Starting phenix.real_space_refine on Sun Jul 5 20:39:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wrb_32721/07_2026/7wrb_32721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrb_32721/07_2026/7wrb_32721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wrb_32721/07_2026/7wrb_32721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrb_32721/07_2026/7wrb_32721.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wrb_32721/07_2026/7wrb_32721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrb_32721/07_2026/7wrb_32721.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wrb_32721/07_2026/7wrb_32721.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wrb_32721/07_2026/7wrb_32721.cif" } resolution = 2.88 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 140 5.16 5 C 19756 2.51 5 N 5040 2.21 5 O 5436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30376 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "B" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "C" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "D" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.90, per 1000 atoms: 0.23 Number of scatterers: 30376 At special positions: 0 Unit cell: (153.114, 153.114, 157.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 140 16.00 O 5436 8.00 N 5040 7.00 C 19756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.02 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.02 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.02 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.02 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=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 8 sheets defined 71.1% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 204 removed outlier: 3.692A pdb=" N ARG A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 309 through 322 removed outlier: 4.044A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.728A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.785A pdb=" N ARG A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 385 removed outlier: 4.512A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 removed outlier: 5.968A pdb=" N HIS A 389 " --> pdb=" O GLU A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.697A pdb=" N TYR A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.507A pdb=" N GLN A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.810A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.853A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 582 removed outlier: 3.719A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 607 through 636 removed outlier: 4.081A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 644 Processing helix chain 'A' and resid 655 through 663 removed outlier: 3.900A pdb=" N ALA A 660 " --> pdb=" O CYS A 656 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.767A pdb=" N ILE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.754A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.992A pdb=" N GLY A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 758 removed outlier: 3.755A pdb=" N VAL A 743 " --> pdb=" O SER A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 790 Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 796 through 817 Processing helix chain 'A' and resid 821 through 847 removed outlier: 3.824A pdb=" N ARG A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 853 through 860 Processing helix chain 'A' and resid 863 through 890 removed outlier: 3.918A pdb=" N ALA A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 904 removed outlier: 3.929A pdb=" N SER A 902 " --> pdb=" O TRP A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 925 through 929 removed outlier: 4.115A pdb=" N HIS A 928 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A 929 " --> pdb=" O PHE A 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 929' Processing helix chain 'A' and resid 952 through 969 Proline residue: A 958 - end of helix Processing helix chain 'A' and resid 969 through 1007 removed outlier: 3.887A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1014 No H-bonds generated for 'chain 'A' and resid 1012 through 1014' Processing helix chain 'A' and resid 1015 through 1030 Processing helix chain 'A' and resid 1046 through 1070 removed outlier: 3.906A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS A1070 " --> pdb=" O LYS A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1104 removed outlier: 3.607A pdb=" N MET A1078 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 204 removed outlier: 3.692A pdb=" N ARG B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 309 through 322 removed outlier: 4.044A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.728A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.785A pdb=" N ARG B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 370 through 385 removed outlier: 4.513A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 removed outlier: 5.969A pdb=" N HIS B 389 " --> pdb=" O GLU B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.698A pdb=" N TYR B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.506A pdb=" N GLN B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.810A pdb=" N ALA B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 532 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.854A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 582 removed outlier: 3.718A pdb=" N VAL B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 607 through 636 removed outlier: 4.081A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP B 636 " --> pdb=" O CYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 644 Processing helix chain 'B' and resid 655 through 663 removed outlier: 3.901A pdb=" N ALA B 660 " --> pdb=" O CYS B 656 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.768A pdb=" N ILE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.755A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.992A pdb=" N GLY B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 758 removed outlier: 3.755A pdb=" N VAL B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 790 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 796 through 817 Processing helix chain 'B' and resid 821 through 847 removed outlier: 3.823A pdb=" N ARG B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 838 " --> pdb=" O LEU B 834 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 853 through 860 Processing helix chain 'B' and resid 863 through 890 removed outlier: 3.919A pdb=" N ALA B 884 " --> pdb=" O ALA B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 904 removed outlier: 3.930A pdb=" N SER B 902 " --> pdb=" O TRP B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 925 through 929 removed outlier: 4.115A pdb=" N HIS B 928 " --> pdb=" O ASP B 925 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS B 929 " --> pdb=" O PHE B 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 925 through 929' Processing helix chain 'B' and resid 952 through 969 Proline residue: B 958 - end of helix Processing helix chain 'B' and resid 969 through 1007 removed outlier: 3.887A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1014 No H-bonds generated for 'chain 'B' and resid 1012 through 1014' Processing helix chain 'B' and resid 1015 through 1030 Processing helix chain 'B' and resid 1046 through 1070 removed outlier: 3.907A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS B1070 " --> pdb=" O LYS B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1104 removed outlier: 3.607A pdb=" N MET B1078 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS B1104 " --> pdb=" O ALA B1100 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 204 removed outlier: 3.693A pdb=" N ARG C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 309 through 322 removed outlier: 4.044A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 removed outlier: 3.728A pdb=" N VAL C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.785A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 370 through 385 removed outlier: 4.513A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 removed outlier: 5.969A pdb=" N HIS C 389 " --> pdb=" O GLU C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 402 through 418 removed outlier: 3.697A pdb=" N TYR C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.506A pdb=" N GLN C 429 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.809A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 470 through 481 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 532 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.854A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 582 removed outlier: 3.719A pdb=" N VAL C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 602 Processing helix chain 'C' and resid 607 through 636 removed outlier: 4.081A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP C 636 " --> pdb=" O CYS C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 644 Processing helix chain 'C' and resid 655 through 663 removed outlier: 3.901A pdb=" N ALA C 660 " --> pdb=" O CYS C 656 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 670 removed outlier: 3.768A pdb=" N ILE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.754A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 removed outlier: 3.992A pdb=" N GLY C 706 " --> pdb=" O PRO C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 758 removed outlier: 3.755A pdb=" N VAL C 743 " --> pdb=" O SER C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 765 through 790 Processing helix chain 'C' and resid 791 through 795 Processing helix chain 'C' and resid 796 through 817 Processing helix chain 'C' and resid 821 through 847 removed outlier: 3.823A pdb=" N ARG C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 838 " --> pdb=" O LEU C 834 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 850 No H-bonds generated for 'chain 'C' and resid 848 through 850' Processing helix chain 'C' and resid 853 through 860 Processing helix chain 'C' and resid 863 through 890 removed outlier: 3.918A pdb=" N ALA C 884 " --> pdb=" O ALA C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 904 removed outlier: 3.929A pdb=" N SER C 902 " --> pdb=" O TRP C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 925 through 929 removed outlier: 4.114A pdb=" N HIS C 928 " --> pdb=" O ASP C 925 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS C 929 " --> pdb=" O PHE C 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 925 through 929' Processing helix chain 'C' and resid 952 through 969 Proline residue: C 958 - end of helix Processing helix chain 'C' and resid 969 through 1007 removed outlier: 3.887A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1014 No H-bonds generated for 'chain 'C' and resid 1012 through 1014' Processing helix chain 'C' and resid 1015 through 1030 Processing helix chain 'C' and resid 1046 through 1070 removed outlier: 3.906A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS C1070 " --> pdb=" O LYS C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1104 removed outlier: 3.608A pdb=" N MET C1078 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS C1104 " --> pdb=" O ALA C1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 136 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 204 removed outlier: 3.693A pdb=" N ARG D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 309 through 322 removed outlier: 4.044A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 343 removed outlier: 3.729A pdb=" N VAL D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU D 342 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.786A pdb=" N ARG D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 370 through 385 removed outlier: 4.513A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 389 removed outlier: 5.970A pdb=" N HIS D 389 " --> pdb=" O GLU D 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 386 through 389' Processing helix chain 'D' and resid 402 through 418 removed outlier: 3.698A pdb=" N TYR D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 removed outlier: 3.506A pdb=" N GLN D 429 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.810A pdb=" N ALA D 442 " --> pdb=" O GLN D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 470 through 481 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 532 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.854A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 582 removed outlier: 3.718A pdb=" N VAL D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 602 Processing helix chain 'D' and resid 607 through 636 removed outlier: 4.081A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP D 636 " --> pdb=" O CYS D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 644 Processing helix chain 'D' and resid 655 through 663 removed outlier: 3.899A pdb=" N ALA D 660 " --> pdb=" O CYS D 656 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 removed outlier: 3.768A pdb=" N ILE D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.754A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 removed outlier: 3.992A pdb=" N GLY D 706 " --> pdb=" O PRO D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 733 through 758 removed outlier: 3.755A pdb=" N VAL D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 790 Processing helix chain 'D' and resid 791 through 795 Processing helix chain 'D' and resid 796 through 817 Processing helix chain 'D' and resid 821 through 847 removed outlier: 3.823A pdb=" N ARG D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE D 838 " --> pdb=" O LEU D 834 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 850 No H-bonds generated for 'chain 'D' and resid 848 through 850' Processing helix chain 'D' and resid 853 through 860 Processing helix chain 'D' and resid 863 through 890 removed outlier: 3.919A pdb=" N ALA D 884 " --> pdb=" O ALA D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 904 removed outlier: 3.929A pdb=" N SER D 902 " --> pdb=" O TRP D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 925 through 929 removed outlier: 4.115A pdb=" N HIS D 928 " --> pdb=" O ASP D 925 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS D 929 " --> pdb=" O PHE D 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 925 through 929' Processing helix chain 'D' and resid 952 through 969 Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 969 through 1007 removed outlier: 3.886A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1014 No H-bonds generated for 'chain 'D' and resid 1012 through 1014' Processing helix chain 'D' and resid 1015 through 1030 Processing helix chain 'D' and resid 1046 through 1070 removed outlier: 3.907A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS D1070 " --> pdb=" O LYS D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1104 removed outlier: 3.607A pdb=" N MET D1078 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS D1104 " --> pdb=" O ALA D1100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 121 removed outlier: 6.265A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL A 328 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS A 303 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU A 330 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA A 305 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AA4, first strand: chain 'B' and resid 116 through 121 removed outlier: 6.264A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL B 328 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS B 303 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU B 330 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA B 305 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AA6, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.264A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL C 328 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS C 303 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU C 330 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA C 305 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AA8, first strand: chain 'D' and resid 116 through 121 removed outlier: 6.263A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL D 328 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS D 303 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU D 330 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA D 305 " --> pdb=" O GLU D 330 " (cutoff:3.500A) 1812 hydrogen bonds defined for protein. 5364 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: 6.16 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9447 1.34 - 1.46: 7395 1.46 - 1.58: 14034 1.58 - 1.70: 0 1.70 - 1.82: 212 Bond restraints: 31088 Sorted by residual: bond pdb=" CA PRO D1014 " pdb=" C PRO D1014 " ideal model delta sigma weight residual 1.518 1.578 -0.060 1.75e-02 3.27e+03 1.17e+01 bond pdb=" CA PRO B1014 " pdb=" C PRO B1014 " ideal model delta sigma weight residual 1.518 1.573 -0.055 1.75e-02 3.27e+03 9.74e+00 bond pdb=" CA PRO C1014 " pdb=" C PRO C1014 " ideal model delta sigma weight residual 1.518 1.572 -0.054 1.75e-02 3.27e+03 9.61e+00 bond pdb=" CA PRO A1014 " pdb=" C PRO A1014 " ideal model delta sigma weight residual 1.518 1.569 -0.051 1.75e-02 3.27e+03 8.62e+00 bond pdb=" CA ILE A1011 " pdb=" C ILE A1011 " ideal model delta sigma weight residual 1.524 1.551 -0.027 1.05e-02 9.07e+03 6.54e+00 ... (remaining 31083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 40435 2.21 - 4.42: 1350 4.42 - 6.63: 233 6.63 - 8.84: 70 8.84 - 11.06: 24 Bond angle restraints: 42112 Sorted by residual: angle pdb=" N SER C 917 " pdb=" CA SER C 917 " pdb=" C SER C 917 " ideal model delta sigma weight residual 111.28 118.73 -7.45 1.09e+00 8.42e-01 4.67e+01 angle pdb=" N SER D 917 " pdb=" CA SER D 917 " pdb=" C SER D 917 " ideal model delta sigma weight residual 111.28 118.68 -7.40 1.09e+00 8.42e-01 4.61e+01 angle pdb=" N SER B 917 " pdb=" CA SER B 917 " pdb=" C SER B 917 " ideal model delta sigma weight residual 111.28 118.64 -7.36 1.09e+00 8.42e-01 4.56e+01 angle pdb=" N SER A 917 " pdb=" CA SER A 917 " pdb=" C SER A 917 " ideal model delta sigma weight residual 111.28 118.62 -7.34 1.09e+00 8.42e-01 4.53e+01 angle pdb=" C PHE C1013 " pdb=" N PRO C1014 " pdb=" CA PRO C1014 " ideal model delta sigma weight residual 119.87 112.89 6.98 1.04e+00 9.25e-01 4.50e+01 ... (remaining 42107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 17049 14.89 - 29.79: 935 29.79 - 44.68: 256 44.68 - 59.58: 12 59.58 - 74.47: 28 Dihedral angle restraints: 18280 sinusoidal: 7368 harmonic: 10912 Sorted by residual: dihedral pdb=" CA ILE D 985 " pdb=" C ILE D 985 " pdb=" N VAL D 986 " pdb=" CA VAL D 986 " ideal model delta harmonic sigma weight residual 180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ILE A 985 " pdb=" C ILE A 985 " pdb=" N VAL A 986 " pdb=" CA VAL A 986 " ideal model delta harmonic sigma weight residual -180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ILE C 985 " pdb=" C ILE C 985 " pdb=" N VAL C 986 " pdb=" CA VAL C 986 " ideal model delta harmonic sigma weight residual 180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 18277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3839 0.066 - 0.132: 741 0.132 - 0.198: 107 0.198 - 0.264: 9 0.264 - 0.330: 12 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CA ARG B 451 " pdb=" N ARG B 451 " pdb=" C ARG B 451 " pdb=" CB ARG B 451 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA PHE D1013 " pdb=" N PHE D1013 " pdb=" C PHE D1013 " pdb=" CB PHE D1013 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA PHE A1013 " pdb=" N PHE A1013 " pdb=" C PHE A1013 " pdb=" CB PHE A1013 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 4705 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A1011 " 0.027 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C ILE A1011 " -0.096 2.00e-02 2.50e+03 pdb=" O ILE A1011 " 0.037 2.00e-02 2.50e+03 pdb=" N PRO A1012 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B1011 " 0.027 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C ILE B1011 " -0.096 2.00e-02 2.50e+03 pdb=" O ILE B1011 " 0.037 2.00e-02 2.50e+03 pdb=" N PRO B1012 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C1011 " 0.027 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C ILE C1011 " -0.096 2.00e-02 2.50e+03 pdb=" O ILE C1011 " 0.037 2.00e-02 2.50e+03 pdb=" N PRO C1012 " 0.032 2.00e-02 2.50e+03 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7939 2.80 - 3.33: 28158 3.33 - 3.85: 48301 3.85 - 4.38: 57078 4.38 - 4.90: 96163 Nonbonded interactions: 237639 Sorted by model distance: nonbonded pdb=" O VAL C1065 " pdb=" OG1 THR C1069 " model vdw 2.276 3.040 nonbonded pdb=" O VAL D1065 " pdb=" OG1 THR D1069 " model vdw 2.276 3.040 nonbonded pdb=" O VAL A1065 " pdb=" OG1 THR A1069 " model vdw 2.276 3.040 nonbonded pdb=" O VAL B1065 " pdb=" OG1 THR B1069 " model vdw 2.276 3.040 nonbonded pdb=" O VAL B 728 " pdb=" OG1 THR B 732 " model vdw 2.278 3.040 ... (remaining 237634 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 28.840 Find NCS groups from input model: 0.450 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:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.006 0.077 31092 Z= 0.266 Angle : 1.011 11.056 42120 Z= 0.575 Chirality : 0.055 0.330 4708 Planarity : 0.007 0.072 5264 Dihedral : 10.444 73.991 11188 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.02 % Favored : 93.87 % Rotamer: Outliers : 0.12 % Allowed : 1.92 % Favored : 97.96 % 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: -3.78 (0.11), residues: 3656 helix: -2.08 (0.08), residues: 2436 sheet: -1.83 (0.34), residues: 200 loop : -3.26 (0.15), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 364 TYR 0.029 0.003 TYR D 808 PHE 0.041 0.003 PHE C 108 TRP 0.026 0.003 TRP A 651 HIS 0.009 0.002 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.27 (31088) covalent geometry : angle 1.00875 / 0.57 (42112) SS BOND : bond 0.01462 / 0.67 ( 4) SS BOND : angle 5.47565 / 3.08 ( 8) hydrogen bonds : bond 0.15707 / 10.58 ( 1812) hydrogen bonds : angle 6.50585 / 4.52 ( 5364) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 912 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8809 (tttt) cc_final: 0.8555 (tptt) REVERT: A 164 ILE cc_start: 0.8621 (mt) cc_final: 0.8329 (mt) REVERT: A 441 LEU cc_start: 0.8574 (tp) cc_final: 0.8135 (mp) REVERT: A 468 LYS cc_start: 0.8182 (mttp) cc_final: 0.7832 (mtpp) REVERT: A 1023 MET cc_start: 0.7117 (mmt) cc_final: 0.6895 (tpt) REVERT: A 1097 LYS cc_start: 0.7838 (mtpt) cc_final: 0.7596 (ttmt) REVERT: B 163 LYS cc_start: 0.8810 (tttt) cc_final: 0.8541 (tptt) REVERT: B 164 ILE cc_start: 0.8584 (mt) cc_final: 0.8269 (mt) REVERT: B 441 LEU cc_start: 0.8551 (tp) cc_final: 0.8062 (mp) REVERT: B 468 LYS cc_start: 0.8184 (mttp) cc_final: 0.7832 (mtpp) REVERT: B 665 ASP cc_start: 0.7647 (t0) cc_final: 0.6691 (t0) REVERT: B 1023 MET cc_start: 0.7134 (mmt) cc_final: 0.6916 (tpt) REVERT: B 1097 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7627 (ttmt) REVERT: C 163 LYS cc_start: 0.8835 (tttt) cc_final: 0.8576 (tptt) REVERT: C 164 ILE cc_start: 0.8588 (mt) cc_final: 0.8255 (mt) REVERT: C 441 LEU cc_start: 0.8580 (tp) cc_final: 0.8083 (mp) REVERT: C 468 LYS cc_start: 0.8195 (mttp) cc_final: 0.7832 (mtpp) REVERT: C 665 ASP cc_start: 0.7645 (t0) cc_final: 0.6636 (t0) REVERT: C 1023 MET cc_start: 0.7110 (mmt) cc_final: 0.6891 (tpt) REVERT: C 1097 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7620 (ttmt) REVERT: D 163 LYS cc_start: 0.8827 (tttt) cc_final: 0.8579 (tptt) REVERT: D 164 ILE cc_start: 0.8591 (mt) cc_final: 0.8257 (mt) REVERT: D 441 LEU cc_start: 0.8587 (tp) cc_final: 0.8129 (mp) REVERT: D 468 LYS cc_start: 0.8193 (mttp) cc_final: 0.7831 (mtpp) REVERT: D 1023 MET cc_start: 0.7099 (mmt) cc_final: 0.6884 (tpt) REVERT: D 1097 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7557 (ttmt) outliers start: 4 outliers final: 4 residues processed: 912 average time/residue: 0.6962 time to fit residues: 738.1912 Evaluate side-chains 455 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 451 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 PHE Chi-restraints excluded: chain B residue 807 PHE Chi-restraints excluded: chain C residue 807 PHE Chi-restraints excluded: chain D residue 807 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.0060 chunk 298 optimal weight: 3.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS A 173 GLN A 185 HIS A 235 HIS ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 987 GLN A1074 ASN A1102 ASN B 136 HIS B 173 GLN B 185 HIS B 235 HIS ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN B 675 GLN B 987 GLN B1074 ASN B1102 ASN C 136 HIS C 173 GLN C 185 HIS C 235 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN C 675 GLN C 987 GLN C1074 ASN C1102 ASN D 136 HIS D 173 GLN D 185 HIS D 235 HIS ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN D 675 GLN D 987 GLN ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN D1102 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.163710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.113810 restraints weight = 54814.745| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.46 r_work: 0.3433 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31092 Z= 0.153 Angle : 0.678 8.115 42120 Z= 0.355 Chirality : 0.042 0.135 4708 Planarity : 0.005 0.051 5264 Dihedral : 5.477 26.165 4008 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.09 % Allowed : 13.82 % Favored : 82.09 % 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: -1.56 (0.13), residues: 3656 helix: -0.20 (0.10), residues: 2460 sheet: -1.60 (0.34), residues: 200 loop : -2.87 (0.16), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 784 TYR 0.024 0.002 TYR D 117 PHE 0.026 0.002 PHE A 779 TRP 0.034 0.002 TRP A 693 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (31088) covalent geometry : angle 0.67709 / 0.35 (42112) SS BOND : bond 0.00676 / 0.31 ( 4) SS BOND : angle 2.23378 / 1.26 ( 8) hydrogen bonds : bond 0.04813 / 3.27 ( 1812) hydrogen bonds : angle 4.55886 / 3.15 ( 5364) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 488 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8941 (tttt) cc_final: 0.8567 (tptt) REVERT: A 164 ILE cc_start: 0.8448 (mt) cc_final: 0.8112 (mt) REVERT: A 441 LEU cc_start: 0.8418 (tp) cc_final: 0.8080 (tt) REVERT: A 575 GLU cc_start: 0.8737 (tp30) cc_final: 0.8527 (mm-30) REVERT: A 642 GLN cc_start: 0.8344 (mt0) cc_final: 0.7869 (mp10) REVERT: A 692 ASN cc_start: 0.6896 (OUTLIER) cc_final: 0.6688 (m110) REVERT: A 815 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.7693 (t80) REVERT: A 1061 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: A 1097 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7858 (ttmt) REVERT: B 163 LYS cc_start: 0.8931 (tttt) cc_final: 0.8549 (tptt) REVERT: B 164 ILE cc_start: 0.8492 (mt) cc_final: 0.8164 (mt) REVERT: B 431 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8358 (mppt) REVERT: B 441 LEU cc_start: 0.8354 (tp) cc_final: 0.8086 (tt) REVERT: B 622 GLU cc_start: 0.8536 (tt0) cc_final: 0.8285 (tt0) REVERT: B 642 GLN cc_start: 0.8349 (mt0) cc_final: 0.7585 (mt0) REVERT: B 692 ASN cc_start: 0.6912 (OUTLIER) cc_final: 0.6695 (m110) REVERT: B 815 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.7704 (t80) REVERT: B 1061 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: B 1097 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7770 (ttmt) REVERT: C 163 LYS cc_start: 0.8937 (tttt) cc_final: 0.8565 (tptt) REVERT: C 164 ILE cc_start: 0.8455 (mt) cc_final: 0.8112 (mt) REVERT: C 383 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7738 (mt-10) REVERT: C 431 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8153 (mppt) REVERT: C 441 LEU cc_start: 0.8312 (tp) cc_final: 0.8032 (tt) REVERT: C 622 GLU cc_start: 0.8538 (tt0) cc_final: 0.8285 (tt0) REVERT: C 815 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.7673 (t80) REVERT: C 1061 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: C 1097 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7737 (ttmt) REVERT: D 163 LYS cc_start: 0.8926 (tttt) cc_final: 0.8561 (tptt) REVERT: D 164 ILE cc_start: 0.8489 (mt) cc_final: 0.8147 (mt) REVERT: D 441 LEU cc_start: 0.8343 (tp) cc_final: 0.8043 (tt) REVERT: D 638 ASP cc_start: 0.8169 (t0) cc_final: 0.7927 (t0) REVERT: D 642 GLN cc_start: 0.8320 (mt0) cc_final: 0.7450 (mt0) REVERT: D 692 ASN cc_start: 0.6914 (OUTLIER) cc_final: 0.6702 (m110) REVERT: D 815 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.7667 (t80) REVERT: D 1004 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7809 (tm-30) REVERT: D 1061 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: D 1097 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7739 (ttmt) outliers start: 136 outliers final: 32 residues processed: 598 average time/residue: 0.6230 time to fit residues: 440.4258 Evaluate side-chains 436 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 391 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 815 PHE Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 815 PHE Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1087 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 75 optimal weight: 0.0770 chunk 165 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 270 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 307 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 4 optimal weight: 30.0000 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN A 235 HIS ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 HIS ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 235 HIS ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN C 235 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 GLN ** C 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN D 235 HIS ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.160465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109088 restraints weight = 54650.712| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.46 r_work: 0.3361 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 31092 Z= 0.204 Angle : 0.697 12.154 42120 Z= 0.355 Chirality : 0.044 0.241 4708 Planarity : 0.004 0.043 5264 Dihedral : 5.126 19.457 4000 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.54 % Allowed : 15.20 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.13), residues: 3656 helix: 0.47 (0.10), residues: 2476 sheet: -1.61 (0.32), residues: 200 loop : -2.70 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 203 TYR 0.025 0.002 TYR D 117 PHE 0.030 0.002 PHE B 752 TRP 0.021 0.002 TRP C 693 HIS 0.010 0.002 HIS D1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (31088) covalent geometry : angle 0.69641 / 0.35 (42112) SS BOND : bond 0.00791 / 0.36 ( 4) SS BOND : angle 2.49154 / 1.40 ( 8) hydrogen bonds : bond 0.04975 / 3.39 ( 1812) hydrogen bonds : angle 4.41932 / 3.05 ( 5364) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 427 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8957 (tttt) cc_final: 0.8594 (tptt) REVERT: A 164 ILE cc_start: 0.8593 (mt) cc_final: 0.8283 (mt) REVERT: A 431 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8278 (mppt) REVERT: A 697 LEU cc_start: 0.8257 (tt) cc_final: 0.8043 (tt) REVERT: B 163 LYS cc_start: 0.8952 (tttt) cc_final: 0.8586 (tptt) REVERT: B 164 ILE cc_start: 0.8578 (mt) cc_final: 0.8267 (mt) REVERT: B 697 LEU cc_start: 0.8254 (tt) cc_final: 0.8041 (tt) REVERT: C 163 LYS cc_start: 0.8961 (tttt) cc_final: 0.8598 (tptt) REVERT: C 164 ILE cc_start: 0.8585 (mt) cc_final: 0.8279 (mt) REVERT: C 383 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7694 (mt-10) REVERT: C 431 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8202 (mppt) REVERT: D 163 LYS cc_start: 0.8971 (tttt) cc_final: 0.8611 (tptt) REVERT: D 164 ILE cc_start: 0.8594 (mt) cc_final: 0.8288 (mt) REVERT: D 431 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8260 (mppt) REVERT: D 1004 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7771 (tm-30) outliers start: 151 outliers final: 71 residues processed: 548 average time/residue: 0.5759 time to fit residues: 377.8062 Evaluate side-chains 458 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 384 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 807 PHE Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 807 PHE Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 807 PHE Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 807 PHE Chi-restraints excluded: chain D residue 815 PHE Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 1087 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 0 optimal weight: 20.0000 chunk 256 optimal weight: 4.9990 chunk 368 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 257 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 262 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 HIS ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 HIS B 257 HIS ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 HIS B 667 HIS C 257 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 HIS C 667 HIS D 257 HIS ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 HIS D 667 HIS D 671 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.161463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110218 restraints weight = 54315.239| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.39 r_work: 0.3378 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31092 Z= 0.153 Angle : 0.665 14.521 42120 Z= 0.336 Chirality : 0.042 0.213 4708 Planarity : 0.004 0.040 5264 Dihedral : 4.897 21.474 4000 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.75 % Allowed : 17.13 % Favored : 78.12 % 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: -0.23 (0.14), residues: 3656 helix: 0.88 (0.10), residues: 2480 sheet: -1.44 (0.33), residues: 196 loop : -2.55 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 451 TYR 0.026 0.001 TYR A 117 PHE 0.029 0.002 PHE C 779 TRP 0.020 0.002 TRP A 453 HIS 0.013 0.001 HIS B1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (31088) covalent geometry : angle 0.66392 / 0.34 (42112) SS BOND : bond 0.00777 / 0.36 ( 4) SS BOND : angle 2.34046 / 1.31 ( 8) hydrogen bonds : bond 0.04381 / 2.99 ( 1812) hydrogen bonds : angle 4.24675 / 2.92 ( 5364) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 427 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8937 (tttt) cc_final: 0.8597 (tptt) REVERT: A 164 ILE cc_start: 0.8461 (mt) cc_final: 0.8158 (mt) REVERT: A 194 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8235 (mt-10) REVERT: A 283 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8828 (mmmm) REVERT: A 337 ASP cc_start: 0.7868 (m-30) cc_final: 0.6984 (t70) REVERT: A 431 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8252 (mppt) REVERT: A 697 LEU cc_start: 0.8233 (tt) cc_final: 0.8012 (tt) REVERT: A 804 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8869 (tt) REVERT: A 1004 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 1097 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7532 (tmtm) REVERT: B 163 LYS cc_start: 0.8952 (tttt) cc_final: 0.8598 (tptt) REVERT: B 164 ILE cc_start: 0.8510 (mt) cc_final: 0.8196 (mt) REVERT: B 194 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8248 (mt-10) REVERT: B 337 ASP cc_start: 0.7879 (m-30) cc_final: 0.6994 (t70) REVERT: B 453 TRP cc_start: 0.5798 (m-10) cc_final: 0.5590 (m-10) REVERT: B 697 LEU cc_start: 0.8246 (tt) cc_final: 0.8023 (tt) REVERT: B 804 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8888 (tt) REVERT: B 863 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8486 (mmt) REVERT: B 1004 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7679 (tm-30) REVERT: C 163 LYS cc_start: 0.8968 (tttt) cc_final: 0.8625 (tptt) REVERT: C 164 ILE cc_start: 0.8528 (mt) cc_final: 0.8217 (mt) REVERT: C 194 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8244 (mt-10) REVERT: C 283 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8740 (mmmm) REVERT: C 337 ASP cc_start: 0.7864 (m-30) cc_final: 0.7036 (t70) REVERT: C 431 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8172 (mppt) REVERT: D 163 LYS cc_start: 0.8954 (tttt) cc_final: 0.8615 (tptt) REVERT: D 164 ILE cc_start: 0.8532 (mt) cc_final: 0.8227 (mt) REVERT: D 194 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8242 (mt-10) REVERT: D 283 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8749 (mmmm) REVERT: D 337 ASP cc_start: 0.7846 (m-30) cc_final: 0.7011 (t70) REVERT: D 431 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8215 (mppt) REVERT: D 804 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8833 (tt) REVERT: D 863 MET cc_start: 0.9093 (mmt) cc_final: 0.8505 (mmt) REVERT: D 1004 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7679 (tm-30) outliers start: 158 outliers final: 68 residues processed: 544 average time/residue: 0.6056 time to fit residues: 391.2914 Evaluate side-chains 481 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 403 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 PHE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 807 PHE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 807 PHE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 851 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 95 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 295 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 343 optimal weight: 5.9990 chunk 323 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 283 optimal weight: 0.8980 chunk 337 optimal weight: 4.9990 chunk 362 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN A1080 HIS B 154 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN B1080 HIS C 154 ASN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN C1080 HIS D 154 ASN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1080 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.158455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.106627 restraints weight = 54652.115| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.41 r_work: 0.3326 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 31092 Z= 0.234 Angle : 0.726 12.816 42120 Z= 0.368 Chirality : 0.045 0.201 4708 Planarity : 0.004 0.039 5264 Dihedral : 4.981 23.484 4000 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.11 % Allowed : 17.64 % Favored : 77.25 % 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: -0.21 (0.14), residues: 3656 helix: 0.90 (0.10), residues: 2476 sheet: -1.41 (0.32), residues: 196 loop : -2.52 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 203 TYR 0.028 0.002 TYR B 117 PHE 0.035 0.002 PHE D 752 TRP 0.025 0.002 TRP D 453 HIS 0.014 0.002 HIS C1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.23 (31088) covalent geometry : angle 0.72529 / 0.37 (42112) SS BOND : bond 0.00973 / 0.44 ( 4) SS BOND : angle 2.80000 / 1.57 ( 8) hydrogen bonds : bond 0.05060 / 3.45 ( 1812) hydrogen bonds : angle 4.38948 / 3.03 ( 5364) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 411 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8966 (tttt) cc_final: 0.8653 (tptt) REVERT: A 164 ILE cc_start: 0.8660 (mt) cc_final: 0.8387 (mt) REVERT: A 283 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8817 (mmmm) REVERT: A 431 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8285 (mppt) REVERT: A 697 LEU cc_start: 0.8255 (tt) cc_final: 0.8041 (tt) REVERT: A 953 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8250 (mm-30) REVERT: A 988 GLU cc_start: 0.8004 (pm20) cc_final: 0.7511 (pm20) REVERT: A 1004 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7729 (tm-30) REVERT: A 1027 LYS cc_start: 0.5076 (mttp) cc_final: 0.4810 (pptt) REVERT: B 163 LYS cc_start: 0.8966 (tttt) cc_final: 0.8650 (tptt) REVERT: B 164 ILE cc_start: 0.8644 (mt) cc_final: 0.8366 (mt) REVERT: B 194 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8233 (mt-10) REVERT: B 431 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8271 (mppt) REVERT: B 445 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7694 (mt-10) REVERT: B 697 LEU cc_start: 0.8290 (tt) cc_final: 0.8072 (tt) REVERT: B 942 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8723 (pp20) REVERT: B 953 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8241 (mm-30) REVERT: B 988 GLU cc_start: 0.7998 (pm20) cc_final: 0.7504 (pm20) REVERT: B 1004 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7733 (tm-30) REVERT: B 1027 LYS cc_start: 0.5094 (mttp) cc_final: 0.4824 (pptt) REVERT: C 163 LYS cc_start: 0.8992 (tttt) cc_final: 0.8649 (tptt) REVERT: C 164 ILE cc_start: 0.8659 (mt) cc_final: 0.8396 (mt) REVERT: C 194 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8264 (mt-10) REVERT: C 283 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8753 (mmmm) REVERT: C 382 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8296 (mppt) REVERT: C 431 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8265 (mppt) REVERT: C 445 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7691 (mt-10) REVERT: C 453 TRP cc_start: 0.5586 (m-10) cc_final: 0.5317 (m-10) REVERT: C 804 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8862 (tt) REVERT: C 988 GLU cc_start: 0.7990 (pm20) cc_final: 0.7491 (pm20) REVERT: C 1004 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 1027 LYS cc_start: 0.5055 (mttp) cc_final: 0.4805 (pptt) REVERT: D 163 LYS cc_start: 0.8969 (tttt) cc_final: 0.8633 (tptt) REVERT: D 164 ILE cc_start: 0.8636 (mt) cc_final: 0.8364 (mt) REVERT: D 283 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8751 (mmmm) REVERT: D 337 ASP cc_start: 0.7986 (m-30) cc_final: 0.7006 (t70) REVERT: D 482 LEU cc_start: 0.6771 (tt) cc_final: 0.6353 (tm) REVERT: D 638 ASP cc_start: 0.8276 (t0) cc_final: 0.8024 (t0) REVERT: D 953 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8260 (mm-30) REVERT: D 988 GLU cc_start: 0.7996 (pm20) cc_final: 0.7495 (pm20) REVERT: D 1004 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7738 (tm-30) REVERT: D 1027 LYS cc_start: 0.5096 (mttp) cc_final: 0.4809 (pptt) REVERT: D 1097 LYS cc_start: 0.7913 (mtmm) cc_final: 0.7403 (ttmt) outliers start: 170 outliers final: 86 residues processed: 526 average time/residue: 0.6056 time to fit residues: 380.7119 Evaluate side-chains 474 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 379 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 1080 HIS Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 1087 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 70 optimal weight: 0.8980 chunk 257 optimal weight: 0.5980 chunk 280 optimal weight: 20.0000 chunk 273 optimal weight: 6.9990 chunk 278 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 154 optimal weight: 0.9990 chunk 172 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN A1080 HIS ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 449 ASN B1080 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1080 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.161886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.111075 restraints weight = 54333.108| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.73 r_work: 0.3365 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31092 Z= 0.125 Angle : 0.671 13.655 42120 Z= 0.331 Chirality : 0.042 0.163 4708 Planarity : 0.004 0.032 5264 Dihedral : 4.737 22.790 4000 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.00 % Allowed : 19.02 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.14), residues: 3656 helix: 1.21 (0.10), residues: 2484 sheet: -1.08 (0.31), residues: 220 loop : -2.51 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 203 TYR 0.029 0.001 TYR B 646 PHE 0.022 0.001 PHE A 779 TRP 0.023 0.001 TRP D 453 HIS 0.017 0.001 HIS C1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (31088) covalent geometry : angle 0.67020 / 0.33 (42112) SS BOND : bond 0.00775 / 0.36 ( 4) SS BOND : angle 1.88203 / 1.06 ( 8) hydrogen bonds : bond 0.04038 / 2.73 ( 1812) hydrogen bonds : angle 4.12639 / 2.85 ( 5364) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 429 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8937 (tttt) cc_final: 0.8617 (tptt) REVERT: A 164 ILE cc_start: 0.8474 (mt) cc_final: 0.8159 (mt) REVERT: A 283 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8884 (mmmm) REVERT: A 431 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8219 (mppt) REVERT: A 445 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7258 (pm20) REVERT: A 607 ASP cc_start: 0.8516 (t0) cc_final: 0.8125 (t0) REVERT: A 697 LEU cc_start: 0.8209 (tt) cc_final: 0.7968 (tt) REVERT: A 815 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.7705 (t80) REVERT: A 863 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8556 (mmt) REVERT: A 953 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8313 (mm-30) REVERT: A 988 GLU cc_start: 0.8025 (pm20) cc_final: 0.7557 (pm20) REVERT: A 1004 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 1027 LYS cc_start: 0.4936 (mttp) cc_final: 0.4719 (pptt) REVERT: A 1061 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: B 163 LYS cc_start: 0.8952 (tttt) cc_final: 0.8619 (tptt) REVERT: B 164 ILE cc_start: 0.8457 (mt) cc_final: 0.8232 (mt) REVERT: B 194 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8308 (mt-10) REVERT: B 282 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8126 (pp20) REVERT: B 283 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8704 (mmmm) REVERT: B 431 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8335 (mppt) REVERT: B 445 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7730 (mt-10) REVERT: B 453 TRP cc_start: 0.5400 (m-10) cc_final: 0.5155 (m-10) REVERT: B 578 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8341 (mmtt) REVERT: B 607 ASP cc_start: 0.8505 (t0) cc_final: 0.8108 (t0) REVERT: B 622 GLU cc_start: 0.8673 (tt0) cc_final: 0.8222 (tp30) REVERT: B 697 LEU cc_start: 0.8214 (tt) cc_final: 0.7976 (tt) REVERT: B 815 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.7692 (t80) REVERT: B 863 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8507 (mmt) REVERT: B 953 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8295 (mm-30) REVERT: B 988 GLU cc_start: 0.8049 (pm20) cc_final: 0.7584 (pm20) REVERT: B 1004 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7753 (tm-30) REVERT: B 1027 LYS cc_start: 0.4996 (mttp) cc_final: 0.4774 (pptt) REVERT: B 1061 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8167 (mt-10) REVERT: C 163 LYS cc_start: 0.8964 (tttt) cc_final: 0.8647 (tptt) REVERT: C 164 ILE cc_start: 0.8561 (mt) cc_final: 0.8258 (mt) REVERT: C 194 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8310 (mt-10) REVERT: C 283 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8823 (mmmm) REVERT: C 431 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8344 (mppt) REVERT: C 445 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7686 (mt-10) REVERT: C 578 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8309 (mmtt) REVERT: C 607 ASP cc_start: 0.8486 (t0) cc_final: 0.8084 (t0) REVERT: C 804 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8824 (tt) REVERT: C 815 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7681 (t80) REVERT: C 863 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8544 (mmt) REVERT: C 988 GLU cc_start: 0.8038 (pm20) cc_final: 0.7574 (pm20) REVERT: C 1004 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7714 (tm-30) REVERT: C 1027 LYS cc_start: 0.5001 (mttp) cc_final: 0.4768 (pptt) REVERT: C 1061 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: C 1078 MET cc_start: 0.5797 (mmt) cc_final: 0.5541 (tpp) REVERT: C 1080 HIS cc_start: 0.8462 (t-170) cc_final: 0.7989 (t-170) REVERT: C 1083 ARG cc_start: 0.7092 (mtt180) cc_final: 0.6863 (mmp80) REVERT: D 163 LYS cc_start: 0.8941 (tttt) cc_final: 0.8613 (tptt) REVERT: D 164 ILE cc_start: 0.8532 (mt) cc_final: 0.8228 (mt) REVERT: D 283 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8823 (mmmm) REVERT: D 337 ASP cc_start: 0.7984 (m-30) cc_final: 0.6979 (t70) REVERT: D 431 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8112 (mppt) REVERT: D 445 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7278 (pm20) REVERT: D 453 TRP cc_start: 0.5342 (m-10) cc_final: 0.5069 (m-10) REVERT: D 578 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8303 (mmtt) REVERT: D 607 ASP cc_start: 0.8554 (t0) cc_final: 0.8165 (t0) REVERT: D 638 ASP cc_start: 0.8232 (t0) cc_final: 0.8006 (t0) REVERT: D 641 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: D 815 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.7688 (t80) REVERT: D 863 MET cc_start: 0.9058 (mmt) cc_final: 0.8517 (mmt) REVERT: D 953 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8277 (mm-30) REVERT: D 988 GLU cc_start: 0.8007 (pm20) cc_final: 0.7547 (pm20) REVERT: D 1004 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7720 (tm-30) REVERT: D 1027 LYS cc_start: 0.5013 (mttp) cc_final: 0.4774 (pptt) REVERT: D 1061 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8199 (mt-10) outliers start: 133 outliers final: 54 residues processed: 523 average time/residue: 0.6204 time to fit residues: 386.3826 Evaluate side-chains 473 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 395 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1080 HIS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 666 GLN Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1080 HIS Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 578 LYS Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 815 PHE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 578 LYS Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 666 GLN Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 815 PHE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1080 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 118 optimal weight: 4.9990 chunk 312 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 chunk 231 optimal weight: 0.0770 chunk 29 optimal weight: 20.0000 chunk 295 optimal weight: 7.9990 chunk 366 optimal weight: 10.0000 chunk 230 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS B 204 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 HIS B1080 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** 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 = 0.4233 r_free = 0.4233 target = 0.161011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109720 restraints weight = 54326.800| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.43 r_work: 0.3367 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31092 Z= 0.152 Angle : 0.686 13.756 42120 Z= 0.339 Chirality : 0.043 0.322 4708 Planarity : 0.004 0.055 5264 Dihedral : 4.665 22.276 4000 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.85 % Allowed : 20.70 % Favored : 75.45 % 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: 0.24 (0.14), residues: 3656 helix: 1.22 (0.10), residues: 2484 sheet: -0.94 (0.32), residues: 220 loop : -2.44 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 203 TYR 0.025 0.001 TYR D 117 PHE 0.033 0.002 PHE D 779 TRP 0.027 0.002 TRP A 786 HIS 0.023 0.001 HIS A1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (31088) covalent geometry : angle 0.68585 / 0.34 (42112) SS BOND : bond 0.00663 / 0.31 ( 4) SS BOND : angle 2.07613 / 1.17 ( 8) hydrogen bonds : bond 0.04221 / 2.87 ( 1812) hydrogen bonds : angle 4.12228 / 2.85 ( 5364) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 394 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8236 (pp) REVERT: A 163 LYS cc_start: 0.8943 (tttt) cc_final: 0.8629 (tptt) REVERT: A 164 ILE cc_start: 0.8472 (mt) cc_final: 0.8167 (mt) REVERT: A 283 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8885 (mmmm) REVERT: A 431 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8219 (mppt) REVERT: A 445 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7309 (pm20) REVERT: A 453 TRP cc_start: 0.5371 (m-10) cc_final: 0.5073 (m-10) REVERT: A 578 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8330 (mmtt) REVERT: A 607 ASP cc_start: 0.8480 (t0) cc_final: 0.8074 (t0) REVERT: A 641 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: A 697 LEU cc_start: 0.8240 (tt) cc_final: 0.7997 (tt) REVERT: A 815 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.7710 (t80) REVERT: A 863 MET cc_start: 0.9122 (mmt) cc_final: 0.8519 (mmt) REVERT: A 953 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8154 (mm-30) REVERT: A 988 GLU cc_start: 0.7940 (pm20) cc_final: 0.7396 (pm20) REVERT: B 132 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8238 (pp) REVERT: B 163 LYS cc_start: 0.8946 (tttt) cc_final: 0.8628 (tptt) REVERT: B 164 ILE cc_start: 0.8457 (mt) cc_final: 0.8139 (mt) REVERT: B 282 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8118 (pp20) REVERT: B 283 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8715 (mmmm) REVERT: B 431 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8238 (mppt) REVERT: B 445 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7738 (mt-10) REVERT: B 453 TRP cc_start: 0.5369 (m-10) cc_final: 0.5162 (m-10) REVERT: B 578 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8357 (mmtt) REVERT: B 607 ASP cc_start: 0.8489 (t0) cc_final: 0.8081 (t0) REVERT: B 641 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: B 697 LEU cc_start: 0.8267 (tt) cc_final: 0.8023 (tt) REVERT: B 863 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8516 (mmt) REVERT: B 953 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8151 (mm-30) REVERT: B 988 GLU cc_start: 0.7879 (pm20) cc_final: 0.7348 (pm20) REVERT: B 1004 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7729 (tm-30) REVERT: C 132 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8233 (pp) REVERT: C 163 LYS cc_start: 0.8958 (tttt) cc_final: 0.8634 (tptt) REVERT: C 164 ILE cc_start: 0.8569 (mt) cc_final: 0.8275 (mt) REVERT: C 283 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8831 (mmmm) REVERT: C 431 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8280 (mppt) REVERT: C 578 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8329 (mmtt) REVERT: C 607 ASP cc_start: 0.8495 (t0) cc_final: 0.8084 (t0) REVERT: C 804 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8884 (tt) REVERT: C 815 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.7691 (t80) REVERT: C 863 MET cc_start: 0.9114 (mmt) cc_final: 0.8501 (mmt) REVERT: C 988 GLU cc_start: 0.7902 (pm20) cc_final: 0.7376 (pm20) REVERT: C 1004 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7728 (tm-30) REVERT: C 1080 HIS cc_start: 0.8468 (t-170) cc_final: 0.8019 (t-170) REVERT: D 132 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8243 (pp) REVERT: D 163 LYS cc_start: 0.8942 (tttt) cc_final: 0.8624 (tptt) REVERT: D 164 ILE cc_start: 0.8524 (mt) cc_final: 0.8218 (mt) REVERT: D 194 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8251 (mt-10) REVERT: D 283 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8827 (mmmm) REVERT: D 337 ASP cc_start: 0.8014 (m-30) cc_final: 0.7003 (t70) REVERT: D 431 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8162 (mppt) REVERT: D 445 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7282 (pm20) REVERT: D 578 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8321 (mmtt) REVERT: D 607 ASP cc_start: 0.8440 (t0) cc_final: 0.8035 (t0) REVERT: D 638 ASP cc_start: 0.8284 (t0) cc_final: 0.8066 (t0) REVERT: D 815 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.7648 (t80) REVERT: D 953 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8135 (mm-30) REVERT: D 988 GLU cc_start: 0.7898 (pm20) cc_final: 0.7390 (pm20) outliers start: 128 outliers final: 65 residues processed: 490 average time/residue: 0.5984 time to fit residues: 350.3137 Evaluate side-chains 457 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 369 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 578 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 815 PHE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 578 LYS Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 615 GLU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 815 PHE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 367 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 168 optimal weight: 0.1980 chunk 174 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 14 optimal weight: 40.0000 chunk 63 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN A1080 HIS ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 HIS C 204 ASN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN D 204 ASN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 ASN D1080 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.160503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109203 restraints weight = 54351.730| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.42 r_work: 0.3357 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 31092 Z= 0.167 Angle : 0.700 13.409 42120 Z= 0.348 Chirality : 0.044 0.324 4708 Planarity : 0.004 0.064 5264 Dihedral : 4.664 22.665 4000 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.82 % Allowed : 21.66 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3656 helix: 1.25 (0.10), residues: 2480 sheet: -0.88 (0.33), residues: 220 loop : -2.40 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 203 TYR 0.026 0.001 TYR C 117 PHE 0.034 0.002 PHE A 776 TRP 0.024 0.002 TRP D 453 HIS 0.008 0.001 HIS C1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (31088) covalent geometry : angle 0.69969 / 0.35 (42112) SS BOND : bond 0.00698 / 0.32 ( 4) SS BOND : angle 2.28892 / 1.29 ( 8) hydrogen bonds : bond 0.04355 / 2.96 ( 1812) hydrogen bonds : angle 4.15225 / 2.87 ( 5364) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 383 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8228 (pp) REVERT: A 163 LYS cc_start: 0.8932 (tttt) cc_final: 0.8616 (tptt) REVERT: A 164 ILE cc_start: 0.8556 (mt) cc_final: 0.8267 (mt) REVERT: A 194 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8184 (mt-10) REVERT: A 283 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8891 (mmmm) REVERT: A 431 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8227 (mppt) REVERT: A 445 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7445 (pm20) REVERT: A 453 TRP cc_start: 0.5425 (m-10) cc_final: 0.5113 (m-10) REVERT: A 578 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8334 (mmtt) REVERT: A 607 ASP cc_start: 0.8463 (t0) cc_final: 0.8039 (t0) REVERT: A 641 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: A 697 LEU cc_start: 0.8239 (tt) cc_final: 0.7997 (tt) REVERT: A 815 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.7672 (t80) REVERT: A 863 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8558 (mmt) REVERT: A 988 GLU cc_start: 0.7911 (pm20) cc_final: 0.7434 (pm20) REVERT: A 1023 MET cc_start: 0.6715 (mmt) cc_final: 0.5705 (tmt) REVERT: A 1027 LYS cc_start: 0.5888 (OUTLIER) cc_final: 0.4954 (mmmm) REVERT: B 132 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8223 (pp) REVERT: B 163 LYS cc_start: 0.8944 (tttt) cc_final: 0.8629 (tptt) REVERT: B 164 ILE cc_start: 0.8484 (mt) cc_final: 0.8178 (mt) REVERT: B 282 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8135 (pp20) REVERT: B 431 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8247 (mppt) REVERT: B 445 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7709 (mt-10) REVERT: B 578 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8355 (mmtt) REVERT: B 607 ASP cc_start: 0.8441 (t0) cc_final: 0.8028 (t0) REVERT: B 622 GLU cc_start: 0.8630 (tt0) cc_final: 0.8253 (tp30) REVERT: B 641 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: B 697 LEU cc_start: 0.8273 (tt) cc_final: 0.8033 (tt) REVERT: B 863 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8458 (mmt) REVERT: B 988 GLU cc_start: 0.7871 (pm20) cc_final: 0.7387 (pm20) REVERT: B 1004 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7751 (tm-30) REVERT: B 1023 MET cc_start: 0.6758 (mmt) cc_final: 0.5748 (tmt) REVERT: B 1027 LYS cc_start: 0.5904 (OUTLIER) cc_final: 0.4986 (mmmm) REVERT: C 132 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8233 (pp) REVERT: C 163 LYS cc_start: 0.8956 (tttt) cc_final: 0.8638 (tptt) REVERT: C 164 ILE cc_start: 0.8583 (mt) cc_final: 0.8297 (mt) REVERT: C 283 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8833 (mmmm) REVERT: C 431 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8227 (mppt) REVERT: C 445 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7720 (mt-10) REVERT: C 578 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8335 (mmtt) REVERT: C 607 ASP cc_start: 0.8439 (t0) cc_final: 0.8022 (t0) REVERT: C 804 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8851 (mt) REVERT: C 815 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.7685 (t80) REVERT: C 988 GLU cc_start: 0.7887 (pm20) cc_final: 0.7415 (pm20) REVERT: C 1004 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7732 (tm-30) REVERT: C 1023 MET cc_start: 0.6744 (mmt) cc_final: 0.5719 (tmt) REVERT: C 1027 LYS cc_start: 0.5903 (OUTLIER) cc_final: 0.4940 (mmmm) REVERT: D 163 LYS cc_start: 0.8946 (tttt) cc_final: 0.8609 (tptt) REVERT: D 164 ILE cc_start: 0.8544 (mt) cc_final: 0.8252 (mt) REVERT: D 194 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8259 (mt-10) REVERT: D 283 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8833 (mmmm) REVERT: D 337 ASP cc_start: 0.8041 (m-30) cc_final: 0.6986 (t70) REVERT: D 445 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7336 (pm20) REVERT: D 453 TRP cc_start: 0.5409 (m-10) cc_final: 0.5147 (m-10) REVERT: D 507 ARG cc_start: 0.7827 (tpp-160) cc_final: 0.7597 (mmm160) REVERT: D 578 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8328 (mmtt) REVERT: D 607 ASP cc_start: 0.8425 (t0) cc_final: 0.8011 (t0) REVERT: D 863 MET cc_start: 0.9130 (mmt) cc_final: 0.8577 (mmt) REVERT: D 988 GLU cc_start: 0.7874 (pm20) cc_final: 0.7404 (pm20) REVERT: D 1023 MET cc_start: 0.6743 (mmt) cc_final: 0.5726 (tmt) REVERT: D 1027 LYS cc_start: 0.5902 (OUTLIER) cc_final: 0.4941 (mmmm) outliers start: 127 outliers final: 72 residues processed: 478 average time/residue: 0.6165 time to fit residues: 353.1182 Evaluate side-chains 453 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 357 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 1027 LYS Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 1027 LYS Chi-restraints excluded: chain B residue 1080 HIS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 578 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 815 PHE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 578 LYS Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 1027 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 33 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 283 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN B1080 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 HIS ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** 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 = 0.4246 r_free = 0.4246 target = 0.162186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.111442 restraints weight = 54403.268| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.41 r_work: 0.3392 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31092 Z= 0.131 Angle : 0.683 13.556 42120 Z= 0.336 Chirality : 0.043 0.324 4708 Planarity : 0.004 0.059 5264 Dihedral : 4.528 21.621 4000 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.16 % Allowed : 22.27 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3656 helix: 1.38 (0.10), residues: 2476 sheet: -0.84 (0.33), residues: 220 loop : -2.32 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 203 TYR 0.026 0.001 TYR C 117 PHE 0.033 0.001 PHE B 779 TRP 0.021 0.002 TRP A 786 HIS 0.034 0.001 HIS B1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (31088) covalent geometry : angle 0.68300 / 0.34 (42112) SS BOND : bond 0.00560 / 0.26 ( 4) SS BOND : angle 1.90154 / 1.07 ( 8) hydrogen bonds : bond 0.03906 / 2.64 ( 1812) hydrogen bonds : angle 4.04017 / 2.79 ( 5364) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 389 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8935 (tttt) cc_final: 0.8625 (tptt) REVERT: A 164 ILE cc_start: 0.8440 (mt) cc_final: 0.8217 (mt) REVERT: A 194 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8236 (mt-10) REVERT: A 203 ARG cc_start: 0.6982 (mtp-110) cc_final: 0.6219 (ttp-170) REVERT: A 283 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8895 (mmmm) REVERT: A 431 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8191 (mppt) REVERT: A 445 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7475 (pm20) REVERT: A 507 ARG cc_start: 0.7777 (tpp-160) cc_final: 0.7553 (mmm160) REVERT: A 578 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8271 (mmtt) REVERT: A 607 ASP cc_start: 0.8401 (t0) cc_final: 0.7970 (t0) REVERT: A 692 ASN cc_start: 0.6934 (OUTLIER) cc_final: 0.6601 (m110) REVERT: A 697 LEU cc_start: 0.8228 (tt) cc_final: 0.7973 (tt) REVERT: A 815 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.7637 (t80) REVERT: A 863 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8586 (mmt) REVERT: A 988 GLU cc_start: 0.7881 (pm20) cc_final: 0.7413 (pm20) REVERT: A 1023 MET cc_start: 0.6815 (mmt) cc_final: 0.5832 (tmt) REVERT: B 163 LYS cc_start: 0.8917 (tttt) cc_final: 0.8615 (tptt) REVERT: B 282 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8174 (pp20) REVERT: B 283 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8748 (mmmm) REVERT: B 395 LYS cc_start: 0.8691 (tppt) cc_final: 0.8427 (mptt) REVERT: B 431 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8167 (mppt) REVERT: B 445 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7764 (mt-10) REVERT: B 507 ARG cc_start: 0.7918 (tpp-160) cc_final: 0.7641 (mmm160) REVERT: B 578 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8263 (mmtt) REVERT: B 607 ASP cc_start: 0.8388 (t0) cc_final: 0.7974 (t0) REVERT: B 622 GLU cc_start: 0.8582 (tt0) cc_final: 0.8187 (tp30) REVERT: B 692 ASN cc_start: 0.6947 (OUTLIER) cc_final: 0.6612 (m110) REVERT: B 697 LEU cc_start: 0.8251 (tt) cc_final: 0.7997 (tt) REVERT: B 815 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.7621 (t80) REVERT: B 863 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8527 (mmt) REVERT: B 988 GLU cc_start: 0.7857 (pm20) cc_final: 0.7373 (pm20) REVERT: B 1004 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7675 (tm-30) REVERT: B 1023 MET cc_start: 0.6811 (mmt) cc_final: 0.5897 (tmt) REVERT: C 163 LYS cc_start: 0.8943 (tttt) cc_final: 0.8601 (tptt) REVERT: C 283 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8820 (mmmm) REVERT: C 395 LYS cc_start: 0.8772 (tppt) cc_final: 0.8528 (mptt) REVERT: C 431 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8221 (mppt) REVERT: C 445 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7675 (mt-10) REVERT: C 453 TRP cc_start: 0.5346 (m-10) cc_final: 0.4936 (m-10) REVERT: C 507 ARG cc_start: 0.7938 (tpp-160) cc_final: 0.7661 (mmm160) REVERT: C 526 LYS cc_start: 0.6115 (pptt) cc_final: 0.5867 (pptt) REVERT: C 578 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8291 (mmtt) REVERT: C 607 ASP cc_start: 0.8422 (t0) cc_final: 0.8012 (t0) REVERT: C 815 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.7615 (t80) REVERT: C 863 MET cc_start: 0.9078 (mmt) cc_final: 0.8496 (mmt) REVERT: C 988 GLU cc_start: 0.7848 (pm20) cc_final: 0.7376 (pm20) REVERT: C 1004 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7678 (tm-30) REVERT: C 1023 MET cc_start: 0.6784 (mmt) cc_final: 0.5879 (tmt) REVERT: C 1059 MET cc_start: 0.6193 (mpt) cc_final: 0.5790 (pmm) REVERT: D 132 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8140 (pp) REVERT: D 163 LYS cc_start: 0.8936 (tttt) cc_final: 0.8617 (tptt) REVERT: D 203 ARG cc_start: 0.6956 (mtp-110) cc_final: 0.6174 (ttp-170) REVERT: D 283 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8829 (mmmm) REVERT: D 337 ASP cc_start: 0.8064 (m-30) cc_final: 0.6981 (t70) REVERT: D 431 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8124 (mppt) REVERT: D 445 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7400 (pm20) REVERT: D 453 TRP cc_start: 0.5378 (m-10) cc_final: 0.5087 (m-10) REVERT: D 507 ARG cc_start: 0.7766 (tpp-160) cc_final: 0.7551 (mmm160) REVERT: D 607 ASP cc_start: 0.8376 (t0) cc_final: 0.7959 (t0) REVERT: D 641 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: D 692 ASN cc_start: 0.6925 (OUTLIER) cc_final: 0.6593 (m110) REVERT: D 815 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.7651 (t80) REVERT: D 863 MET cc_start: 0.9139 (mmt) cc_final: 0.8562 (mmt) REVERT: D 988 GLU cc_start: 0.7848 (pm20) cc_final: 0.7368 (pm20) REVERT: D 1023 MET cc_start: 0.6803 (mmt) cc_final: 0.5883 (tmt) outliers start: 105 outliers final: 59 residues processed: 472 average time/residue: 0.6378 time to fit residues: 358.0547 Evaluate side-chains 443 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 362 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 1080 HIS Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 578 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 815 PHE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 1080 HIS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 815 PHE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 940 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 301 optimal weight: 20.0000 chunk 338 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 283 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 310 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1080 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.160424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108905 restraints weight = 53971.624| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.40 r_work: 0.3356 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31092 Z= 0.180 Angle : 0.725 13.102 42120 Z= 0.361 Chirality : 0.045 0.318 4708 Planarity : 0.004 0.058 5264 Dihedral : 4.597 22.112 4000 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.76 % Allowed : 23.29 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3656 helix: 1.28 (0.10), residues: 2468 sheet: -0.80 (0.33), residues: 220 loop : -2.30 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 203 TYR 0.027 0.001 TYR D 117 PHE 0.037 0.002 PHE D 807 TRP 0.031 0.002 TRP A 525 HIS 0.034 0.001 HIS B1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (31088) covalent geometry : angle 0.72421 / 0.36 (42112) SS BOND : bond 0.00713 / 0.33 ( 4) SS BOND : angle 2.34462 / 1.32 ( 8) hydrogen bonds : bond 0.04423 / 3.00 ( 1812) hydrogen bonds : angle 4.15015 / 2.87 ( 5364) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 373 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8145 (pp) REVERT: A 163 LYS cc_start: 0.8934 (tttt) cc_final: 0.8626 (tptt) REVERT: A 164 ILE cc_start: 0.8548 (mt) cc_final: 0.8251 (mt) REVERT: A 194 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8254 (mt-10) REVERT: A 283 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8905 (mmmm) REVERT: A 395 LYS cc_start: 0.8731 (mppt) cc_final: 0.8480 (mptt) REVERT: A 431 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8205 (mppt) REVERT: A 445 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7488 (pm20) REVERT: A 507 ARG cc_start: 0.7910 (tpp-160) cc_final: 0.7632 (mmm160) REVERT: A 578 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8331 (mmtt) REVERT: A 607 ASP cc_start: 0.8412 (t0) cc_final: 0.7972 (t0) REVERT: A 697 LEU cc_start: 0.8236 (tt) cc_final: 0.7990 (tt) REVERT: A 988 GLU cc_start: 0.7882 (pm20) cc_final: 0.7444 (pm20) REVERT: A 1023 MET cc_start: 0.6885 (mmt) cc_final: 0.5879 (tmt) REVERT: B 163 LYS cc_start: 0.8937 (tttt) cc_final: 0.8598 (tptt) REVERT: B 164 ILE cc_start: 0.8486 (mt) cc_final: 0.8230 (mt) REVERT: B 282 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8137 (pp20) REVERT: B 283 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8756 (mmmm) REVERT: B 431 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8202 (mppt) REVERT: B 445 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7709 (mt-10) REVERT: B 507 ARG cc_start: 0.8029 (tpp-160) cc_final: 0.7699 (mmm160) REVERT: B 578 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8359 (mmtt) REVERT: B 607 ASP cc_start: 0.8399 (t0) cc_final: 0.7968 (t0) REVERT: B 622 GLU cc_start: 0.8662 (tt0) cc_final: 0.8254 (tp30) REVERT: B 641 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: B 697 LEU cc_start: 0.8269 (tt) cc_final: 0.8021 (tt) REVERT: B 863 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8428 (mmt) REVERT: B 988 GLU cc_start: 0.7863 (pm20) cc_final: 0.7414 (pm20) REVERT: B 1004 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7714 (tm-30) REVERT: B 1023 MET cc_start: 0.6899 (mmt) cc_final: 0.5944 (tmt) REVERT: C 132 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8164 (pp) REVERT: C 163 LYS cc_start: 0.8985 (tttt) cc_final: 0.8654 (tptt) REVERT: C 164 ILE cc_start: 0.8534 (mt) cc_final: 0.8262 (mt) REVERT: C 283 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8853 (mmmm) REVERT: C 395 LYS cc_start: 0.8707 (tppt) cc_final: 0.8465 (mptt) REVERT: C 445 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7707 (mt-10) REVERT: C 453 TRP cc_start: 0.5280 (m-10) cc_final: 0.4928 (m-10) REVERT: C 507 ARG cc_start: 0.8033 (tpp-160) cc_final: 0.7703 (mmm160) REVERT: C 578 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8336 (mmtt) REVERT: C 607 ASP cc_start: 0.8427 (t0) cc_final: 0.7985 (t0) REVERT: C 863 MET cc_start: 0.9135 (mmt) cc_final: 0.8520 (mmt) REVERT: C 988 GLU cc_start: 0.7870 (pm20) cc_final: 0.7419 (pm20) REVERT: C 1004 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7830 (tm-30) REVERT: C 1023 MET cc_start: 0.6897 (mmt) cc_final: 0.5932 (tmt) REVERT: D 132 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8151 (pp) REVERT: D 163 LYS cc_start: 0.8959 (tttt) cc_final: 0.8619 (tptt) REVERT: D 164 ILE cc_start: 0.8509 (mt) cc_final: 0.8249 (mt) REVERT: D 283 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8847 (mmmm) REVERT: D 431 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8139 (mppt) REVERT: D 445 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7389 (pm20) REVERT: D 607 ASP cc_start: 0.8417 (t0) cc_final: 0.7986 (t0) REVERT: D 988 GLU cc_start: 0.7876 (pm20) cc_final: 0.7440 (pm20) REVERT: D 1023 MET cc_start: 0.6872 (mmt) cc_final: 0.5853 (tmt) outliers start: 92 outliers final: 60 residues processed: 447 average time/residue: 0.6165 time to fit residues: 329.2692 Evaluate side-chains 433 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 358 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 578 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 615 GLU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 128 optimal weight: 1.9990 chunk 115 optimal weight: 0.0170 chunk 369 optimal weight: 20.0000 chunk 283 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 348 optimal weight: 1.9990 chunk 320 optimal weight: 0.8980 chunk 271 optimal weight: 6.9990 chunk 282 optimal weight: 0.0470 chunk 70 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** 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 = 0.4258 r_free = 0.4258 target = 0.163290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.112852 restraints weight = 54435.085| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.45 r_work: 0.3409 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 31092 Z= 0.128 Angle : 0.703 13.010 42120 Z= 0.346 Chirality : 0.043 0.304 4708 Planarity : 0.004 0.062 5264 Dihedral : 4.463 21.201 4000 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.88 % Allowed : 23.20 % Favored : 73.92 % 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: 0.42 (0.14), residues: 3656 helix: 1.33 (0.10), residues: 2484 sheet: -0.74 (0.32), residues: 220 loop : -2.34 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B1083 TYR 0.027 0.001 TYR B 117 PHE 0.037 0.001 PHE D 807 TRP 0.034 0.002 TRP A 525 HIS 0.009 0.001 HIS B1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (31088) covalent geometry : angle 0.70267 / 0.35 (42112) SS BOND : bond 0.00556 / 0.25 ( 4) SS BOND : angle 1.72441 / 0.97 ( 8) hydrogen bonds : bond 0.03817 / 2.57 ( 1812) hydrogen bonds : angle 4.01219 / 2.78 ( 5364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15367.16 seconds wall clock time: 261 minutes 17.81 seconds (15677.81 seconds total)