND : angle 0.87076 ( 182) hydrogen bonds : bond 0.03942 ( 633) hydrogen bonds : angle 5.37753 ( 1839) Misc. bond : bond 0.18216 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 236 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASN cc_start: 0.7304 (t0) cc_final: 0.7079 (p0) REVERT: A 188 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: A 339 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6758 (pm20) REVERT: A 754 HIS cc_start: 0.8450 (OUTLIER) cc_final: 0.7881 (t-90) REVERT: A 813 ASP cc_start: 0.6118 (OUTLIER) cc_final: 0.5887 (m-30) REVERT: B 649 MET cc_start: 0.8059 (ptt) cc_final: 0.7267 (ptt) REVERT: B 659 MET cc_start: 0.8692 (tmm) cc_final: 0.8300 (tmm) REVERT: B 914 LEU cc_start: 0.8830 (tp) cc_final: 0.8624 (tt) REVERT: B 927 ASN cc_start: 0.8415 (t0) cc_final: 0.8164 (t0) REVERT: C 280 GLU cc_start: 0.7626 (mt-10) cc_final: 0.6474 (pm20) REVERT: C 295 TRP cc_start: 0.2060 (OUTLIER) cc_final: 0.1075 (t-100) REVERT: C 373 LEU cc_start: 0.8849 (tt) cc_final: 0.8647 (tp) REVERT: C 564 GLU cc_start: 0.8304 (mt-10) cc_final: 0.6990 (pp20) REVERT: C 612 TRP cc_start: 0.8172 (OUTLIER) cc_final: 0.7736 (m-10) REVERT: D 76 ASP cc_start: 0.7747 (t0) cc_final: 0.6731 (t0) REVERT: D 141 TYR cc_start: 0.7892 (t80) cc_final: 0.7385 (t80) REVERT: E 8 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7700 (mt-10) REVERT: E 20 ASN cc_start: 0.8502 (p0) cc_final: 0.8059 (p0) REVERT: E 100 ASP cc_start: 0.8991 (t70) cc_final: 0.8681 (t70) REVERT: E 101 PRO cc_start: 0.8654 (Cg_exo) cc_final: 0.8224 (Cg_endo) REVERT: E 102 GLU cc_start: 0.7572 (mp0) cc_final: 0.7172 (mp0) REVERT: E 104 PHE cc_start: 0.8233 (m-80) cc_final: 0.7968 (m-80) REVERT: E 118 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.7402 (m170) REVERT: F 218 ARG cc_start: 0.8191 (tpp-160) cc_final: 0.7920 (tpp-160) REVERT: F 284 MET cc_start: 0.4692 (ppp) cc_final: 0.4409 (ppp) REVERT: F 319 ASP cc_start: 0.7891 (p0) cc_final: 0.7610 (p0) REVERT: F 330 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6494 (p90) outliers start: 98 outliers final: 62 residues processed: 309 average time/residue: 0.1324 time to fit residues: 68.0930 Evaluate side-chains 288 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 612 TRP Chi-restraints excluded: chain C residue 647 ARG Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 773 HIS Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 336 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 128 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS C 773 HIS F 123 HIS F 136 GLN F 144 ASN ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.095376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.080884 restraints weight = 92699.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.082389 restraints weight = 62174.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.083155 restraints weight = 47443.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.083333 restraints weight = 41938.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.083416 restraints weight = 38137.662| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.212 22772 Z= 0.151 Angle : 0.598 9.041 30953 Z= 0.311 Chirality : 0.042 0.160 3256 Planarity : 0.004 0.052 4018 Dihedral : 6.322 81.809 3103 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.80 % Rotamer: Outliers : 4.26 % Allowed : 18.58 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 2886 helix: 1.33 (0.23), residues: 542 sheet: -0.94 (0.30), residues: 287 loop : -0.84 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 412 TYR 0.023 0.002 TYR F 330 PHE 0.023 0.001 PHE E 104 TRP 0.028 0.001 TRP F 310 HIS 0.010 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00343 (22679) covalent geometry : angle 0.59727 (30771) SS BOND : bond 0.00308 ( 91) SS BOND : angle 0.73251 ( 182) hydrogen bonds : bond 0.03521 ( 633) hydrogen bonds : angle 5.14644 ( 1839) Misc. bond : bond 0.15016 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 240 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASN cc_start: 0.7420 (t0) cc_final: 0.7127 (p0) REVERT: A 188 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7735 (m-80) REVERT: A 339 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6798 (pm20) REVERT: A 546 GLN cc_start: 0.8382 (tm-30) cc_final: 0.8137 (tm-30) REVERT: A 623 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8097 (tt0) REVERT: A 754 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.7849 (t-90) REVERT: A 813 ASP cc_start: 0.6194 (OUTLIER) cc_final: 0.5988 (m-30) REVERT: B 649 MET cc_start: 0.8030 (ptt) cc_final: 0.7264 (ptt) REVERT: B 914 LEU cc_start: 0.8867 (tp) cc_final: 0.8657 (tt) REVERT: B 927 ASN cc_start: 0.8407 (t0) cc_final: 0.8157 (t0) REVERT: C 280 GLU cc_start: 0.7644 (mt-10) cc_final: 0.6476 (pm20) REVERT: C 295 TRP cc_start: 0.2031 (OUTLIER) cc_final: 0.0985 (t-100) REVERT: C 564 GLU cc_start: 0.8320 (mt-10) cc_final: 0.6910 (pp20) REVERT: C 612 TRP cc_start: 0.8235 (OUTLIER) cc_final: 0.7700 (m-10) REVERT: C 649 MET cc_start: 0.8095 (ttp) cc_final: 0.7532 (mtp) REVERT: C 840 GLU cc_start: 0.5898 (mp0) cc_final: 0.5430 (mm-30) REVERT: D 76 ASP cc_start: 0.7840 (t0) cc_final: 0.6759 (t0) REVERT: D 141 TYR cc_start: 0.7928 (t80) cc_final: 0.7454 (t80) REVERT: E 8 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7731 (mt-10) REVERT: E 20 ASN cc_start: 0.8561 (p0) cc_final: 0.8206 (p0) REVERT: E 100 ASP cc_start: 0.8977 (t70) cc_final: 0.8560 (t70) REVERT: E 101 PRO cc_start: 0.8773 (Cg_exo) cc_final: 0.8394 (Cg_endo) REVERT: E 102 GLU cc_start: 0.7573 (mp0) cc_final: 0.7137 (mp0) REVERT: E 104 PHE cc_start: 0.8285 (m-80) cc_final: 0.7981 (m-80) REVERT: E 118 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.7436 (m170) REVERT: F 218 ARG cc_start: 0.8200 (tpp-160) cc_final: 0.7890 (tpp-160) REVERT: F 247 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8257 (mt0) REVERT: F 284 MET cc_start: 0.4773 (ppp) cc_final: 0.4461 (ppp) REVERT: F 319 ASP cc_start: 0.7893 (p0) cc_final: 0.7639 (p0) outliers start: 101 outliers final: 72 residues processed: 310 average time/residue: 0.1296 time to fit residues: 66.9265 Evaluate side-chains 302 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 222 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 HIS Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 612 TRP Chi-restraints excluded: chain C residue 647 ARG Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 336 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 275 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 287 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 229 optimal weight: 0.5980 chunk 274 optimal weight: 8.9990 chunk 285 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 GLN ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS F 123 HIS F 272 GLN ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.096812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.082883 restraints weight = 92217.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.084006 restraints weight = 64085.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.084667 restraints weight = 45548.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.084955 restraints weight = 42538.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.084982 restraints weight = 38351.346| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 22772 Z= 0.112 Angle : 0.561 7.817 30953 Z= 0.290 Chirality : 0.041 0.184 3256 Planarity : 0.004 0.062 4018 Dihedral : 6.040 81.018 3103 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.92 % Favored : 95.05 % Rotamer: Outliers : 3.46 % Allowed : 19.72 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 2886 helix: 1.53 (0.24), residues: 538 sheet: -0.88 (0.31), residues: 278 loop : -0.79 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 476 TYR 0.021 0.001 TYR F 330 PHE 0.017 0.001 PHE E 104 TRP 0.020 0.001 TRP F 310 HIS 0.010 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00258 (22679) covalent geometry : angle 0.56038 (30771) SS BOND : bond 0.00280 ( 91) SS BOND : angle 0.64265 ( 182) hydrogen bonds : bond 0.03117 ( 633) hydrogen bonds : angle 4.79892 ( 1839) Misc. bond : bond 0.07364 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 255 time to evaluate : 0.821 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: 0.5810 (tmm) cc_final: 0.5610 (tmm) REVERT: A 188 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: A 546 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 623 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8085 (tt0) REVERT: A 740 TRP cc_start: 0.6286 (m100) cc_final: 0.5520 (m100) REVERT: A 754 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.7837 (t-90) REVERT: A 813 ASP cc_start: 0.5846 (OUTLIER) cc_final: 0.5638 (m-30) REVERT: A 927 ASN cc_start: 0.7817 (t0) cc_final: 0.7613 (t0) REVERT: B 649 MET cc_start: 0.7945 (ptt) cc_final: 0.7696 (ptp) REVERT: B 927 ASN cc_start: 0.8446 (t0) cc_final: 0.8163 (t0) REVERT: C 280 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6505 (pm20) REVERT: C 295 TRP cc_start: 0.1949 (OUTLIER) cc_final: 0.0899 (t-100) REVERT: C 564 GLU cc_start: 0.8365 (mt-10) cc_final: 0.6745 (pp20) REVERT: C 612 TRP cc_start: 0.8132 (OUTLIER) cc_final: 0.7626 (m-10) REVERT: C 649 MET cc_start: 0.8003 (ttp) cc_final: 0.7631 (mtp) REVERT: C 840 GLU cc_start: 0.5717 (mp0) cc_final: 0.5392 (mm-30) REVERT: D 74 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.9002 (t) REVERT: D 76 ASP cc_start: 0.7825 (t0) cc_final: 0.6750 (t0) REVERT: D 117 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7725 (mm-30) REVERT: E 8 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7639 (mt-10) REVERT: E 20 ASN cc_start: 0.8666 (p0) cc_final: 0.8335 (p0) REVERT: E 91 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8021 (mm-30) REVERT: E 100 ASP cc_start: 0.8986 (t70) cc_final: 0.8507 (t70) REVERT: E 102 GLU cc_start: 0.7616 (mp0) cc_final: 0.7311 (mp0) REVERT: E 104 PHE cc_start: 0.8298 (m-80) cc_final: 0.7942 (m-80) REVERT: E 118 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7399 (m-70) REVERT: F 218 ARG cc_start: 0.8095 (tpp-160) cc_final: 0.7785 (tpp-160) REVERT: F 247 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8231 (mt0) REVERT: F 284 MET cc_start: 0.4597 (ppp) cc_final: 0.4211 (ppp) REVERT: F 319 ASP cc_start: 0.7821 (p0) cc_final: 0.7565 (p0) outliers start: 82 outliers final: 57 residues processed: 314 average time/residue: 0.1323 time to fit residues: 69.2098 Evaluate side-chains 291 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 994 ASN Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 612 TRP Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 336 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 201 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 237 optimal weight: 0.0570 chunk 35 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 overall best weight: 1.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS F 123 HIS ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.095247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.080911 restraints weight = 93163.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.081949 restraints weight = 68326.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.082832 restraints weight = 48286.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.083122 restraints weight = 43174.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.083126 restraints weight = 38733.956| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 22772 Z= 0.151 Angle : 0.590 8.701 30953 Z= 0.307 Chirality : 0.042 0.167 3256 Planarity : 0.004 0.060 4018 Dihedral : 6.062 80.875 3096 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 4.55 % Allowed : 19.76 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.15), residues: 2886 helix: 1.44 (0.23), residues: 544 sheet: -1.02 (0.31), residues: 272 loop : -0.86 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 476 TYR 0.023 0.001 TYR F 330 PHE 0.013 0.001 PHE D 118 TRP 0.041 0.001 TRP C 847 HIS 0.011 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00349 (22679) covalent geometry : angle 0.58892 (30771) SS BOND : bond 0.00280 ( 91) SS BOND : angle 0.78815 ( 182) hydrogen bonds : bond 0.03222 ( 633) hydrogen bonds : angle 4.92699 ( 1839) Misc. bond : bond 0.12044 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 225 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: A 546 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 623 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8115 (tt0) REVERT: A 649 MET cc_start: 0.6596 (tpp) cc_final: 0.5849 (tpp) REVERT: A 754 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.7846 (t-90) REVERT: A 1005 LEU cc_start: 0.9221 (pp) cc_final: 0.8737 (mm) REVERT: B 649 MET cc_start: 0.8092 (ptt) cc_final: 0.7329 (ptt) REVERT: B 927 ASN cc_start: 0.8489 (t0) cc_final: 0.8210 (t0) REVERT: C 318 ARG cc_start: 0.7007 (ppt170) cc_final: 0.6683 (ptt90) REVERT: C 564 GLU cc_start: 0.8373 (mt-10) cc_final: 0.6909 (pp20) REVERT: C 612 TRP cc_start: 0.8172 (OUTLIER) cc_final: 0.7720 (m-10) REVERT: C 649 MET cc_start: 0.8140 (ttp) cc_final: 0.7733 (ttp) REVERT: C 773 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7469 (p-80) REVERT: D 74 VAL cc_start: 0.9333 (OUTLIER) cc_final: 0.9038 (t) REVERT: D 76 ASP cc_start: 0.7898 (t0) cc_final: 0.6818 (t0) REVERT: E 8 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7762 (mt-10) REVERT: E 20 ASN cc_start: 0.8676 (p0) cc_final: 0.8395 (p0) REVERT: E 100 ASP cc_start: 0.9051 (t70) cc_final: 0.8527 (t70) REVERT: E 102 GLU cc_start: 0.7513 (mp0) cc_final: 0.7214 (mp0) REVERT: E 104 PHE cc_start: 0.8323 (m-80) cc_final: 0.7977 (m-80) REVERT: E 118 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7385 (m170) REVERT: F 218 ARG cc_start: 0.8188 (tpp-160) cc_final: 0.7500 (tpp80) REVERT: F 247 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8194 (mt0) REVERT: F 284 MET cc_start: 0.4933 (ppp) cc_final: 0.4621 (ppp) outliers start: 108 outliers final: 75 residues processed: 304 average time/residue: 0.1273 time to fit residues: 65.3644 Evaluate side-chains 296 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 214 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 994 ASN Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 612 TRP Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 773 HIS Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1008 CYS Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 336 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 115 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 117 optimal weight: 0.4980 chunk 268 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 GLN C 754 HIS F 123 HIS ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.095834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.081343 restraints weight = 95601.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.082920 restraints weight = 66552.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.083265 restraints weight = 45464.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.083364 restraints weight = 40278.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.083474 restraints weight = 37436.629| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.216 22772 Z= 0.158 Angle : 0.601 9.569 30953 Z= 0.312 Chirality : 0.042 0.173 3256 Planarity : 0.004 0.053 4018 Dihedral : 6.151 81.438 3096 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 4.38 % Allowed : 20.14 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 2886 helix: 1.41 (0.23), residues: 545 sheet: -1.11 (0.30), residues: 281 loop : -0.91 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 584 TYR 0.023 0.002 TYR F 330 PHE 0.013 0.001 PHE C 842 TRP 0.028 0.001 TRP C 847 HIS 0.012 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00364 (22679) covalent geometry : angle 0.59950 (30771) SS BOND : bond 0.00297 ( 91) SS BOND : angle 0.83675 ( 182) hydrogen bonds : bond 0.03204 ( 633) hydrogen bonds : angle 4.90613 ( 1839) Misc. bond : bond 0.15297 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 220 time to evaluate : 1.051 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 188 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: A 546 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8189 (tm-30) REVERT: A 623 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8106 (tt0) REVERT: A 640 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6216 (tptp) REVERT: A 649 MET cc_start: 0.6653 (tpp) cc_final: 0.5837 (tpp) REVERT: A 754 HIS cc_start: 0.8343 (OUTLIER) cc_final: 0.7829 (t-90) REVERT: A 927 ASN cc_start: 0.7854 (t0) cc_final: 0.7613 (t0) REVERT: A 1005 LEU cc_start: 0.9183 (pp) cc_final: 0.8727 (mm) REVERT: B 649 MET cc_start: 0.8063 (ptt) cc_final: 0.7286 (ptt) REVERT: B 927 ASN cc_start: 0.8451 (t0) cc_final: 0.8175 (t0) REVERT: C 564 GLU cc_start: 0.8380 (mt-10) cc_final: 0.6943 (pp20) REVERT: C 612 TRP cc_start: 0.8172 (OUTLIER) cc_final: 0.7760 (m-10) REVERT: C 649 MET cc_start: 0.8143 (ttp) cc_final: 0.7905 (ttp) REVERT: C 773 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7516 (p-80) REVERT: C 840 GLU cc_start: 0.5932 (mp0) cc_final: 0.5719 (mp0) REVERT: D 74 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9182 (t) REVERT: D 76 ASP cc_start: 0.7874 (t0) cc_final: 0.6809 (t0) REVERT: E 8 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7757 (mt-10) REVERT: E 20 ASN cc_start: 0.8615 (p0) cc_final: 0.7924 (p0) REVERT: E 104 PHE cc_start: 0.8308 (m-80) cc_final: 0.7926 (m-80) REVERT: F 218 ARG cc_start: 0.8200 (tpp-160) cc_final: 0.7517 (tpp80) REVERT: F 247 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8243 (mt0) REVERT: F 284 MET cc_start: 0.4710 (ppp) cc_final: 0.4386 (ppp) outliers start: 104 outliers final: 82 residues processed: 295 average time/residue: 0.1331 time to fit residues: 64.9840 Evaluate side-chains 298 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 209 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 994 ASN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 612 TRP Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 773 HIS Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1008 CYS Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 336 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 203 optimal weight: 0.0870 chunk 235 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 128 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 216 optimal weight: 0.1980 chunk 284 optimal weight: 8.9990 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 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 GLN ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS F 123 HIS ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.097955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.083697 restraints weight = 96040.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.085252 restraints weight = 67012.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.085577 restraints weight = 46012.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.085852 restraints weight = 41003.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.085924 restraints weight = 38373.082| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 22772 Z= 0.104 Angle : 0.572 7.860 30953 Z= 0.292 Chirality : 0.041 0.153 3256 Planarity : 0.004 0.055 4018 Dihedral : 5.892 80.892 3094 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.18 % Rotamer: Outliers : 3.75 % Allowed : 21.15 % Favored : 75.09 % 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: -0.60 (0.15), residues: 2886 helix: 1.50 (0.23), residues: 546 sheet: -1.08 (0.29), residues: 310 loop : -0.85 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 584 TYR 0.021 0.001 TYR D 141 PHE 0.015 0.001 PHE E 104 TRP 0.023 0.001 TRP C 847 HIS 0.013 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00243 (22679) covalent geometry : angle 0.57188 (30771) SS BOND : bond 0.00184 ( 91) SS BOND : angle 0.65888 ( 182) hydrogen bonds : bond 0.02853 ( 633) hydrogen bonds : angle 4.65722 ( 1839) Misc. bond : bond 0.05888 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 231 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: A 546 GLN cc_start: 0.8341 (tm-30) cc_final: 0.8036 (tm-30) REVERT: A 623 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8096 (tt0) REVERT: A 649 MET cc_start: 0.6459 (tpp) cc_final: 0.6139 (tpp) REVERT: A 740 TRP cc_start: 0.6571 (m100) cc_final: 0.5923 (m100) REVERT: A 754 HIS cc_start: 0.8260 (OUTLIER) cc_final: 0.7787 (t-90) REVERT: A 927 ASN cc_start: 0.7766 (t0) cc_final: 0.7512 (t0) REVERT: A 1005 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8765 (mm) REVERT: B 927 ASN cc_start: 0.8470 (t0) cc_final: 0.8176 (t0) REVERT: C 537 ASN cc_start: 0.8230 (p0) cc_final: 0.7858 (p0) REVERT: C 612 TRP cc_start: 0.8063 (OUTLIER) cc_final: 0.7562 (m-10) REVERT: C 649 MET cc_start: 0.8093 (ttp) cc_final: 0.7607 (mtp) REVERT: C 773 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.7339 (p-80) REVERT: C 840 GLU cc_start: 0.5683 (mp0) cc_final: 0.5387 (mm-30) REVERT: D 74 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.8979 (t) REVERT: D 76 ASP cc_start: 0.7844 (t0) cc_final: 0.6735 (t0) REVERT: D 117 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7681 (mm-30) REVERT: E 8 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7913 (mt-10) REVERT: E 20 ASN cc_start: 0.8533 (p0) cc_final: 0.8146 (p0) REVERT: E 100 ASP cc_start: 0.8973 (t70) cc_final: 0.8452 (t70) REVERT: E 102 GLU cc_start: 0.7379 (mp0) cc_final: 0.7097 (mp0) REVERT: E 104 PHE cc_start: 0.8289 (m-80) cc_final: 0.7954 (m-80) REVERT: E 118 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7311 (m170) REVERT: F 218 ARG cc_start: 0.8058 (tpp-160) cc_final: 0.7408 (tpp80) outliers start: 89 outliers final: 65 residues processed: 297 average time/residue: 0.1363 time to fit residues: 67.2558 Evaluate side-chains 291 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 219 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 541 TRP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1020 HIS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 608 CYS Chi-restraints excluded: chain C residue 612 TRP Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 773 HIS Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 1008 CYS Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 154 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS ** B 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS C 932 GLN ** C 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 HIS ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.086347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.067471 restraints weight = 81598.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.069406 restraints weight = 49719.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.070702 restraints weight = 35635.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.071561 restraints weight = 28518.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.072102 restraints weight = 24669.053| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.445 22772 Z= 0.294 Angle : 0.735 11.057 30953 Z= 0.387 Chirality : 0.045 0.220 3256 Planarity : 0.005 0.061 4018 Dihedral : 6.649 82.456 3094 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.79 % Favored : 93.17 % Rotamer: Outliers : 4.05 % Allowed : 21.11 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 2886 helix: 1.05 (0.22), residues: 546 sheet: -1.33 (0.29), residues: 291 loop : -1.13 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 647 TYR 0.029 0.002 TYR F 330 PHE 0.016 0.002 PHE B 842 TRP 0.029 0.002 TRP B1013 HIS 0.013 0.002 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00659 (22679) covalent geometry : angle 0.73275 (30771) SS BOND : bond 0.00540 ( 91) SS BOND : angle 1.10589 ( 182) hydrogen bonds : bond 0.03858 ( 633) hydrogen bonds : angle 5.29203 ( 1839) Misc. bond : bond 0.31459 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 215 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: A 477 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7373 (tm-30) REVERT: A 495 HIS cc_start: 0.5565 (OUTLIER) cc_final: 0.4234 (t70) REVERT: A 546 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8209 (tm-30) REVERT: A 609 ASN cc_start: 0.6815 (m-40) cc_final: 0.6486 (m110) REVERT: A 623 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8082 (tt0) REVERT: A 649 MET cc_start: 0.6638 (tpp) cc_final: 0.5792 (tpp) REVERT: A 754 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.7886 (t-90) REVERT: A 984 PHE cc_start: 0.7759 (m-10) cc_final: 0.7541 (m-10) REVERT: A 1005 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8824 (mm) REVERT: B 927 ASN cc_start: 0.8535 (t0) cc_final: 0.8265 (t0) REVERT: C 537 ASN cc_start: 0.8299 (p0) cc_final: 0.7955 (p0) REVERT: C 564 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7111 (pp20) REVERT: C 773 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7813 (p-80) REVERT: E 8 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7728 (mt-10) REVERT: E 20 ASN cc_start: 0.8567 (p0) cc_final: 0.8116 (p0) REVERT: E 100 ASP cc_start: 0.9074 (t70) cc_final: 0.8622 (t70) REVERT: E 102 GLU cc_start: 0.7481 (mp0) cc_final: 0.7225 (mp0) REVERT: E 104 PHE cc_start: 0.8388 (m-80) cc_final: 0.8052 (m-80) REVERT: F 218 ARG cc_start: 0.8417 (tpp-160) cc_final: 0.7627 (tpp80) REVERT: F 247 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8357 (mt0) REVERT: F 284 MET cc_start: 0.5122 (ppp) cc_final: 0.4538 (ppp) outliers start: 96 outliers final: 72 residues processed: 287 average time/residue: 0.1317 time to fit residues: 62.8817 Evaluate side-chains 287 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 209 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 994 ASN Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 919 GLU Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 773 HIS Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 888 MET Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 932 GLN Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 984 PHE Chi-restraints excluded: chain C residue 1008 CYS Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 0 optimal weight: 20.0000 chunk 192 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 269 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 234 optimal weight: 7.9990 chunk 217 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.095877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.081620 restraints weight = 95814.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.083262 restraints weight = 66661.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.083427 restraints weight = 44945.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.083612 restraints weight = 41561.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.083650 restraints weight = 38573.085| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.223 22772 Z= 0.131 Angle : 0.637 14.630 30953 Z= 0.325 Chirality : 0.043 0.210 3256 Planarity : 0.004 0.055 4018 Dihedral : 6.310 82.910 3094 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.11 % Rotamer: Outliers : 2.99 % Allowed : 22.08 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.15), residues: 2886 helix: 1.35 (0.23), residues: 549 sheet: -1.22 (0.29), residues: 291 loop : -1.03 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 727 TYR 0.022 0.002 TYR D 141 PHE 0.026 0.001 PHE A 979 TRP 0.063 0.002 TRP F 310 HIS 0.010 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00308 (22679) covalent geometry : angle 0.63563 (30771) SS BOND : bond 0.00241 ( 91) SS BOND : angle 0.81897 ( 182) hydrogen bonds : bond 0.03146 ( 633) hydrogen bonds : angle 4.85337 ( 1839) Misc. bond : bond 0.15792 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 220 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: A 546 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 609 ASN cc_start: 0.6762 (m-40) cc_final: 0.6462 (m110) REVERT: A 623 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8093 (tt0) REVERT: A 649 MET cc_start: 0.6769 (tpp) cc_final: 0.6083 (tpp) REVERT: A 754 HIS cc_start: 0.8334 (OUTLIER) cc_final: 0.7746 (t-90) REVERT: A 927 ASN cc_start: 0.7928 (t0) cc_final: 0.7681 (t0) REVERT: A 1005 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8801 (mm) REVERT: B 927 ASN cc_start: 0.8462 (t0) cc_final: 0.8175 (t0) REVERT: C 537 ASN cc_start: 0.8229 (p0) cc_final: 0.7833 (p0) REVERT: C 564 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7009 (pp20) REVERT: C 773 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.7377 (p-80) REVERT: C 811 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8065 (pptt) REVERT: C 886 ILE cc_start: 0.8703 (pt) cc_final: 0.8282 (mm) REVERT: D 76 ASP cc_start: 0.7948 (t0) cc_final: 0.6771 (t0) REVERT: D 117 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7864 (mm-30) REVERT: E 20 ASN cc_start: 0.8567 (p0) cc_final: 0.8156 (p0) REVERT: E 100 ASP cc_start: 0.9076 (t70) cc_final: 0.8595 (t70) REVERT: E 102 GLU cc_start: 0.7398 (mp0) cc_final: 0.7148 (mp0) REVERT: E 104 PHE cc_start: 0.8297 (m-80) cc_final: 0.8002 (m-80) REVERT: E 118 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7353 (m-70) REVERT: F 218 ARG cc_start: 0.8209 (tpp-160) cc_final: 0.7859 (tpp-160) REVERT: F 247 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: F 284 MET cc_start: 0.4603 (ppp) cc_final: 0.4163 (ppp) outliers start: 71 outliers final: 59 residues processed: 274 average time/residue: 0.1310 time to fit residues: 59.6101 Evaluate side-chains 274 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 773 HIS Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 984 PHE Chi-restraints excluded: chain C residue 1008 CYS Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 241 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 281 CYS Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 239 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 285 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS C 932 GLN ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.095285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.080808 restraints weight = 96011.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.082277 restraints weight = 66421.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.082558 restraints weight = 46909.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.082711 restraints weight = 41334.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.082739 restraints weight = 38573.332| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 22772 Z= 0.154 Angle : 0.637 13.363 30953 Z= 0.328 Chirality : 0.043 0.165 3256 Planarity : 0.004 0.053 4018 Dihedral : 6.292 82.554 3094 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.21 % Rotamer: Outliers : 3.29 % Allowed : 22.25 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.15), residues: 2886 helix: 1.37 (0.23), residues: 544 sheet: -1.14 (0.29), residues: 292 loop : -1.03 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 727 TYR 0.021 0.002 TYR D 141 PHE 0.045 0.002 PHE A 984 TRP 0.050 0.002 TRP F 310 HIS 0.010 0.001 HIS F 123 Details of bonding type rmsd covalent geometry : bond 0.00358 (22679) covalent geometry : angle 0.63519 (30771) SS BOND : bond 0.00275 ( 91) SS BOND : angle 0.84226 ( 182) hydrogen bonds : bond 0.03124 ( 633) hydrogen bonds : angle 4.87690 ( 1839) Misc. bond : bond 0.17002 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3078.88 seconds wall clock time: 54 minutes 29.36 seconds (3269.36 seconds total)