Starting phenix.real_space_refine on Thu Jun 26 04:13:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrb_32721/06_2025/7wrb_32721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrb_32721/06_2025/7wrb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wrb_32721/06_2025/7wrb_32721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrb_32721/06_2025/7wrb_32721.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrb_32721/06_2025/7wrb_32721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrb_32721/06_2025/7wrb_32721.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.37, per 1000 atoms: 0.57 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: 6.57 Conformation dependent library (CDL) restraints added in 3.4 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: 2.86 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: 11.46 Time building geometry restraints manager: 7.99 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: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.170 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 64.520 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.140 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.003 TRP A 651 HIS 0.009 0.002 HIS D 257 PHE 0.041 0.003 PHE C 108 TYR 0.029 0.003 TYR D 808 ARG 0.005 0.001 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.15707 ( 1812) hydrogen bonds : angle 6.50585 ( 5364) SS BOND : bond 0.01462 ( 4) SS BOND : angle 5.47565 ( 8) covalent geometry : bond 0.00578 (31088) covalent geometry : angle 1.00875 (42112) *********************** 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 : 3.378 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: 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: 0.8270 (mt) REVERT: B 441 LEU cc_start: 0.8551 (tp) cc_final: 0.8063 (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: 0.7135 (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: 0.8258 (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: 1.4940 time to fit residues: 1582.8389 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 : 3.383 ------------------------------------------------------------------------------- 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 314 optimal weight: 8.9990 chunk 281 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 291 optimal weight: 30.0000 chunk 112 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 337 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 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 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 675 GLN D 987 GLN D1074 ASN D1102 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.160666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110059 restraints weight = 54346.958| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.46 r_work: 0.3371 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 31092 Z= 0.219 Angle : 0.731 8.275 42120 Z= 0.383 Chirality : 0.044 0.140 4708 Planarity : 0.005 0.053 5264 Dihedral : 5.577 26.744 4008 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.81 % Allowed : 13.97 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3656 helix: -0.21 (0.10), residues: 2468 sheet: -1.75 (0.33), residues: 200 loop : -3.00 (0.16), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 693 HIS 0.006 0.001 HIS A 138 PHE 0.029 0.002 PHE A 779 TYR 0.026 0.002 TYR D 117 ARG 0.008 0.001 ARG B 784 Details of bonding type rmsd hydrogen bonds : bond 0.05389 ( 1812) hydrogen bonds : angle 4.66031 ( 5364) SS BOND : bond 0.00789 ( 4) SS BOND : angle 2.88718 ( 8) covalent geometry : bond 0.00522 (31088) covalent geometry : angle 0.72951 (42112) *********************** 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 631 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 471 time to evaluate : 4.110 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: A 146 ILE cc_start: 0.8506 (mt) cc_final: 0.8252 (tt) REVERT: A 163 LYS cc_start: 0.8969 (tttt) cc_final: 0.8578 (tptt) REVERT: A 164 ILE cc_start: 0.8515 (mt) cc_final: 0.8218 (mt) REVERT: A 302 VAL cc_start: 0.9054 (t) cc_final: 0.8829 (p) REVERT: A 441 LEU cc_start: 0.8468 (tp) cc_final: 0.8204 (tt) REVERT: A 815 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7659 (t80) REVERT: B 139 LEU cc_start: 0.8371 (pp) cc_final: 0.7895 (tm) REVERT: B 146 ILE cc_start: 0.8442 (mt) cc_final: 0.8208 (tt) REVERT: B 163 LYS cc_start: 0.8961 (tttt) cc_final: 0.8563 (tptt) REVERT: B 164 ILE cc_start: 0.8575 (mt) cc_final: 0.8274 (mt) REVERT: B 302 VAL cc_start: 0.9023 (t) cc_final: 0.8808 (p) REVERT: B 431 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8425 (mppt) REVERT: B 441 LEU cc_start: 0.8440 (tp) cc_final: 0.8208 (tt) REVERT: B 815 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.7657 (t80) REVERT: C 139 LEU cc_start: 0.8378 (pp) cc_final: 0.7905 (tm) REVERT: C 146 ILE cc_start: 0.8488 (mt) cc_final: 0.8245 (tt) REVERT: C 163 LYS cc_start: 0.8971 (tttt) cc_final: 0.8586 (tptt) REVERT: C 164 ILE cc_start: 0.8583 (mt) cc_final: 0.8285 (mt) REVERT: C 302 VAL cc_start: 0.9024 (t) cc_final: 0.8808 (p) REVERT: C 431 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8192 (mppt) REVERT: C 441 LEU cc_start: 0.8432 (tp) cc_final: 0.8204 (tt) REVERT: C 622 GLU cc_start: 0.8607 (tt0) cc_final: 0.8360 (tt0) REVERT: C 665 ASP cc_start: 0.8513 (t0) cc_final: 0.8271 (t0) REVERT: C 815 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.7650 (t80) REVERT: D 139 LEU cc_start: 0.8365 (pp) cc_final: 0.7939 (tm) REVERT: D 146 ILE cc_start: 0.8545 (mt) cc_final: 0.8275 (tt) REVERT: D 163 LYS cc_start: 0.8975 (tttt) cc_final: 0.8591 (tptt) REVERT: D 164 ILE cc_start: 0.8616 (mt) cc_final: 0.8328 (mt) REVERT: D 302 VAL cc_start: 0.9035 (t) cc_final: 0.8807 (p) REVERT: D 431 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8429 (mppt) REVERT: D 441 LEU cc_start: 0.8478 (tp) cc_final: 0.8160 (tt) REVERT: D 815 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.7648 (t80) REVERT: D 1004 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7805 (tm-30) outliers start: 160 outliers final: 57 residues processed: 588 average time/residue: 1.8677 time to fit residues: 1312.4620 Evaluate side-chains 447 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 383 time to evaluate : 10.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 462 MET 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 662 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 851 ARG 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 327 VAL Chi-restraints excluded: chain B residue 424 ASP 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 615 GLU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 639 LEU 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 814 VAL 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 304 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 464 THR 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 692 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 815 PHE Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 462 MET 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 791 VAL Chi-restraints excluded: chain D residue 814 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 288 optimal weight: 5.9990 chunk 260 optimal weight: 0.7980 chunk 1 optimal weight: 30.0000 chunk 353 optimal weight: 0.6980 chunk 203 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 284 optimal weight: 9.9990 chunk 277 optimal weight: 9.9990 chunk 26 optimal weight: 0.0470 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 199 ASN ** 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 438 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 635 ASN A 671 GLN B 107 GLN B 199 ASN ** 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 438 GLN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN B 635 ASN B 671 GLN C 107 GLN C 199 ASN ** 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 438 GLN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 635 ASN C 671 GLN ** C 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 GLN D 199 ASN ** 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 438 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN D 635 ASN D 671 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.163759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.113500 restraints weight = 54447.635| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.45 r_work: 0.3423 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31092 Z= 0.126 Angle : 0.639 10.958 42120 Z= 0.325 Chirality : 0.042 0.259 4708 Planarity : 0.004 0.043 5264 Dihedral : 4.959 20.112 4000 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.54 % Allowed : 16.11 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3656 helix: 0.56 (0.10), residues: 2488 sheet: -1.52 (0.32), residues: 232 loop : -2.61 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 693 HIS 0.010 0.001 HIS C1080 PHE 0.023 0.001 PHE D 487 TYR 0.024 0.001 TYR C 117 ARG 0.008 0.001 ARG D 203 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 1812) hydrogen bonds : angle 4.23174 ( 5364) SS BOND : bond 0.00534 ( 4) SS BOND : angle 1.67207 ( 8) covalent geometry : bond 0.00275 (31088) covalent geometry : angle 0.63847 (42112) *********************** 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 630 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 479 time to evaluate : 3.573 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: symmetry clash REVERT: A 163 LYS cc_start: 0.8918 (tttt) cc_final: 0.8559 (tptt) REVERT: A 164 ILE cc_start: 0.8425 (mt) cc_final: 0.8188 (mt) REVERT: A 337 ASP cc_start: 0.7742 (m-30) cc_final: 0.6888 (t70) REVERT: A 431 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8239 (mppt) REVERT: A 441 LEU cc_start: 0.8382 (tp) cc_final: 0.8090 (tt) REVERT: A 692 ASN cc_start: 0.6885 (OUTLIER) cc_final: 0.6601 (m110) REVERT: B 163 LYS cc_start: 0.8931 (tttt) cc_final: 0.8559 (tptt) REVERT: B 164 ILE cc_start: 0.8442 (mt) cc_final: 0.8210 (mt) REVERT: B 194 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8197 (mt-10) REVERT: B 431 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8237 (mppt) REVERT: B 692 ASN cc_start: 0.6898 (OUTLIER) cc_final: 0.6613 (m110) REVERT: B 1097 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7570 (tmtm) REVERT: C 163 LYS cc_start: 0.8926 (tttt) cc_final: 0.8568 (tptt) REVERT: C 194 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8261 (mt-10) REVERT: C 431 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8198 (mppt) REVERT: C 575 GLU cc_start: 0.8754 (tp30) cc_final: 0.8538 (mm-30) REVERT: C 622 GLU cc_start: 0.8549 (tt0) cc_final: 0.8283 (tt0) REVERT: C 665 ASP cc_start: 0.8493 (t0) cc_final: 0.8264 (t0) REVERT: C 692 ASN cc_start: 0.6916 (OUTLIER) cc_final: 0.6632 (m110) REVERT: C 1061 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: D 163 LYS cc_start: 0.8928 (tttt) cc_final: 0.8571 (tptt) REVERT: D 164 ILE cc_start: 0.8501 (mt) cc_final: 0.8164 (mt) REVERT: D 194 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8286 (mt-10) REVERT: D 431 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8240 (mppt) REVERT: D 441 LEU cc_start: 0.8491 (tp) cc_final: 0.8183 (tt) REVERT: D 575 GLU cc_start: 0.8938 (tp30) cc_final: 0.8605 (tp30) REVERT: D 692 ASN cc_start: 0.6903 (OUTLIER) cc_final: 0.6619 (m110) REVERT: D 1004 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7743 (tm-30) REVERT: D 1061 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8113 (mt-10) outliers start: 151 outliers final: 40 residues processed: 592 average time/residue: 1.3924 time to fit residues: 979.7378 Evaluate side-chains 468 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 418 time to evaluate : 4.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 431 LYS 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 692 ASN Chi-restraints excluded: chain A residue 807 PHE Chi-restraints excluded: chain A residue 851 ARG 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 431 LYS Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 516 TYR 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 807 PHE Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 516 TYR 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 807 PHE Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 1061 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 361 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 chunk 333 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 237 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** 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 429 GLN A 500 HIS A 510 GLN ** A 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 429 GLN B 500 HIS B 510 GLN 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 429 GLN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 HIS C 510 GLN D 257 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** D 500 HIS D 510 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.163522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.112945 restraints weight = 54937.320| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.46 r_work: 0.3419 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31092 Z= 0.125 Angle : 0.646 12.637 42120 Z= 0.325 Chirality : 0.041 0.227 4708 Planarity : 0.004 0.038 5264 Dihedral : 4.698 19.837 4000 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.21 % Allowed : 17.46 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3656 helix: 0.90 (0.10), residues: 2492 sheet: -1.59 (0.30), residues: 232 loop : -2.57 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 693 HIS 0.013 0.001 HIS C1080 PHE 0.027 0.001 PHE C 779 TYR 0.024 0.001 TYR A 117 ARG 0.005 0.000 ARG C1079 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 1812) hydrogen bonds : angle 4.09817 ( 5364) SS BOND : bond 0.00736 ( 4) SS BOND : angle 2.06820 ( 8) covalent geometry : bond 0.00279 (31088) covalent geometry : angle 0.64547 (42112) *********************** 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 580 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 440 time to evaluate : 3.569 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: A 163 LYS cc_start: 0.8924 (tttt) cc_final: 0.8590 (tptt) REVERT: A 164 ILE cc_start: 0.8480 (mt) cc_final: 0.8101 (mt) REVERT: A 194 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8313 (mt-10) REVERT: A 283 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8716 (mmmm) REVERT: A 337 ASP cc_start: 0.7858 (m-30) cc_final: 0.7015 (t70) REVERT: A 692 ASN cc_start: 0.6945 (OUTLIER) cc_final: 0.6649 (m110) REVERT: A 815 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.7723 (t80) REVERT: A 863 MET cc_start: 0.9101 (mmt) cc_final: 0.8556 (mmt) REVERT: A 1004 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7743 (tm-30) REVERT: A 1061 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: A 1097 LYS cc_start: 0.7877 (mttt) cc_final: 0.7329 (tmtm) REVERT: B 163 LYS cc_start: 0.8936 (tttt) cc_final: 0.8586 (tptt) REVERT: B 194 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8357 (mt-10) REVERT: B 283 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8716 (mmmm) REVERT: B 337 ASP cc_start: 0.7804 (m-30) cc_final: 0.6938 (t70) REVERT: B 431 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8246 (mppt) REVERT: B 692 ASN cc_start: 0.6907 (OUTLIER) cc_final: 0.6610 (m110) REVERT: B 863 MET cc_start: 0.9103 (mmt) cc_final: 0.8559 (mmt) REVERT: B 1004 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7742 (tm-30) REVERT: B 1061 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: C 163 LYS cc_start: 0.8947 (tttt) cc_final: 0.8612 (tptt) REVERT: C 164 ILE cc_start: 0.8379 (mt) cc_final: 0.8084 (mt) REVERT: C 283 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8715 (mmmm) REVERT: C 337 ASP cc_start: 0.7806 (m-30) cc_final: 0.6889 (t70) REVERT: C 431 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8204 (mppt) REVERT: C 575 GLU cc_start: 0.8787 (tp30) cc_final: 0.8551 (tp30) REVERT: C 622 GLU cc_start: 0.8529 (tt0) cc_final: 0.8294 (tt0) REVERT: C 665 ASP cc_start: 0.8370 (t0) cc_final: 0.8082 (t0) REVERT: C 692 ASN cc_start: 0.6934 (OUTLIER) cc_final: 0.6636 (m110) REVERT: C 863 MET cc_start: 0.9100 (mmt) cc_final: 0.8554 (mmt) REVERT: C 1004 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7743 (tm-30) REVERT: C 1061 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: C 1097 LYS cc_start: 0.7862 (mttt) cc_final: 0.7289 (tmtm) REVERT: D 163 LYS cc_start: 0.8935 (tttt) cc_final: 0.8600 (tptt) REVERT: D 164 ILE cc_start: 0.8460 (mt) cc_final: 0.8105 (mt) REVERT: D 194 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8319 (mt-10) REVERT: D 283 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8712 (mmmm) REVERT: D 337 ASP cc_start: 0.7782 (m-30) cc_final: 0.6896 (t70) REVERT: D 431 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8294 (mppt) REVERT: D 692 ASN cc_start: 0.6917 (OUTLIER) cc_final: 0.6617 (m110) REVERT: D 815 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.7740 (t80) REVERT: D 863 MET cc_start: 0.9094 (mmt) cc_final: 0.8545 (mmt) REVERT: D 1004 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7739 (tm-30) REVERT: D 1061 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: D 1097 LYS cc_start: 0.7890 (mttt) cc_final: 0.7349 (tmtm) outliers start: 140 outliers final: 54 residues processed: 550 average time/residue: 1.3358 time to fit residues: 875.9272 Evaluate side-chains 483 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 412 time to evaluate : 3.484 ------------------------------------------------------------------------------- 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 283 LYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 569 ILE 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 846 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 1061 GLU 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 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 584 THR 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 851 ARG Chi-restraints excluded: chain B residue 1061 GLU 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 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 584 THR Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 851 ARG 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 185 HIS Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 569 ILE 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 815 PHE Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 1061 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 238 optimal weight: 0.8980 chunk 336 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 327 optimal weight: 0.9990 chunk 230 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 269 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 318 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 667 HIS A1080 HIS B 154 ASN B 257 HIS ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN B 667 HIS B1080 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 667 HIS C1080 HIS D 154 ASN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 GLN D 667 HIS D1080 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.160505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109208 restraints weight = 54394.495| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.40 r_work: 0.3366 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31092 Z= 0.184 Angle : 0.681 13.340 42120 Z= 0.346 Chirality : 0.043 0.176 4708 Planarity : 0.004 0.049 5264 Dihedral : 4.741 21.014 4000 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.75 % Allowed : 18.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3656 helix: 1.02 (0.10), residues: 2476 sheet: -1.47 (0.31), residues: 232 loop : -2.26 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 453 HIS 0.013 0.002 HIS B1080 PHE 0.031 0.002 PHE D 752 TYR 0.026 0.001 TYR C 117 ARG 0.012 0.001 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 1812) hydrogen bonds : angle 4.22528 ( 5364) SS BOND : bond 0.00884 ( 4) SS BOND : angle 2.57425 ( 8) covalent geometry : bond 0.00439 (31088) covalent geometry : angle 0.67990 (42112) *********************** 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 597 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 439 time to evaluate : 3.842 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: A 163 LYS cc_start: 0.8956 (tttt) cc_final: 0.8642 (tptt) REVERT: A 164 ILE cc_start: 0.8604 (mt) cc_final: 0.8305 (mt) REVERT: A 194 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8329 (mt-10) REVERT: A 431 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8216 (mppt) REVERT: A 622 GLU cc_start: 0.8588 (tt0) cc_final: 0.8116 (tp30) REVERT: A 1004 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 1078 MET cc_start: 0.5718 (OUTLIER) cc_final: 0.5325 (tpp) REVERT: B 163 LYS cc_start: 0.8965 (tttt) cc_final: 0.8603 (tptt) REVERT: B 164 ILE cc_start: 0.8602 (mt) cc_final: 0.8367 (mt) REVERT: B 194 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8328 (mt-10) REVERT: B 1004 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 163 LYS cc_start: 0.8975 (tttt) cc_final: 0.8627 (tptt) REVERT: C 164 ILE cc_start: 0.8585 (mt) cc_final: 0.8334 (mt) REVERT: C 575 GLU cc_start: 0.8853 (tp30) cc_final: 0.8607 (tp30) REVERT: C 1004 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7697 (tm-30) REVERT: C 1078 MET cc_start: 0.5449 (mmm) cc_final: 0.5097 (tpp) REVERT: D 163 LYS cc_start: 0.8973 (tttt) cc_final: 0.8627 (tptt) REVERT: D 164 ILE cc_start: 0.8570 (mt) cc_final: 0.8269 (mt) REVERT: D 194 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8328 (mt-10) REVERT: D 337 ASP cc_start: 0.7931 (m-30) cc_final: 0.6954 (t70) REVERT: D 1004 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7698 (tm-30) outliers start: 158 outliers final: 85 residues processed: 551 average time/residue: 1.3359 time to fit residues: 881.8906 Evaluate side-chains 483 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 396 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 277 LEU 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 418 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 569 ILE 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 697 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain A residue 1080 HIS Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 356 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 662 GLU Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 851 ARG 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 185 HIS Chi-restraints excluded: chain C residue 277 LEU 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 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 584 THR Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 1087 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 277 LEU 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 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 569 ILE 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 697 LEU Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 1080 HIS 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 57 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 345 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 357 optimal weight: 0.9990 chunk 269 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN B 185 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 ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 449 ASN C1080 HIS ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 ASN D1080 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.161708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.110423 restraints weight = 54517.243| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.44 r_work: 0.3389 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31092 Z= 0.138 Angle : 0.667 13.823 42120 Z= 0.332 Chirality : 0.043 0.294 4708 Planarity : 0.004 0.059 5264 Dihedral : 4.655 21.667 4000 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.36 % Allowed : 19.50 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3656 helix: 1.17 (0.10), residues: 2480 sheet: -1.16 (0.31), residues: 224 loop : -2.41 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 453 HIS 0.012 0.001 HIS C1080 PHE 0.032 0.002 PHE B 779 TYR 0.027 0.001 TYR B 646 ARG 0.006 0.000 ARG C 203 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 1812) hydrogen bonds : angle 4.10964 ( 5364) SS BOND : bond 0.00652 ( 4) SS BOND : angle 2.26852 ( 8) covalent geometry : bond 0.00321 (31088) covalent geometry : angle 0.66653 (42112) *********************** 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 563 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 418 time to evaluate : 3.668 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: A 163 LYS cc_start: 0.8942 (tttt) cc_final: 0.8621 (tptt) REVERT: A 164 ILE cc_start: 0.8569 (mt) cc_final: 0.8265 (mt) REVERT: A 194 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8269 (mt-10) REVERT: A 334 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7140 (mm-40) REVERT: A 337 ASP cc_start: 0.7916 (m-30) cc_final: 0.7433 (p0) REVERT: A 431 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8211 (mppt) REVERT: A 445 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7422 (pm20) REVERT: A 622 GLU cc_start: 0.8600 (tt0) cc_final: 0.8151 (tp30) REVERT: A 988 GLU cc_start: 0.7924 (pm20) cc_final: 0.7353 (pm20) REVERT: A 1027 LYS cc_start: 0.5058 (mttp) cc_final: 0.4800 (pptt) REVERT: B 163 LYS cc_start: 0.8952 (tttt) cc_final: 0.8611 (tptt) REVERT: B 194 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8341 (mt-10) REVERT: B 445 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: B 607 ASP cc_start: 0.8477 (t0) cc_final: 0.8034 (t0) REVERT: B 622 GLU cc_start: 0.8620 (tt0) cc_final: 0.8157 (tp30) REVERT: B 638 ASP cc_start: 0.8216 (t0) cc_final: 0.7843 (t0) REVERT: B 641 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: B 666 GLN cc_start: 0.8741 (pt0) cc_final: 0.8446 (pt0) REVERT: B 988 GLU cc_start: 0.7915 (pm20) cc_final: 0.7341 (pm20) REVERT: B 1027 LYS cc_start: 0.5073 (mttp) cc_final: 0.4806 (pptt) REVERT: C 163 LYS cc_start: 0.8955 (tttt) cc_final: 0.8611 (tptt) REVERT: C 431 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8251 (mppt) REVERT: C 445 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: C 575 GLU cc_start: 0.8846 (tp30) cc_final: 0.8505 (tp30) REVERT: C 607 ASP cc_start: 0.8446 (t0) cc_final: 0.8019 (t0) REVERT: C 641 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: C 942 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8647 (pp20) REVERT: C 988 GLU cc_start: 0.7905 (pm20) cc_final: 0.7328 (pm20) REVERT: C 1027 LYS cc_start: 0.5024 (mttp) cc_final: 0.4785 (pptt) REVERT: D 163 LYS cc_start: 0.8966 (tttt) cc_final: 0.8629 (tptt) REVERT: D 164 ILE cc_start: 0.8544 (mt) cc_final: 0.8221 (mt) REVERT: D 194 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8321 (mt-10) REVERT: D 337 ASP cc_start: 0.7931 (m-30) cc_final: 0.6917 (t70) REVERT: D 445 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7102 (pm20) REVERT: D 607 ASP cc_start: 0.8485 (t0) cc_final: 0.8059 (t0) REVERT: D 622 GLU cc_start: 0.8663 (tt0) cc_final: 0.8242 (tp30) REVERT: D 641 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: D 863 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8504 (mmt) REVERT: D 942 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8653 (pp20) REVERT: D 988 GLU cc_start: 0.7926 (pm20) cc_final: 0.7354 (pm20) REVERT: D 1027 LYS cc_start: 0.5063 (mttp) cc_final: 0.4783 (pptt) outliers start: 145 outliers final: 66 residues processed: 516 average time/residue: 1.4301 time to fit residues: 884.7240 Evaluate side-chains 478 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 400 time to evaluate : 3.716 ------------------------------------------------------------------------------- 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 304 PHE Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 356 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 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 846 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 445 GLU 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 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 846 ILE Chi-restraints excluded: chain B residue 849 VAL 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 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 445 GLU 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 584 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 942 GLU 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 304 PHE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 445 GLU 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 846 ILE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 942 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 40 optimal weight: 8.9990 chunk 353 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 172 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 HIS B 185 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** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1080 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.162307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.111382 restraints weight = 54356.301| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.43 r_work: 0.3397 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31092 Z= 0.136 Angle : 0.683 15.359 42120 Z= 0.338 Chirality : 0.043 0.317 4708 Planarity : 0.004 0.063 5264 Dihedral : 4.570 21.260 4000 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.12 % Allowed : 20.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3656 helix: 1.26 (0.10), residues: 2480 sheet: -1.26 (0.31), residues: 232 loop : -2.28 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 786 HIS 0.024 0.001 HIS C1080 PHE 0.032 0.001 PHE B 779 TYR 0.026 0.001 TYR D 117 ARG 0.012 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 1812) hydrogen bonds : angle 4.05074 ( 5364) SS BOND : bond 0.00601 ( 4) SS BOND : angle 1.93233 ( 8) covalent geometry : bond 0.00318 (31088) covalent geometry : angle 0.68219 (42112) *********************** 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 538 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 401 time to evaluate : 3.489 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: A 163 LYS cc_start: 0.8953 (tttt) cc_final: 0.8626 (tptt) REVERT: A 164 ILE cc_start: 0.8563 (mt) cc_final: 0.8261 (mt) REVERT: A 194 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8262 (mt-10) REVERT: A 431 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8168 (mppt) REVERT: A 445 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7438 (pm20) REVERT: A 692 ASN cc_start: 0.6933 (OUTLIER) cc_final: 0.6510 (m110) REVERT: A 863 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8549 (mmt) REVERT: A 988 GLU cc_start: 0.7871 (pm20) cc_final: 0.7323 (pm20) REVERT: A 1027 LYS cc_start: 0.4994 (mttp) cc_final: 0.4768 (pptt) REVERT: A 1061 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: B 163 LYS cc_start: 0.8954 (tttt) cc_final: 0.8614 (tptt) REVERT: B 164 ILE cc_start: 0.8517 (mt) cc_final: 0.8222 (mt) REVERT: B 194 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8336 (mt-10) REVERT: B 431 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8206 (mppt) REVERT: B 445 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7128 (pm20) REVERT: B 607 ASP cc_start: 0.8466 (t0) cc_final: 0.8006 (t0) REVERT: B 622 GLU cc_start: 0.8632 (tt0) cc_final: 0.8138 (tp30) REVERT: B 666 GLN cc_start: 0.8720 (pt0) cc_final: 0.8411 (pt0) REVERT: B 692 ASN cc_start: 0.6941 (OUTLIER) cc_final: 0.6527 (m110) REVERT: B 815 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.7721 (t80) REVERT: B 863 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8522 (mmt) REVERT: B 988 GLU cc_start: 0.7897 (pm20) cc_final: 0.7351 (pm20) REVERT: C 163 LYS cc_start: 0.8972 (tttt) cc_final: 0.8615 (tptt) REVERT: C 164 ILE cc_start: 0.8439 (mt) cc_final: 0.8173 (mt) REVERT: C 431 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8223 (mppt) REVERT: C 575 GLU cc_start: 0.8819 (tp30) cc_final: 0.8467 (tp30) REVERT: C 607 ASP cc_start: 0.8462 (t0) cc_final: 0.7998 (t0) REVERT: C 638 ASP cc_start: 0.8167 (t0) cc_final: 0.7963 (t0) REVERT: C 641 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: C 692 ASN cc_start: 0.7018 (OUTLIER) cc_final: 0.6624 (m110) REVERT: C 815 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.7743 (t80) REVERT: C 988 GLU cc_start: 0.7882 (pm20) cc_final: 0.7340 (pm20) REVERT: D 163 LYS cc_start: 0.8964 (tttt) cc_final: 0.8623 (tptt) REVERT: D 164 ILE cc_start: 0.8541 (mt) cc_final: 0.8322 (mt) REVERT: D 337 ASP cc_start: 0.7949 (m-30) cc_final: 0.7029 (t70) REVERT: D 607 ASP cc_start: 0.8375 (t0) cc_final: 0.7953 (t0) REVERT: D 692 ASN cc_start: 0.6790 (OUTLIER) cc_final: 0.6362 (m110) REVERT: D 863 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8554 (mmt) REVERT: D 988 GLU cc_start: 0.7880 (pm20) cc_final: 0.7338 (pm20) REVERT: D 1061 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8132 (mt-10) outliers start: 137 outliers final: 65 residues processed: 503 average time/residue: 1.3173 time to fit residues: 796.3913 Evaluate side-chains 458 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 377 time to evaluate : 3.154 ------------------------------------------------------------------------------- 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 199 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LYS 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 662 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 846 ILE 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 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 277 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 445 GLU 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 783 VAL Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 846 ILE 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 133 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 277 LEU 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 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 692 ASN Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 815 PHE Chi-restraints excluded: chain C residue 849 VAL 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 356 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 431 LYS 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 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 846 ILE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1080 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 43 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 255 optimal weight: 0.9980 chunk 332 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 350 optimal weight: 1.9990 chunk 334 optimal weight: 0.0770 chunk 283 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 365 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN B 185 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** B1080 HIS C 185 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** 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 480 ASN D1080 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.160555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109416 restraints weight = 54648.988| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.44 r_work: 0.3362 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 31092 Z= 0.181 Angle : 0.711 13.047 42120 Z= 0.357 Chirality : 0.045 0.304 4708 Planarity : 0.004 0.052 5264 Dihedral : 4.634 22.125 4000 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.40 % Allowed : 21.94 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3656 helix: 1.23 (0.10), residues: 2484 sheet: -0.97 (0.32), residues: 224 loop : -2.32 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 453 HIS 0.025 0.001 HIS D1080 PHE 0.034 0.002 PHE B 779 TYR 0.027 0.001 TYR D 117 ARG 0.013 0.001 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 1812) hydrogen bonds : angle 4.15616 ( 5364) SS BOND : bond 0.00858 ( 4) SS BOND : angle 2.46972 ( 8) covalent geometry : bond 0.00437 (31088) covalent geometry : angle 0.71052 (42112) *********************** 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 505 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 392 time to evaluate : 3.711 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: 0.8966 (tttt) cc_final: 0.8658 (tptt) REVERT: A 164 ILE cc_start: 0.8611 (mt) cc_final: 0.8324 (mt) REVERT: A 194 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8283 (mt-10) REVERT: A 431 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8210 (mppt) REVERT: A 445 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7478 (pm20) REVERT: A 453 TRP cc_start: 0.5299 (m-10) cc_final: 0.4942 (m-10) REVERT: A 622 GLU cc_start: 0.8595 (tt0) cc_final: 0.8229 (tp30) REVERT: A 988 GLU cc_start: 0.7846 (pm20) cc_final: 0.7319 (pm20) REVERT: A 1059 MET cc_start: 0.6410 (mpt) cc_final: 0.5927 (pmm) REVERT: B 163 LYS cc_start: 0.8972 (tttt) cc_final: 0.8647 (tptt) REVERT: B 194 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8317 (mt-10) REVERT: B 445 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: B 507 ARG cc_start: 0.7889 (tpp-160) cc_final: 0.7687 (mmm160) REVERT: B 607 ASP cc_start: 0.8426 (t0) cc_final: 0.7946 (t0) REVERT: B 666 GLN cc_start: 0.8770 (pt0) cc_final: 0.8466 (pt0) REVERT: B 988 GLU cc_start: 0.7852 (pm20) cc_final: 0.7320 (pm20) REVERT: B 1023 MET cc_start: 0.6881 (mmt) cc_final: 0.5863 (tmt) REVERT: B 1027 LYS cc_start: 0.5880 (OUTLIER) cc_final: 0.4933 (mmmm) REVERT: B 1059 MET cc_start: 0.6357 (mpt) cc_final: 0.5894 (pmm) REVERT: C 163 LYS cc_start: 0.8990 (tttt) cc_final: 0.8647 (tptt) REVERT: C 164 ILE cc_start: 0.8537 (mt) cc_final: 0.8259 (mt) REVERT: C 575 GLU cc_start: 0.8863 (tp30) cc_final: 0.8529 (tp30) REVERT: C 607 ASP cc_start: 0.8435 (t0) cc_final: 0.7956 (t0) REVERT: C 641 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: C 988 GLU cc_start: 0.7858 (pm20) cc_final: 0.7307 (pm20) REVERT: C 1023 MET cc_start: 0.6917 (mmt) cc_final: 0.5873 (tmt) REVERT: C 1027 LYS cc_start: 0.5860 (OUTLIER) cc_final: 0.4923 (mmmm) REVERT: C 1059 MET cc_start: 0.6437 (mpt) cc_final: 0.5968 (pmm) REVERT: D 163 LYS cc_start: 0.8980 (tttt) cc_final: 0.8639 (tptt) REVERT: D 164 ILE cc_start: 0.8567 (mt) cc_final: 0.8265 (mt) REVERT: D 337 ASP cc_start: 0.7989 (m-30) cc_final: 0.7044 (t70) REVERT: D 431 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8187 (mppt) REVERT: D 453 TRP cc_start: 0.5246 (m-10) cc_final: 0.4793 (m-10) REVERT: D 607 ASP cc_start: 0.8422 (t0) cc_final: 0.7967 (t0) REVERT: D 622 GLU cc_start: 0.8614 (tt0) cc_final: 0.8232 (tp30) REVERT: D 988 GLU cc_start: 0.7829 (pm20) cc_final: 0.7300 (pm20) REVERT: D 1023 MET cc_start: 0.6807 (mmt) cc_final: 0.5633 (tmt) REVERT: D 1027 LYS cc_start: 0.5876 (OUTLIER) cc_final: 0.4913 (mmmm) outliers start: 113 outliers final: 69 residues processed: 474 average time/residue: 1.7392 time to fit residues: 991.6385 Evaluate side-chains 440 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 364 time to evaluate : 4.753 ------------------------------------------------------------------------------- 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 328 VAL Chi-restraints excluded: chain A residue 356 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 521 LEU 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 849 VAL 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 277 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 445 GLU 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 704 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 849 VAL 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 133 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 304 PHE 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 439 LEU 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 692 ASN Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 783 VAL 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 304 PHE Chi-restraints excluded: chain D residue 356 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 516 TYR 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 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 14 optimal weight: 10.0000 chunk 214 optimal weight: 0.9980 chunk 287 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 204 optimal weight: 20.0000 chunk 365 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 30.0000 chunk 237 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 204 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS A1080 HIS B 185 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 C 154 ASN C 185 HIS C 204 ASN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN C 559 HIS D 204 ASN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 ASN D 559 HIS D1080 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.155948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.104336 restraints weight = 54429.736| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.59 r_work: 0.3272 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 31092 Z= 0.340 Angle : 0.858 12.636 42120 Z= 0.439 Chirality : 0.051 0.264 4708 Planarity : 0.005 0.051 5264 Dihedral : 5.212 26.658 4000 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.79 % Allowed : 21.51 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3656 helix: 0.72 (0.10), residues: 2468 sheet: -1.20 (0.34), residues: 200 loop : -2.47 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 453 HIS 0.047 0.002 HIS B1080 PHE 0.043 0.003 PHE A 752 TYR 0.031 0.002 TYR A 117 ARG 0.012 0.001 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.05984 ( 1812) hydrogen bonds : angle 4.65337 ( 5364) SS BOND : bond 0.00991 ( 4) SS BOND : angle 3.38436 ( 8) covalent geometry : bond 0.00820 (31088) covalent geometry : angle 0.85682 (42112) *********************** 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 499 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 373 time to evaluate : 6.560 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: A 163 LYS cc_start: 0.9000 (tttt) cc_final: 0.8649 (tptt) REVERT: A 164 ILE cc_start: 0.8674 (mt) cc_final: 0.8449 (mt) REVERT: A 431 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8262 (mppt) REVERT: A 641 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: A 988 GLU cc_start: 0.7921 (pm20) cc_final: 0.7448 (pm20) REVERT: A 1023 MET cc_start: 0.6772 (mmt) cc_final: 0.5773 (tmt) REVERT: A 1059 MET cc_start: 0.6668 (mpt) cc_final: 0.6177 (pmm) REVERT: B 163 LYS cc_start: 0.9004 (tttt) cc_final: 0.8652 (tptt) REVERT: B 431 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8246 (mppt) REVERT: B 453 TRP cc_start: 0.5679 (m-10) cc_final: 0.5384 (m-10) REVERT: B 607 ASP cc_start: 0.8586 (t0) cc_final: 0.8092 (t0) REVERT: B 622 GLU cc_start: 0.8749 (tt0) cc_final: 0.8352 (tp30) REVERT: B 988 GLU cc_start: 0.7968 (pm20) cc_final: 0.7496 (pm20) REVERT: B 1023 MET cc_start: 0.6803 (mmt) cc_final: 0.5775 (tmt) REVERT: B 1059 MET cc_start: 0.6511 (mpt) cc_final: 0.5905 (pmm) REVERT: C 163 LYS cc_start: 0.8968 (tttt) cc_final: 0.8622 (tptt) REVERT: C 382 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8221 (mppt) REVERT: C 431 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8254 (mppt) REVERT: C 518 ASP cc_start: 0.7742 (m-30) cc_final: 0.7472 (m-30) REVERT: C 607 ASP cc_start: 0.8582 (t0) cc_final: 0.8085 (t0) REVERT: C 622 GLU cc_start: 0.8745 (tt0) cc_final: 0.8351 (tp30) REVERT: C 988 GLU cc_start: 0.7956 (pm20) cc_final: 0.7483 (pm20) REVERT: C 1023 MET cc_start: 0.6759 (mmt) cc_final: 0.5792 (tmt) REVERT: C 1059 MET cc_start: 0.6636 (mpt) cc_final: 0.6090 (pmm) REVERT: C 1061 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8254 (mt-10) REVERT: D 163 LYS cc_start: 0.8950 (tttt) cc_final: 0.8609 (tptt) REVERT: D 164 ILE cc_start: 0.8677 (mt) cc_final: 0.8445 (mt) REVERT: D 431 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8258 (mppt) REVERT: D 518 ASP cc_start: 0.7704 (m-30) cc_final: 0.7393 (m-30) REVERT: D 607 ASP cc_start: 0.8594 (t0) cc_final: 0.8098 (t0) REVERT: D 622 GLU cc_start: 0.8701 (tt0) cc_final: 0.8328 (tp30) REVERT: D 641 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: D 988 GLU cc_start: 0.7955 (pm20) cc_final: 0.7491 (pm20) REVERT: D 1023 MET cc_start: 0.6851 (mmt) cc_final: 0.5782 (tmt) REVERT: D 1059 MET cc_start: 0.6660 (mpt) cc_final: 0.6275 (pmm) outliers start: 126 outliers final: 70 residues processed: 462 average time/residue: 2.2371 time to fit residues: 1285.1401 Evaluate side-chains 429 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 351 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 356 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 526 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 783 VAL Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 1080 HIS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 356 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 526 LYS 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 783 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 CYS 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 304 PHE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 439 LEU 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 526 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 692 ASN Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 1061 GLU 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 304 PHE Chi-restraints excluded: chain D residue 356 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 516 TYR Chi-restraints excluded: chain D residue 526 LYS 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 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 299 optimal weight: 20.0000 chunk 263 optimal weight: 0.6980 chunk 239 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 290 optimal weight: 0.0170 chunk 324 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 overall best weight: 2.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 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** B1080 HIS C 185 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN C 799 ASN C1080 HIS ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 ASN D 799 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.158975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107982 restraints weight = 54335.163| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.64 r_work: 0.3326 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31092 Z= 0.180 Angle : 0.747 12.410 42120 Z= 0.376 Chirality : 0.045 0.296 4708 Planarity : 0.004 0.060 5264 Dihedral : 4.966 25.386 4000 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.67 % Allowed : 22.96 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3656 helix: 1.03 (0.10), residues: 2480 sheet: -0.90 (0.35), residues: 192 loop : -2.44 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 453 HIS 0.027 0.001 HIS A1080 PHE 0.035 0.002 PHE D 807 TYR 0.034 0.002 TYR C 191 ARG 0.014 0.001 ARG D 203 Details of bonding type rmsd hydrogen bonds : bond 0.04724 ( 1812) hydrogen bonds : angle 4.36780 ( 5364) SS BOND : bond 0.00755 ( 4) SS BOND : angle 2.67905 ( 8) covalent geometry : bond 0.00434 (31088) covalent geometry : angle 0.74623 (42112) ********************** 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 463 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 374 time to evaluate : 3.492 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: 0.8965 (tttt) cc_final: 0.8616 (tptt) REVERT: A 164 ILE cc_start: 0.8597 (mt) cc_final: 0.8343 (mt) REVERT: A 194 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8220 (mt-10) REVERT: A 431 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8232 (mppt) REVERT: A 445 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7358 (pm20) REVERT: A 507 ARG cc_start: 0.7972 (tpp-160) cc_final: 0.7588 (mmm160) REVERT: A 622 GLU cc_start: 0.8639 (tt0) cc_final: 0.8396 (tp30) REVERT: A 641 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: A 815 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.7571 (t80) REVERT: A 863 MET cc_start: 0.9165 (mmt) cc_final: 0.8577 (mmt) REVERT: A 988 GLU cc_start: 0.7968 (pm20) cc_final: 0.7505 (pm20) REVERT: A 1023 MET cc_start: 0.6804 (mmt) cc_final: 0.5785 (tmt) REVERT: A 1059 MET cc_start: 0.6644 (mpt) cc_final: 0.6255 (pmm) REVERT: B 163 LYS cc_start: 0.8941 (tttt) cc_final: 0.8582 (tptt) REVERT: B 194 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8241 (mt-10) REVERT: B 507 ARG cc_start: 0.7905 (tpp-160) cc_final: 0.7559 (mmm160) REVERT: B 607 ASP cc_start: 0.8512 (t0) cc_final: 0.8044 (t0) REVERT: B 622 GLU cc_start: 0.8649 (tt0) cc_final: 0.8247 (tp30) REVERT: B 863 MET cc_start: 0.9149 (mmt) cc_final: 0.8549 (mmt) REVERT: B 988 GLU cc_start: 0.7943 (pm20) cc_final: 0.7479 (pm20) REVERT: B 1023 MET cc_start: 0.6779 (mmt) cc_final: 0.5801 (tmt) REVERT: C 163 LYS cc_start: 0.8953 (tttt) cc_final: 0.8589 (tptt) REVERT: C 431 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8208 (mppt) REVERT: C 607 ASP cc_start: 0.8509 (t0) cc_final: 0.8047 (t0) REVERT: C 622 GLU cc_start: 0.8707 (tt0) cc_final: 0.8323 (tp30) REVERT: C 863 MET cc_start: 0.9165 (mmt) cc_final: 0.8570 (mmt) REVERT: C 988 GLU cc_start: 0.7953 (pm20) cc_final: 0.7531 (pm20) REVERT: C 1023 MET cc_start: 0.6743 (mmt) cc_final: 0.5819 (tmt) REVERT: D 163 LYS cc_start: 0.8986 (tttt) cc_final: 0.8623 (tptt) REVERT: D 164 ILE cc_start: 0.8570 (mt) cc_final: 0.8296 (mt) REVERT: D 453 TRP cc_start: 0.5388 (m-10) cc_final: 0.4985 (m-10) REVERT: D 607 ASP cc_start: 0.8534 (t0) cc_final: 0.8086 (t0) REVERT: D 622 GLU cc_start: 0.8637 (tt0) cc_final: 0.8270 (tp30) REVERT: D 641 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: D 815 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.7575 (t80) REVERT: D 863 MET cc_start: 0.9156 (mmt) cc_final: 0.8559 (mmt) REVERT: D 988 GLU cc_start: 0.7955 (pm20) cc_final: 0.7492 (pm20) REVERT: D 1023 MET cc_start: 0.6785 (mmt) cc_final: 0.5689 (tmt) REVERT: D 1027 LYS cc_start: 0.5879 (OUTLIER) cc_final: 0.5025 (mmmm) outliers start: 89 outliers final: 63 residues processed: 448 average time/residue: 1.6246 time to fit residues: 882.0707 Evaluate side-chains 426 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 356 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 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 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 929 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 445 GLU 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 526 LYS 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 783 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 CYS 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 382 LYS Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 526 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 692 ASN 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 133 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 356 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 1027 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 285 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 349 optimal weight: 0.6980 chunk 169 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 60 optimal weight: 0.0870 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1080 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.162015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.111642 restraints weight = 54148.885| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.37 r_work: 0.3402 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31092 Z= 0.137 Angle : 0.720 15.701 42120 Z= 0.358 Chirality : 0.044 0.294 4708 Planarity : 0.004 0.062 5264 Dihedral : 4.699 22.467 4000 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.07 % Allowed : 23.86 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3656 helix: 1.21 (0.10), residues: 2496 sheet: -0.98 (0.33), residues: 224 loop : -2.35 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 525 HIS 0.013 0.001 HIS D1080 PHE 0.039 0.001 PHE C 807 TYR 0.032 0.001 TYR C 191 ARG 0.017 0.001 ARG B1083 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1812) hydrogen bonds : angle 4.16455 ( 5364) SS BOND : bond 0.00557 ( 4) SS BOND : angle 2.06829 ( 8) covalent geometry : bond 0.00308 (31088) covalent geometry : angle 0.71933 (42112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34848.09 seconds wall clock time: 616 minutes 7.76 seconds (36967.76 seconds total)