Starting phenix.real_space_refine on Sun Jul 5 20:59:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wrd_32723/07_2026/7wrd_32723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrd_32723/07_2026/7wrd_32723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wrd_32723/07_2026/7wrd_32723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrd_32723/07_2026/7wrd_32723.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wrd_32723/07_2026/7wrd_32723.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wrd_32723/07_2026/7wrd_32723.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wrd_32723/07_2026/7wrd_32723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrd_32723/07_2026/7wrd_32723.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 19820 2.51 5 N 5052 2.21 5 O 5452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30468 Number of models: 1 Model: "" Number of chains: 2 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: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 8.76, per 1000 atoms: 0.29 Number of scatterers: 30468 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 5452 8.00 N 5052 7.00 C 19820 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=2.01 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.01 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.01 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.1 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: 180 helices and 4 sheets defined 70.2% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 removed outlier: 3.912A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 204 removed outlier: 3.730A 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: 3.545A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.772A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.561A pdb=" N ARG A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 4.272A pdb=" N VAL A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 367' Processing helix chain 'A' and resid 370 through 386 removed outlier: 4.120A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.727A pdb=" N ASN A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.503A pdb=" N TRP A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.743A 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 480 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 503 through 516 Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.627A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 582 removed outlier: 3.689A 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: 3.831A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.738A 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: 3.512A pdb=" N ALA A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.824A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 759 removed outlier: 3.525A pdb=" N ASP A 759 " --> pdb=" O VAL A 755 " (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: 4.205A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.418A 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 861 removed outlier: 3.955A pdb=" N GLN A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 890 Processing helix chain 'A' and resid 895 through 904 removed outlier: 3.880A 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: 3.718A pdb=" N HIS A 928 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 3.761A 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: 3.656A pdb=" N LEU A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 977 " --> pdb=" O ASN A 973 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.781A 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 removed outlier: 3.698A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1071 removed outlier: 3.891A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A1071 " --> pdb=" O ILE A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1104 removed outlier: 3.714A pdb=" N LYS A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.912A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 204 removed outlier: 3.731A 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: 3.546A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.772A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.561A pdb=" N ARG B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 removed outlier: 4.272A pdb=" N VAL B 366 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 367' Processing helix chain 'B' and resid 370 through 386 removed outlier: 4.120A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.727A pdb=" N ASN B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.504A pdb=" N TRP B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.743A 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 480 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 503 through 516 Processing helix chain 'B' and resid 518 through 532 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.627A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 582 removed outlier: 3.689A 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: 3.830A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.739A 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: 3.512A pdb=" N ALA B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.825A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 705 Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 759 removed outlier: 3.525A pdb=" N ASP B 759 " --> pdb=" O VAL B 755 " (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: 4.206A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.418A 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 861 removed outlier: 3.955A pdb=" N GLN B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 890 Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.880A 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: 3.718A pdb=" N HIS B 928 " --> pdb=" O ASP B 925 " (cutoff:3.500A) removed outlier: 3.761A 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: 3.657A pdb=" N LEU B 975 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 977 " --> pdb=" O ASN B 973 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.781A 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 removed outlier: 3.698A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1071 removed outlier: 3.891A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA B1071 " --> pdb=" O ILE B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1104 removed outlier: 3.715A pdb=" N LYS B1104 " --> pdb=" O ALA B1100 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 136 removed outlier: 3.910A pdb=" N LEU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 204 removed outlier: 3.730A 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: 3.546A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 341 removed outlier: 3.772A pdb=" N VAL C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.562A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 removed outlier: 4.272A pdb=" N VAL C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 362 through 367' Processing helix chain 'C' and resid 370 through 386 removed outlier: 4.119A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 418 removed outlier: 3.726A pdb=" N ASN C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.503A pdb=" N TRP C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.743A 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 480 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 503 through 516 Processing helix chain 'C' and resid 518 through 532 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.627A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 582 removed outlier: 3.689A 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: 3.830A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.739A 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: 3.512A pdb=" N ALA C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.824A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 705 Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 759 removed outlier: 3.525A pdb=" N ASP C 759 " --> pdb=" O VAL C 755 " (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: 4.206A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.418A 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 861 removed outlier: 3.954A pdb=" N GLN C 861 " --> pdb=" O ILE C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 890 Processing helix chain 'C' and resid 895 through 904 removed outlier: 3.880A 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: 3.717A pdb=" N HIS C 928 " --> pdb=" O ASP C 925 " (cutoff:3.500A) removed outlier: 3.761A 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: 3.657A pdb=" N LEU C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 977 " --> pdb=" O ASN C 973 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 5.878A 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: 3.849A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.780A 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 removed outlier: 3.698A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1071 removed outlier: 3.891A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA C1071 " --> pdb=" O ILE C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1104 removed outlier: 3.715A pdb=" N LYS C1104 " --> pdb=" O ALA C1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 136 removed outlier: 3.912A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 204 removed outlier: 3.731A 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: 3.546A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 341 removed outlier: 3.772A pdb=" N VAL D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.562A pdb=" N ARG D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 367 removed outlier: 4.271A pdb=" N VAL D 366 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 362 through 367' Processing helix chain 'D' and resid 370 through 386 removed outlier: 4.119A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 418 removed outlier: 3.726A pdb=" N ASN D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 removed outlier: 3.502A pdb=" N TRP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.744A 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 480 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 503 through 516 Processing helix chain 'D' and resid 518 through 532 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.627A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 582 removed outlier: 3.689A 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: 3.830A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.738A 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: 3.512A pdb=" N ALA D 663 " --> pdb=" O LEU D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.825A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 705 Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 733 through 759 removed outlier: 3.525A pdb=" N ASP D 759 " --> pdb=" O VAL D 755 " (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: 4.206A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.418A 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 861 removed outlier: 3.954A pdb=" N GLN D 861 " --> pdb=" O ILE D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 890 Processing helix chain 'D' and resid 895 through 904 removed outlier: 3.882A 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: 3.717A pdb=" N HIS D 928 " --> pdb=" O ASP D 925 " (cutoff:3.500A) removed outlier: 3.760A 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: 3.656A pdb=" N LEU D 975 " --> pdb=" O LEU D 971 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 977 " --> pdb=" O ASN D 973 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 5.878A 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: 3.849A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.781A 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 removed outlier: 3.698A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1046 through 1071 removed outlier: 3.891A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA D1071 " --> pdb=" O ILE D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1104 removed outlier: 3.715A pdb=" N LYS D1104 " --> pdb=" O ALA D1100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 removed outlier: 5.964A pdb=" N ALA A 211 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU A 261 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY A 213 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A 263 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA A 215 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE A 179 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE A 214 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR A 181 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL A 328 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N CYS A 303 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 119 through 121 removed outlier: 5.964A pdb=" N ALA B 211 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU B 261 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY B 213 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL B 263 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA B 215 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE B 179 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE B 214 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR B 181 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL B 328 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS B 303 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 119 through 121 removed outlier: 5.964A pdb=" N ALA C 211 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU C 261 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY C 213 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL C 263 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA C 215 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE C 179 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE C 214 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR C 181 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL C 328 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS C 303 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 121 removed outlier: 5.964A pdb=" N ALA D 211 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU D 261 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLY D 213 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL D 263 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA D 215 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE D 179 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE D 214 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR D 181 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL D 328 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS D 303 " --> pdb=" O VAL D 328 " (cutoff:3.500A) 1756 hydrogen bonds defined for protein. 5232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.42 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4884 1.30 - 1.43: 8700 1.43 - 1.56: 17388 1.56 - 1.69: 4 1.69 - 1.82: 212 Bond restraints: 31188 Sorted by residual: bond pdb=" N21 KX7 B1202 " pdb=" O23 KX7 B1202 " ideal model delta sigma weight residual 1.208 1.397 -0.189 2.00e-02 2.50e+03 8.89e+01 bond pdb=" N21 KX7 A1202 " pdb=" O23 KX7 A1202 " ideal model delta sigma weight residual 1.208 1.397 -0.189 2.00e-02 2.50e+03 8.89e+01 bond pdb=" N21 KX7 C1202 " pdb=" O23 KX7 C1202 " ideal model delta sigma weight residual 1.208 1.396 -0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" N21 KX7 D1202 " pdb=" O23 KX7 D1202 " ideal model delta sigma weight residual 1.208 1.396 -0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" C05 KX7 D1202 " pdb=" N07 KX7 D1202 " ideal model delta sigma weight residual 1.355 1.489 -0.134 2.00e-02 2.50e+03 4.48e+01 ... (remaining 31183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 39810 2.08 - 4.15: 2008 4.15 - 6.23: 304 6.23 - 8.31: 110 8.31 - 10.39: 20 Bond angle restraints: 42252 Sorted by residual: angle pdb=" C ILE C1011 " pdb=" N PRO C1012 " pdb=" CA PRO C1012 " ideal model delta sigma weight residual 119.78 127.01 -7.23 1.03e+00 9.43e-01 4.93e+01 angle pdb=" C ILE D1011 " pdb=" N PRO D1012 " pdb=" CA PRO D1012 " ideal model delta sigma weight residual 119.78 126.99 -7.21 1.03e+00 9.43e-01 4.91e+01 angle pdb=" C ILE B1011 " pdb=" N PRO B1012 " pdb=" CA PRO B1012 " ideal model delta sigma weight residual 119.78 126.96 -7.18 1.03e+00 9.43e-01 4.85e+01 angle pdb=" C ILE A1011 " pdb=" N PRO A1012 " pdb=" CA PRO A1012 " ideal model delta sigma weight residual 119.78 126.95 -7.17 1.03e+00 9.43e-01 4.84e+01 angle pdb=" N LEU C 704 " pdb=" CA LEU C 704 " pdb=" C LEU C 704 " ideal model delta sigma weight residual 113.16 107.07 6.09 1.24e+00 6.50e-01 2.41e+01 ... (remaining 42247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 17135 15.01 - 30.03: 886 30.03 - 45.04: 239 45.04 - 60.05: 12 60.05 - 75.07: 32 Dihedral angle restraints: 18304 sinusoidal: 7392 harmonic: 10912 Sorted by residual: dihedral pdb=" CA PRO B 916 " pdb=" C PRO B 916 " pdb=" N SER B 917 " pdb=" CA SER B 917 " ideal model delta harmonic sigma weight residual -180.00 -150.43 -29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA PRO C 916 " pdb=" C PRO C 916 " pdb=" N SER C 917 " pdb=" CA SER C 917 " ideal model delta harmonic sigma weight residual -180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PRO A 916 " pdb=" C PRO A 916 " pdb=" N SER A 917 " pdb=" CA SER A 917 " ideal model delta harmonic sigma weight residual -180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2933 0.049 - 0.099: 1359 0.099 - 0.148: 308 0.148 - 0.197: 88 0.197 - 0.246: 20 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CA ILE B 324 " pdb=" N ILE B 324 " pdb=" C ILE B 324 " pdb=" CB ILE B 324 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE C 324 " pdb=" N ILE C 324 " pdb=" C ILE C 324 " pdb=" CB ILE C 324 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA ILE A 324 " pdb=" N ILE A 324 " pdb=" C ILE A 324 " pdb=" CB ILE A 324 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 4705 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 454 " -0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C GLU D 454 " 0.072 2.00e-02 2.50e+03 pdb=" O GLU D 454 " -0.027 2.00e-02 2.50e+03 pdb=" N SER D 455 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 454 " 0.020 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" C GLU B 454 " -0.072 2.00e-02 2.50e+03 pdb=" O GLU B 454 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 455 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 454 " 0.020 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" C GLU A 454 " -0.072 2.00e-02 2.50e+03 pdb=" O GLU A 454 " 0.027 2.00e-02 2.50e+03 pdb=" N SER A 455 " 0.024 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6407 2.77 - 3.31: 28243 3.31 - 3.84: 48688 3.84 - 4.37: 57425 4.37 - 4.90: 97837 Nonbonded interactions: 238600 Sorted by model distance: nonbonded pdb=" O VAL C 728 " pdb=" OG1 THR C 732 " model vdw 2.242 3.040 nonbonded pdb=" O VAL B 728 " pdb=" OG1 THR B 732 " model vdw 2.243 3.040 nonbonded pdb=" O VAL A 728 " pdb=" OG1 THR A 732 " model vdw 2.243 3.040 nonbonded pdb=" O VAL D 728 " pdb=" OG1 THR D 732 " model vdw 2.243 3.040 nonbonded pdb=" O VAL A1065 " pdb=" OG1 THR A1069 " model vdw 2.250 3.040 ... (remaining 238595 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 27.570 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.009 0.189 31192 Z= 0.395 Angle : 1.082 10.386 42260 Z= 0.601 Chirality : 0.059 0.246 4708 Planarity : 0.007 0.066 5280 Dihedral : 10.611 75.066 11212 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.80 % Favored : 93.98 % Rotamer: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.11), residues: 3656 helix: -2.03 (0.08), residues: 2396 sheet: -1.88 (0.33), residues: 200 loop : -2.92 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 829 TYR 0.040 0.004 TYR A 772 PHE 0.037 0.004 PHE B 832 TRP 0.028 0.004 TRP B 740 HIS 0.010 0.003 HIS A 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00914 / 0.40 (31188) covalent geometry : angle 1.07922 / 0.60 (42252) SS BOND : bond 0.01778 / 0.81 ( 4) SS BOND : angle 5.22624 / 2.92 ( 8) hydrogen bonds : bond 0.14339 / 9.50 ( 1756) hydrogen bonds : angle 6.37465 / 4.38 ( 5232) *********************** 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 774 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 770 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8642 (ttmm) cc_final: 0.7870 (ttmm) REVERT: A 277 LEU cc_start: 0.8180 (tp) cc_final: 0.7924 (tm) REVERT: A 510 GLN cc_start: 0.7819 (mt0) cc_final: 0.7517 (mt0) REVERT: A 758 MET cc_start: 0.8681 (mtp) cc_final: 0.8410 (mtm) REVERT: A 1026 LYS cc_start: 0.5441 (tmmt) cc_final: 0.5079 (mptm) REVERT: B 190 LYS cc_start: 0.8635 (ttmm) cc_final: 0.7867 (ttmm) REVERT: B 277 LEU cc_start: 0.8178 (tp) cc_final: 0.7929 (tm) REVERT: B 510 GLN cc_start: 0.7822 (mt0) cc_final: 0.7519 (mt0) REVERT: B 758 MET cc_start: 0.8682 (mtp) cc_final: 0.8417 (mtm) REVERT: B 1026 LYS cc_start: 0.5441 (tmmt) cc_final: 0.5079 (mptm) REVERT: C 190 LYS cc_start: 0.8635 (ttmm) cc_final: 0.7868 (ttmm) REVERT: C 277 LEU cc_start: 0.8180 (tp) cc_final: 0.7927 (tm) REVERT: C 337 ASP cc_start: 0.7104 (m-30) cc_final: 0.6892 (t0) REVERT: C 510 GLN cc_start: 0.7818 (mt0) cc_final: 0.7512 (mt0) REVERT: C 758 MET cc_start: 0.8685 (mtp) cc_final: 0.8417 (mtm) REVERT: C 1026 LYS cc_start: 0.5418 (tmmt) cc_final: 0.5059 (mptm) REVERT: D 190 LYS cc_start: 0.8642 (ttmm) cc_final: 0.7872 (ttmm) REVERT: D 277 LEU cc_start: 0.8185 (tp) cc_final: 0.7930 (tm) REVERT: D 337 ASP cc_start: 0.7116 (m-30) cc_final: 0.6897 (t0) REVERT: D 510 GLN cc_start: 0.7817 (mt0) cc_final: 0.7519 (mt0) REVERT: D 758 MET cc_start: 0.8682 (mtp) cc_final: 0.8410 (mtm) REVERT: D 1026 LYS cc_start: 0.5429 (tmmt) cc_final: 0.5070 (mptm) outliers start: 4 outliers final: 0 residues processed: 774 average time/residue: 0.6659 time to fit residues: 600.8855 Evaluate side-chains 379 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.0070 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS A 199 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN A 666 GLN A 671 GLN A 675 GLN A 861 GLN A 987 GLN B 136 HIS B 199 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN B 572 ASN B 666 GLN B 671 GLN B 675 GLN B 861 GLN B 987 GLN B1050 ASN C 136 HIS C 199 ASN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN C 572 ASN C 666 GLN C 671 GLN C 675 GLN C 861 GLN C 987 GLN D 136 HIS D 199 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN D 572 ASN D 666 GLN D 671 GLN D 675 GLN D 861 GLN D 987 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.172886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.126702 restraints weight = 47959.533| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.50 r_work: 0.3416 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31192 Z= 0.146 Angle : 0.643 8.139 42260 Z= 0.336 Chirality : 0.041 0.140 4708 Planarity : 0.005 0.046 5280 Dihedral : 5.920 55.986 4024 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.25 % Allowed : 13.25 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.13), residues: 3656 helix: -0.01 (0.10), residues: 2472 sheet: -1.59 (0.34), residues: 200 loop : -2.76 (0.16), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 167 TYR 0.018 0.002 TYR A 191 PHE 0.019 0.001 PHE A 165 TRP 0.017 0.002 TRP D 798 HIS 0.004 0.001 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (31188) covalent geometry : angle 0.64285 / 0.34 (42252) SS BOND : bond 0.00596 / 0.27 ( 4) SS BOND : angle 2.10152 / 1.17 ( 8) hydrogen bonds : bond 0.04953 / 3.37 ( 1756) hydrogen bonds : angle 4.34041 / 3.02 ( 5232) *********************** 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 585 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 477 time to evaluate : 1.135 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: A 189 MET cc_start: 0.7189 (mtm) cc_final: 0.6875 (mtm) REVERT: A 190 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8250 (ptmt) REVERT: A 217 TRP cc_start: 0.7842 (t-100) cc_final: 0.7499 (t-100) REVERT: A 402 GLU cc_start: 0.7739 (pp20) cc_final: 0.7487 (pp20) REVERT: A 451 ARG cc_start: 0.5771 (pmt-80) cc_final: 0.5469 (ppt170) REVERT: A 510 GLN cc_start: 0.7743 (mt0) cc_final: 0.7369 (mt0) REVERT: A 518 ASP cc_start: 0.7778 (t70) cc_final: 0.7528 (t70) REVERT: A 574 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8072 (tppt) REVERT: A 665 ASP cc_start: 0.8208 (t0) cc_final: 0.7961 (t0) REVERT: A 758 MET cc_start: 0.9032 (mtp) cc_final: 0.8745 (mtm) REVERT: A 989 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7465 (t0) REVERT: B 123 ASP cc_start: 0.6782 (m-30) cc_final: 0.5960 (p0) REVERT: B 189 MET cc_start: 0.7190 (mtm) cc_final: 0.6878 (mtm) REVERT: B 190 LYS cc_start: 0.8621 (ttmm) cc_final: 0.8248 (ptmt) REVERT: B 217 TRP cc_start: 0.7839 (t-100) cc_final: 0.7498 (t-100) REVERT: B 364 ARG cc_start: 0.7229 (tpm170) cc_final: 0.7022 (mmm-85) REVERT: B 402 GLU cc_start: 0.7741 (pp20) cc_final: 0.7490 (pp20) REVERT: B 451 ARG cc_start: 0.5760 (pmt-80) cc_final: 0.5436 (ppt170) REVERT: B 510 GLN cc_start: 0.7766 (mt0) cc_final: 0.7392 (mt0) REVERT: B 518 ASP cc_start: 0.7746 (t70) cc_final: 0.7525 (t70) REVERT: B 574 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8130 (tppt) REVERT: B 665 ASP cc_start: 0.8212 (t0) cc_final: 0.7959 (t0) REVERT: B 758 MET cc_start: 0.9026 (mtp) cc_final: 0.8740 (mtm) REVERT: B 989 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7469 (t0) REVERT: C 189 MET cc_start: 0.7177 (mtm) cc_final: 0.6862 (mtm) REVERT: C 190 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8250 (ptmt) REVERT: C 217 TRP cc_start: 0.7835 (t-100) cc_final: 0.7492 (t-100) REVERT: C 364 ARG cc_start: 0.7225 (tpm170) cc_final: 0.7023 (mmm-85) REVERT: C 402 GLU cc_start: 0.7723 (pp20) cc_final: 0.7489 (pp20) REVERT: C 451 ARG cc_start: 0.5766 (pmt-80) cc_final: 0.5451 (ppt170) REVERT: C 510 GLN cc_start: 0.7773 (mt0) cc_final: 0.7401 (mt0) REVERT: C 574 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8129 (tppt) REVERT: C 665 ASP cc_start: 0.8210 (t0) cc_final: 0.7985 (t0) REVERT: C 758 MET cc_start: 0.9037 (mtp) cc_final: 0.8821 (mtm) REVERT: C 989 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7485 (t0) REVERT: D 189 MET cc_start: 0.7171 (mtm) cc_final: 0.6857 (mtm) REVERT: D 190 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8247 (ptmt) REVERT: D 217 TRP cc_start: 0.7840 (t-100) cc_final: 0.7490 (t-100) REVERT: D 402 GLU cc_start: 0.7729 (pp20) cc_final: 0.7494 (pp20) REVERT: D 451 ARG cc_start: 0.5765 (pmt-80) cc_final: 0.5454 (ppt170) REVERT: D 510 GLN cc_start: 0.7770 (mt0) cc_final: 0.7414 (mt0) REVERT: D 518 ASP cc_start: 0.7790 (t70) cc_final: 0.7545 (t70) REVERT: D 574 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8123 (tppt) REVERT: D 665 ASP cc_start: 0.8200 (t0) cc_final: 0.7949 (t0) REVERT: D 758 MET cc_start: 0.9038 (mtp) cc_final: 0.8821 (mtm) REVERT: D 847 PHE cc_start: 0.7715 (m-10) cc_final: 0.7482 (m-10) REVERT: D 989 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7487 (t0) outliers start: 108 outliers final: 25 residues processed: 559 average time/residue: 0.6317 time to fit residues: 413.9759 Evaluate side-chains 416 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 383 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 574 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 64 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 278 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 23 optimal weight: 0.0030 chunk 244 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 666 GLN A 676 ASN A 741 ASN B 259 HIS ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN B 676 ASN B 741 ASN C 259 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN C 676 ASN C 741 ASN D 259 HIS ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN D 676 ASN D 741 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.169761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124762 restraints weight = 47431.679| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.24 r_work: 0.3393 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31192 Z= 0.163 Angle : 0.640 7.891 42260 Z= 0.329 Chirality : 0.041 0.130 4708 Planarity : 0.004 0.040 5280 Dihedral : 5.604 54.817 4024 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.46 % Allowed : 14.51 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3656 helix: 0.76 (0.10), residues: 2452 sheet: -1.57 (0.35), residues: 200 loop : -2.48 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1079 TYR 0.015 0.002 TYR A 186 PHE 0.022 0.002 PHE D 752 TRP 0.020 0.002 TRP B 786 HIS 0.005 0.001 HIS D 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (31188) covalent geometry : angle 0.63839 / 0.33 (42252) SS BOND : bond 0.00201 / 0.09 ( 4) SS BOND : angle 2.86133 / 1.60 ( 8) hydrogen bonds : bond 0.05014 / 3.44 ( 1756) hydrogen bonds : angle 4.10545 / 2.86 ( 5232) *********************** 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 532 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 417 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.6910 (m-30) cc_final: 0.5998 (p0) REVERT: A 163 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8404 (ptmt) REVERT: A 189 MET cc_start: 0.7262 (mtm) cc_final: 0.6794 (mtm) REVERT: A 190 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8464 (ptmt) REVERT: A 294 ASN cc_start: 0.7951 (p0) cc_final: 0.7609 (p0) REVERT: A 353 MET cc_start: 0.5426 (mpp) cc_final: 0.5145 (pmm) REVERT: A 396 MET cc_start: 0.6638 (mpm) cc_final: 0.6418 (mpp) REVERT: A 402 GLU cc_start: 0.7932 (pp20) cc_final: 0.7644 (pp20) REVERT: A 689 ASP cc_start: 0.7801 (p0) cc_final: 0.7436 (p0) REVERT: A 732 THR cc_start: 0.8135 (m) cc_final: 0.7918 (p) REVERT: A 758 MET cc_start: 0.9187 (mtp) cc_final: 0.8935 (mtm) REVERT: A 797 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6276 (mt) REVERT: A 802 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: A 804 LEU cc_start: 0.8805 (tp) cc_final: 0.8543 (mt) REVERT: A 897 ARG cc_start: 0.8739 (mtt180) cc_final: 0.7634 (mmt180) REVERT: A 988 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6578 (pm20) REVERT: A 989 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.7238 (t0) REVERT: A 1023 MET cc_start: 0.6191 (mmp) cc_final: 0.4374 (ttm) REVERT: A 1047 ASN cc_start: 0.6765 (m-40) cc_final: 0.6322 (t0) REVERT: B 123 ASP cc_start: 0.6906 (m-30) cc_final: 0.6004 (p0) REVERT: B 163 LYS cc_start: 0.8736 (ttpt) cc_final: 0.8404 (ptmt) REVERT: B 189 MET cc_start: 0.7265 (mtm) cc_final: 0.6792 (mtm) REVERT: B 190 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8468 (ptmt) REVERT: B 294 ASN cc_start: 0.7950 (p0) cc_final: 0.7605 (p0) REVERT: B 353 MET cc_start: 0.5418 (mpp) cc_final: 0.5141 (pmm) REVERT: B 396 MET cc_start: 0.6607 (mpm) cc_final: 0.6386 (mpp) REVERT: B 402 GLU cc_start: 0.7937 (pp20) cc_final: 0.7651 (pp20) REVERT: B 689 ASP cc_start: 0.7777 (p0) cc_final: 0.7412 (p0) REVERT: B 732 THR cc_start: 0.8126 (m) cc_final: 0.7910 (p) REVERT: B 758 MET cc_start: 0.9186 (mtp) cc_final: 0.8932 (mtm) REVERT: B 797 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6272 (mt) REVERT: B 802 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7300 (m-30) REVERT: B 804 LEU cc_start: 0.8802 (tp) cc_final: 0.8542 (mt) REVERT: B 897 ARG cc_start: 0.8737 (mtt180) cc_final: 0.7629 (mmt180) REVERT: B 988 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6589 (pm20) REVERT: B 989 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.7238 (t0) REVERT: B 1023 MET cc_start: 0.6196 (mmp) cc_final: 0.4367 (ttm) REVERT: B 1047 ASN cc_start: 0.6917 (m-40) cc_final: 0.6493 (t0) REVERT: C 123 ASP cc_start: 0.6900 (m-30) cc_final: 0.6000 (p0) REVERT: C 163 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8388 (ptmt) REVERT: C 189 MET cc_start: 0.7273 (mtm) cc_final: 0.6798 (mtm) REVERT: C 190 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8465 (ptmt) REVERT: C 294 ASN cc_start: 0.7937 (p0) cc_final: 0.7558 (p0) REVERT: C 353 MET cc_start: 0.5412 (mpp) cc_final: 0.5137 (pmm) REVERT: C 396 MET cc_start: 0.6600 (mpm) cc_final: 0.6386 (mpp) REVERT: C 402 GLU cc_start: 0.7930 (pp20) cc_final: 0.7640 (pp20) REVERT: C 689 ASP cc_start: 0.7661 (p0) cc_final: 0.7285 (p0) REVERT: C 726 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7509 (m-10) REVERT: C 758 MET cc_start: 0.9183 (mtp) cc_final: 0.8929 (mtm) REVERT: C 797 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6264 (mt) REVERT: C 804 LEU cc_start: 0.8782 (tp) cc_final: 0.8556 (mt) REVERT: C 897 ARG cc_start: 0.8751 (mtt180) cc_final: 0.7633 (mmt180) REVERT: C 1023 MET cc_start: 0.6193 (mmp) cc_final: 0.4372 (ttm) REVERT: C 1047 ASN cc_start: 0.6859 (m-40) cc_final: 0.6466 (t0) REVERT: D 123 ASP cc_start: 0.6901 (m-30) cc_final: 0.5991 (p0) REVERT: D 163 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8388 (ptmt) REVERT: D 189 MET cc_start: 0.7262 (mtm) cc_final: 0.6786 (mtm) REVERT: D 190 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8421 (ptmt) REVERT: D 294 ASN cc_start: 0.7945 (p0) cc_final: 0.7587 (p0) REVERT: D 353 MET cc_start: 0.5411 (mpp) cc_final: 0.5137 (pmm) REVERT: D 402 GLU cc_start: 0.7932 (pp20) cc_final: 0.7640 (pp20) REVERT: D 689 ASP cc_start: 0.7743 (p0) cc_final: 0.7384 (p0) REVERT: D 726 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7507 (m-10) REVERT: D 732 THR cc_start: 0.8143 (m) cc_final: 0.7926 (p) REVERT: D 758 MET cc_start: 0.9191 (mtp) cc_final: 0.8940 (mtm) REVERT: D 797 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6268 (mt) REVERT: D 802 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: D 804 LEU cc_start: 0.8798 (tp) cc_final: 0.8545 (mt) REVERT: D 897 ARG cc_start: 0.8751 (mtt180) cc_final: 0.7635 (mmt180) REVERT: D 1023 MET cc_start: 0.6187 (mmp) cc_final: 0.4368 (ttm) REVERT: D 1047 ASN cc_start: 0.6769 (m-40) cc_final: 0.6339 (t0) outliers start: 115 outliers final: 45 residues processed: 502 average time/residue: 0.5904 time to fit residues: 349.7620 Evaluate side-chains 408 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 350 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 574 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 726 TYR Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 726 TYR Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 942 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 13 optimal weight: 20.0000 chunk 371 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 333 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 297 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN A 671 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN B 671 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN C 671 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN D 671 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.167212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121444 restraints weight = 47301.704| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.38 r_work: 0.3348 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31192 Z= 0.213 Angle : 0.684 8.067 42260 Z= 0.352 Chirality : 0.044 0.136 4708 Planarity : 0.004 0.040 5280 Dihedral : 5.669 55.338 4024 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.24 % Allowed : 15.26 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3656 helix: 0.80 (0.10), residues: 2468 sheet: -1.78 (0.35), residues: 188 loop : -2.30 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 310 TYR 0.033 0.002 TYR B 191 PHE 0.025 0.002 PHE C1013 TRP 0.023 0.002 TRP A 786 HIS 0.008 0.001 HIS C 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (31188) covalent geometry : angle 0.68325 / 0.35 (42252) SS BOND : bond 0.00558 / 0.26 ( 4) SS BOND : angle 2.82502 / 1.58 ( 8) hydrogen bonds : bond 0.05468 / 3.78 ( 1756) hydrogen bonds : angle 4.14737 / 2.89 ( 5232) *********************** 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 510 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 369 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8384 (ptmt) REVERT: A 294 ASN cc_start: 0.8080 (p0) cc_final: 0.7742 (p0) REVERT: A 353 MET cc_start: 0.5913 (mpp) cc_final: 0.5594 (pmm) REVERT: A 364 ARG cc_start: 0.7350 (tpm170) cc_final: 0.6967 (ttm110) REVERT: A 402 GLU cc_start: 0.7976 (pp20) cc_final: 0.7571 (pp20) REVERT: A 507 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7351 (tpm170) REVERT: A 566 ILE cc_start: 0.8993 (mt) cc_final: 0.8791 (mp) REVERT: A 627 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8616 (mt-10) REVERT: A 689 ASP cc_start: 0.7966 (p0) cc_final: 0.7573 (p0) REVERT: A 726 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7411 (m-10) REVERT: A 732 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7953 (p) REVERT: A 758 MET cc_start: 0.9181 (mtp) cc_final: 0.8918 (mtm) REVERT: A 794 PHE cc_start: 0.8128 (m-10) cc_final: 0.7921 (m-10) REVERT: A 802 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: A 804 LEU cc_start: 0.8878 (tp) cc_final: 0.8667 (mt) REVERT: A 897 ARG cc_start: 0.8780 (mtt180) cc_final: 0.7734 (mmt180) REVERT: A 988 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6256 (pm20) REVERT: A 989 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7368 (t0) REVERT: A 1047 ASN cc_start: 0.6841 (m-40) cc_final: 0.6380 (t0) REVERT: B 163 LYS cc_start: 0.8755 (ttpt) cc_final: 0.8384 (ptmt) REVERT: B 294 ASN cc_start: 0.8083 (p0) cc_final: 0.7744 (p0) REVERT: B 353 MET cc_start: 0.5933 (mpp) cc_final: 0.5614 (pmm) REVERT: B 364 ARG cc_start: 0.7348 (tpm170) cc_final: 0.7077 (mmm-85) REVERT: B 402 GLU cc_start: 0.7966 (pp20) cc_final: 0.7561 (pp20) REVERT: B 507 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7349 (tpm170) REVERT: B 574 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8351 (tppt) REVERT: B 616 GLU cc_start: 0.8258 (tp30) cc_final: 0.8048 (tt0) REVERT: B 627 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: B 689 ASP cc_start: 0.7951 (p0) cc_final: 0.7560 (p0) REVERT: B 726 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7414 (m-10) REVERT: B 732 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7959 (p) REVERT: B 758 MET cc_start: 0.9188 (mtp) cc_final: 0.8925 (mtm) REVERT: B 794 PHE cc_start: 0.8121 (m-10) cc_final: 0.7910 (m-10) REVERT: B 802 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: B 804 LEU cc_start: 0.8881 (tp) cc_final: 0.8669 (mt) REVERT: B 897 ARG cc_start: 0.8770 (mtt180) cc_final: 0.7718 (mmt180) REVERT: B 988 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6256 (pm20) REVERT: B 989 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7369 (t0) REVERT: B 1047 ASN cc_start: 0.6845 (m-40) cc_final: 0.6406 (t0) REVERT: C 163 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8369 (ptmt) REVERT: C 294 ASN cc_start: 0.8004 (p0) cc_final: 0.7645 (p0) REVERT: C 353 MET cc_start: 0.5939 (mpp) cc_final: 0.5616 (pmm) REVERT: C 364 ARG cc_start: 0.7358 (tpm170) cc_final: 0.7072 (mmm-85) REVERT: C 402 GLU cc_start: 0.7980 (pp20) cc_final: 0.7578 (pp20) REVERT: C 507 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7344 (tpm170) REVERT: C 574 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8347 (tppt) REVERT: C 616 GLU cc_start: 0.8245 (tp30) cc_final: 0.8043 (tt0) REVERT: C 627 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8549 (mt-10) REVERT: C 689 ASP cc_start: 0.7955 (p0) cc_final: 0.7559 (p0) REVERT: C 726 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7451 (m-10) REVERT: C 732 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7958 (p) REVERT: C 758 MET cc_start: 0.9161 (mtp) cc_final: 0.8903 (mtm) REVERT: C 804 LEU cc_start: 0.8843 (tp) cc_final: 0.8632 (mt) REVERT: C 988 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6349 (pm20) REVERT: C 1047 ASN cc_start: 0.6816 (m-40) cc_final: 0.6400 (t0) REVERT: D 163 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8372 (ptmt) REVERT: D 294 ASN cc_start: 0.7991 (p0) cc_final: 0.7637 (p0) REVERT: D 353 MET cc_start: 0.5922 (mpp) cc_final: 0.5603 (pmm) REVERT: D 364 ARG cc_start: 0.7395 (tpm170) cc_final: 0.7006 (ttm110) REVERT: D 402 GLU cc_start: 0.7993 (pp20) cc_final: 0.7591 (pp20) REVERT: D 507 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7343 (tpm170) REVERT: D 574 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8354 (tppt) REVERT: D 616 GLU cc_start: 0.8250 (tp30) cc_final: 0.8042 (tt0) REVERT: D 627 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8599 (mt-10) REVERT: D 689 ASP cc_start: 0.8014 (p0) cc_final: 0.7621 (p0) REVERT: D 726 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7444 (m-10) REVERT: D 732 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7965 (p) REVERT: D 758 MET cc_start: 0.9177 (mtp) cc_final: 0.8911 (mtm) REVERT: D 794 PHE cc_start: 0.8116 (m-10) cc_final: 0.7909 (m-10) REVERT: D 802 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: D 804 LEU cc_start: 0.8875 (tp) cc_final: 0.8661 (mt) REVERT: D 897 ARG cc_start: 0.8774 (mtt180) cc_final: 0.7724 (mmt180) REVERT: D 988 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6343 (pm20) REVERT: D 1047 ASN cc_start: 0.6838 (m-40) cc_final: 0.6374 (t0) outliers start: 141 outliers final: 59 residues processed: 467 average time/residue: 0.5544 time to fit residues: 307.6323 Evaluate side-chains 419 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 332 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 574 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 726 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 726 TYR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 988 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 134 optimal weight: 0.9980 chunk 349 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 348 optimal weight: 0.9980 chunk 340 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 336 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.169038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.122634 restraints weight = 47159.446| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.29 r_work: 0.3350 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31192 Z= 0.141 Angle : 0.622 7.932 42260 Z= 0.316 Chirality : 0.041 0.133 4708 Planarity : 0.004 0.038 5280 Dihedral : 5.310 49.947 4024 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.88 % Allowed : 16.71 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3656 helix: 1.07 (0.10), residues: 2472 sheet: -1.55 (0.36), residues: 188 loop : -2.23 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 167 TYR 0.017 0.002 TYR D 191 PHE 0.016 0.001 PHE A 165 TRP 0.024 0.002 TRP C 786 HIS 0.004 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (31188) covalent geometry : angle 0.62208 / 0.32 (42252) SS BOND : bond 0.00437 / 0.20 ( 4) SS BOND : angle 1.76153 / 0.98 ( 8) hydrogen bonds : bond 0.04495 / 3.09 ( 1756) hydrogen bonds : angle 3.95019 / 2.76 ( 5232) *********************** 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 493 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 364 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7272 (m-30) cc_final: 0.6104 (p0) REVERT: A 163 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8397 (ptmt) REVERT: A 294 ASN cc_start: 0.8049 (p0) cc_final: 0.7685 (p0) REVERT: A 353 MET cc_start: 0.6136 (mpp) cc_final: 0.5817 (pmm) REVERT: A 364 ARG cc_start: 0.7439 (tpm170) cc_final: 0.6994 (ttm170) REVERT: A 402 GLU cc_start: 0.7736 (pp20) cc_final: 0.7524 (pp20) REVERT: A 457 ASP cc_start: 0.7402 (p0) cc_final: 0.7072 (OUTLIER) REVERT: A 459 GLN cc_start: 0.6652 (mp10) cc_final: 0.6198 (mm-40) REVERT: A 566 ILE cc_start: 0.8938 (mt) cc_final: 0.8696 (mp) REVERT: A 627 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8591 (mt-10) REVERT: A 689 ASP cc_start: 0.7927 (p0) cc_final: 0.7528 (p0) REVERT: A 732 THR cc_start: 0.8255 (m) cc_final: 0.7953 (p) REVERT: A 758 MET cc_start: 0.9206 (mtp) cc_final: 0.8962 (mtm) REVERT: A 794 PHE cc_start: 0.8029 (m-10) cc_final: 0.7802 (m-10) REVERT: A 797 LEU cc_start: 0.7040 (pt) cc_final: 0.6396 (mt) REVERT: A 802 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7342 (m-30) REVERT: A 804 LEU cc_start: 0.8786 (tp) cc_final: 0.8558 (mt) REVERT: A 863 MET cc_start: 0.8683 (mmt) cc_final: 0.8361 (mmt) REVERT: A 897 ARG cc_start: 0.8634 (mtt180) cc_final: 0.7509 (mmt180) REVERT: A 988 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6268 (pm20) REVERT: A 989 ASN cc_start: 0.7595 (OUTLIER) cc_final: 0.7375 (t0) REVERT: A 1023 MET cc_start: 0.6235 (mmp) cc_final: 0.4324 (ttm) REVERT: A 1046 ARG cc_start: 0.7913 (ttm170) cc_final: 0.7167 (mtp85) REVERT: A 1051 GLU cc_start: 0.8148 (tp30) cc_final: 0.7869 (tp30) REVERT: B 163 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8389 (ptmt) REVERT: B 294 ASN cc_start: 0.8029 (p0) cc_final: 0.7666 (p0) REVERT: B 353 MET cc_start: 0.6137 (mpp) cc_final: 0.5819 (pmm) REVERT: B 364 ARG cc_start: 0.7379 (tpm170) cc_final: 0.6892 (ttm110) REVERT: B 402 GLU cc_start: 0.7732 (pp20) cc_final: 0.7518 (pp20) REVERT: B 457 ASP cc_start: 0.7438 (p0) cc_final: 0.7049 (p0) REVERT: B 459 GLN cc_start: 0.6972 (mp10) cc_final: 0.6621 (mm-40) REVERT: B 574 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8285 (tppt) REVERT: B 627 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8549 (mt-10) REVERT: B 689 ASP cc_start: 0.7877 (p0) cc_final: 0.7500 (p0) REVERT: B 732 THR cc_start: 0.8249 (m) cc_final: 0.7946 (p) REVERT: B 758 MET cc_start: 0.9204 (mtp) cc_final: 0.8962 (mtm) REVERT: B 794 PHE cc_start: 0.8017 (m-10) cc_final: 0.7789 (m-10) REVERT: B 797 LEU cc_start: 0.7046 (pt) cc_final: 0.6401 (mt) REVERT: B 802 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: B 804 LEU cc_start: 0.8778 (tp) cc_final: 0.8547 (mt) REVERT: B 863 MET cc_start: 0.8674 (mmt) cc_final: 0.8354 (mmt) REVERT: B 897 ARG cc_start: 0.8620 (mtt180) cc_final: 0.7494 (mmt180) REVERT: B 988 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6293 (pm20) REVERT: B 989 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7387 (t0) REVERT: B 1023 MET cc_start: 0.6240 (mmp) cc_final: 0.4340 (ttm) REVERT: B 1046 ARG cc_start: 0.7935 (ttm170) cc_final: 0.7174 (mtp85) REVERT: B 1047 ASN cc_start: 0.6707 (m-40) cc_final: 0.6504 (t0) REVERT: C 163 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8397 (ptmt) REVERT: C 294 ASN cc_start: 0.8003 (p0) cc_final: 0.7643 (p0) REVERT: C 353 MET cc_start: 0.6129 (mpp) cc_final: 0.5812 (pmm) REVERT: C 364 ARG cc_start: 0.7410 (tpm170) cc_final: 0.6901 (ttm110) REVERT: C 402 GLU cc_start: 0.7693 (pp20) cc_final: 0.7477 (pp20) REVERT: C 457 ASP cc_start: 0.7340 (p0) cc_final: 0.7001 (OUTLIER) REVERT: C 459 GLN cc_start: 0.6640 (mp10) cc_final: 0.6185 (mm-40) REVERT: C 574 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8256 (tppt) REVERT: C 627 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8550 (mt-10) REVERT: C 689 ASP cc_start: 0.7900 (p0) cc_final: 0.7504 (p0) REVERT: C 732 THR cc_start: 0.8254 (m) cc_final: 0.7950 (p) REVERT: C 758 MET cc_start: 0.9198 (mtp) cc_final: 0.8957 (mtm) REVERT: C 797 LEU cc_start: 0.7329 (pt) cc_final: 0.6677 (mt) REVERT: C 863 MET cc_start: 0.8713 (mmt) cc_final: 0.8384 (mmt) REVERT: C 897 ARG cc_start: 0.8630 (mtt180) cc_final: 0.7505 (mmt180) REVERT: C 988 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6451 (pm20) REVERT: C 1023 MET cc_start: 0.6250 (mmp) cc_final: 0.4326 (ttm) REVERT: C 1046 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7165 (mtp85) REVERT: C 1047 ASN cc_start: 0.6713 (m-40) cc_final: 0.6509 (t0) REVERT: D 163 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8393 (ptmt) REVERT: D 294 ASN cc_start: 0.7996 (p0) cc_final: 0.7638 (p0) REVERT: D 353 MET cc_start: 0.6137 (mpp) cc_final: 0.5819 (pmm) REVERT: D 364 ARG cc_start: 0.7456 (tpm170) cc_final: 0.6970 (ttm170) REVERT: D 396 MET cc_start: 0.6643 (mpm) cc_final: 0.6428 (mpp) REVERT: D 402 GLU cc_start: 0.7740 (pp20) cc_final: 0.7529 (pp20) REVERT: D 457 ASP cc_start: 0.7436 (p0) cc_final: 0.7061 (p0) REVERT: D 459 GLN cc_start: 0.6994 (mp10) cc_final: 0.6634 (mm-40) REVERT: D 574 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8255 (tppt) REVERT: D 627 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8581 (mt-10) REVERT: D 689 ASP cc_start: 0.7922 (p0) cc_final: 0.7526 (p0) REVERT: D 732 THR cc_start: 0.8249 (m) cc_final: 0.7947 (p) REVERT: D 758 MET cc_start: 0.9212 (mtp) cc_final: 0.8970 (mtm) REVERT: D 794 PHE cc_start: 0.8021 (m-10) cc_final: 0.7797 (m-10) REVERT: D 797 LEU cc_start: 0.7042 (pt) cc_final: 0.6364 (mt) REVERT: D 798 TRP cc_start: 0.7675 (m100) cc_final: 0.7452 (m100) REVERT: D 802 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: D 804 LEU cc_start: 0.8772 (tp) cc_final: 0.8541 (mt) REVERT: D 863 MET cc_start: 0.8704 (mmt) cc_final: 0.8371 (mmt) REVERT: D 897 ARG cc_start: 0.8627 (mtt180) cc_final: 0.7502 (mmt180) REVERT: D 988 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: D 1023 MET cc_start: 0.6222 (mmp) cc_final: 0.4321 (ttm) REVERT: D 1046 ARG cc_start: 0.7904 (ttm170) cc_final: 0.7139 (mtp85) REVERT: D 1051 GLU cc_start: 0.8179 (tp30) cc_final: 0.7907 (tp30) outliers start: 129 outliers final: 58 residues processed: 466 average time/residue: 0.5713 time to fit residues: 317.8651 Evaluate side-chains 389 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 317 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 574 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 988 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 323 optimal weight: 0.9980 chunk 344 optimal weight: 6.9990 chunk 182 optimal weight: 0.1980 chunk 117 optimal weight: 5.9990 chunk 303 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 187 optimal weight: 0.1980 chunk 214 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN A 818 HIS ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN B 818 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN C 818 HIS ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN D 818 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.170961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125313 restraints weight = 47023.927| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.22 r_work: 0.3387 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31192 Z= 0.127 Angle : 0.606 10.250 42260 Z= 0.307 Chirality : 0.040 0.134 4708 Planarity : 0.003 0.039 5280 Dihedral : 5.171 52.337 4024 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.88 % Allowed : 18.00 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3656 helix: 1.31 (0.11), residues: 2464 sheet: -1.41 (0.38), residues: 188 loop : -2.11 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 167 TYR 0.035 0.001 TYR D 191 PHE 0.014 0.001 PHE B 165 TRP 0.027 0.001 TRP B 786 HIS 0.004 0.001 HIS D 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (31188) covalent geometry : angle 0.60513 / 0.31 (42252) SS BOND : bond 0.00466 / 0.21 ( 4) SS BOND : angle 2.52788 / 1.41 ( 8) hydrogen bonds : bond 0.04134 / 2.84 ( 1756) hydrogen bonds : angle 3.87259 / 2.70 ( 5232) *********************** 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 484 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 355 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8414 (ptmt) REVERT: A 294 ASN cc_start: 0.8031 (p0) cc_final: 0.7686 (p0) REVERT: A 353 MET cc_start: 0.6249 (mpp) cc_final: 0.5933 (pmm) REVERT: A 402 GLU cc_start: 0.7722 (pp20) cc_final: 0.7484 (pp20) REVERT: A 457 ASP cc_start: 0.7229 (p0) cc_final: 0.6887 (p0) REVERT: A 459 GLN cc_start: 0.6758 (mp10) cc_final: 0.6371 (mm-40) REVERT: A 480 ASN cc_start: 0.7880 (m-40) cc_final: 0.7385 (m-40) REVERT: A 566 ILE cc_start: 0.8951 (mt) cc_final: 0.8701 (mp) REVERT: A 627 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8521 (mt-10) REVERT: A 666 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: A 689 ASP cc_start: 0.7825 (p0) cc_final: 0.7480 (p0) REVERT: A 726 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7541 (m-10) REVERT: A 758 MET cc_start: 0.9186 (mtp) cc_final: 0.8966 (mtm) REVERT: A 794 PHE cc_start: 0.7998 (m-10) cc_final: 0.7709 (m-10) REVERT: A 797 LEU cc_start: 0.7256 (pt) cc_final: 0.6584 (mt) REVERT: A 802 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7249 (m-30) REVERT: A 804 LEU cc_start: 0.8778 (tp) cc_final: 0.8523 (mt) REVERT: A 863 MET cc_start: 0.8635 (mmt) cc_final: 0.8323 (mmt) REVERT: A 897 ARG cc_start: 0.8623 (mtt180) cc_final: 0.7515 (mmt180) REVERT: A 985 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7329 (mp) REVERT: A 988 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6172 (pm20) REVERT: A 1023 MET cc_start: 0.6286 (mmp) cc_final: 0.4306 (ttm) REVERT: A 1048 GLU cc_start: 0.7167 (pm20) cc_final: 0.6858 (mp0) REVERT: B 163 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8412 (ptmt) REVERT: B 294 ASN cc_start: 0.8039 (p0) cc_final: 0.7691 (p0) REVERT: B 353 MET cc_start: 0.6260 (mpp) cc_final: 0.5942 (pmm) REVERT: B 364 ARG cc_start: 0.7364 (tpm170) cc_final: 0.6894 (ttm110) REVERT: B 402 GLU cc_start: 0.7715 (pp20) cc_final: 0.7475 (pp20) REVERT: B 627 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: B 666 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: B 689 ASP cc_start: 0.7805 (p0) cc_final: 0.7462 (p0) REVERT: B 726 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7526 (m-10) REVERT: B 758 MET cc_start: 0.9203 (mtp) cc_final: 0.8986 (mtm) REVERT: B 794 PHE cc_start: 0.8012 (m-10) cc_final: 0.7762 (m-10) REVERT: B 797 LEU cc_start: 0.7266 (pt) cc_final: 0.6589 (mt) REVERT: B 802 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7253 (m-30) REVERT: B 804 LEU cc_start: 0.8778 (tp) cc_final: 0.8523 (mt) REVERT: B 863 MET cc_start: 0.8625 (mmt) cc_final: 0.8310 (mmt) REVERT: B 897 ARG cc_start: 0.8629 (mtt180) cc_final: 0.7519 (mmt180) REVERT: B 985 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7330 (mp) REVERT: B 988 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6173 (pm20) REVERT: B 1023 MET cc_start: 0.6289 (mmp) cc_final: 0.4289 (ttm) REVERT: B 1046 ARG cc_start: 0.7419 (ttm170) cc_final: 0.7184 (mtp85) REVERT: B 1047 ASN cc_start: 0.6545 (m-40) cc_final: 0.5771 (t0) REVERT: B 1048 GLU cc_start: 0.7115 (pm20) cc_final: 0.6631 (mp0) REVERT: C 163 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8377 (ptmt) REVERT: C 294 ASN cc_start: 0.8003 (p0) cc_final: 0.7685 (p0) REVERT: C 353 MET cc_start: 0.6221 (mpp) cc_final: 0.5912 (pmm) REVERT: C 364 ARG cc_start: 0.7297 (tpm170) cc_final: 0.6861 (ttm170) REVERT: C 402 GLU cc_start: 0.7696 (pp20) cc_final: 0.7476 (pp20) REVERT: C 457 ASP cc_start: 0.7234 (p0) cc_final: 0.6893 (p0) REVERT: C 459 GLN cc_start: 0.6753 (mp10) cc_final: 0.6348 (mm-40) REVERT: C 574 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8335 (tppt) REVERT: C 627 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8460 (mt-10) REVERT: C 666 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8505 (mt0) REVERT: C 689 ASP cc_start: 0.7814 (p0) cc_final: 0.7475 (p0) REVERT: C 726 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7530 (m-10) REVERT: C 732 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7813 (p) REVERT: C 758 MET cc_start: 0.9188 (mtp) cc_final: 0.8976 (mtm) REVERT: C 797 LEU cc_start: 0.7387 (pt) cc_final: 0.6748 (mt) REVERT: C 863 MET cc_start: 0.8643 (mmt) cc_final: 0.8301 (mmt) REVERT: C 897 ARG cc_start: 0.8640 (mtt180) cc_final: 0.7523 (mmt180) REVERT: C 985 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7320 (mp) REVERT: C 988 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6336 (pm20) REVERT: C 1023 MET cc_start: 0.6286 (mmp) cc_final: 0.4292 (ttm) REVERT: C 1046 ARG cc_start: 0.7452 (ttm170) cc_final: 0.7202 (mtp85) REVERT: C 1047 ASN cc_start: 0.6554 (m-40) cc_final: 0.5787 (t0) REVERT: C 1048 GLU cc_start: 0.7217 (pm20) cc_final: 0.6765 (mp0) REVERT: D 163 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8412 (ptmt) REVERT: D 294 ASN cc_start: 0.7930 (p0) cc_final: 0.7547 (p0) REVERT: D 353 MET cc_start: 0.6240 (mpp) cc_final: 0.5927 (pmm) REVERT: D 396 MET cc_start: 0.6624 (mpm) cc_final: 0.6390 (mpp) REVERT: D 402 GLU cc_start: 0.7721 (pp20) cc_final: 0.7484 (pp20) REVERT: D 627 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8533 (mt-10) REVERT: D 689 ASP cc_start: 0.7814 (p0) cc_final: 0.7468 (p0) REVERT: D 726 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7527 (m-10) REVERT: D 758 MET cc_start: 0.9190 (mtp) cc_final: 0.8969 (mtm) REVERT: D 794 PHE cc_start: 0.7998 (m-10) cc_final: 0.7745 (m-10) REVERT: D 797 LEU cc_start: 0.7216 (pt) cc_final: 0.6561 (mt) REVERT: D 802 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: D 804 LEU cc_start: 0.8775 (tp) cc_final: 0.8518 (mt) REVERT: D 863 MET cc_start: 0.8613 (mmt) cc_final: 0.8263 (mmt) REVERT: D 897 ARG cc_start: 0.8617 (mtt180) cc_final: 0.7506 (mmt180) REVERT: D 985 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7347 (mp) REVERT: D 988 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6201 (pm20) REVERT: D 1023 MET cc_start: 0.6267 (mmp) cc_final: 0.4289 (ttm) REVERT: D 1048 GLU cc_start: 0.7149 (pm20) cc_final: 0.6815 (mp0) outliers start: 129 outliers final: 54 residues processed: 451 average time/residue: 0.5842 time to fit residues: 311.9852 Evaluate side-chains 402 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 324 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 666 GLN Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 574 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 726 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 726 TYR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 988 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 98 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 351 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 341 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 295 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.166947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120128 restraints weight = 47058.617| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.49 r_work: 0.3324 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31192 Z= 0.199 Angle : 0.692 12.424 42260 Z= 0.349 Chirality : 0.043 0.177 4708 Planarity : 0.004 0.043 5280 Dihedral : 5.365 52.994 4024 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.54 % Allowed : 18.12 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3656 helix: 1.13 (0.11), residues: 2464 sheet: -1.48 (0.37), residues: 188 loop : -2.12 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1081 TYR 0.028 0.002 TYR B 191 PHE 0.024 0.002 PHE B 807 TRP 0.030 0.002 TRP C 786 HIS 0.006 0.001 HIS D 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (31188) covalent geometry : angle 0.69135 / 0.35 (42252) SS BOND : bond 0.00559 / 0.26 ( 4) SS BOND : angle 2.82244 / 1.58 ( 8) hydrogen bonds : bond 0.05192 / 3.59 ( 1756) hydrogen bonds : angle 4.07961 / 2.84 ( 5232) *********************** 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 482 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 331 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8431 (ptpt) REVERT: A 294 ASN cc_start: 0.8031 (p0) cc_final: 0.7684 (p0) REVERT: A 330 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: A 364 ARG cc_start: 0.7333 (tpm170) cc_final: 0.6987 (mmm-85) REVERT: A 402 GLU cc_start: 0.7714 (pp20) cc_final: 0.7481 (pp20) REVERT: A 451 ARG cc_start: 0.5826 (OUTLIER) cc_final: 0.5425 (ppt170) REVERT: A 507 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7266 (tpm170) REVERT: A 566 ILE cc_start: 0.8998 (mt) cc_final: 0.8748 (mp) REVERT: A 574 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8186 (tppt) REVERT: A 627 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8619 (mt-10) REVERT: A 666 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8579 (mt0) REVERT: A 689 ASP cc_start: 0.7923 (p0) cc_final: 0.7590 (p0) REVERT: A 726 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7489 (m-10) REVERT: A 732 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7585 (p) REVERT: A 758 MET cc_start: 0.9204 (mtp) cc_final: 0.8957 (mtm) REVERT: A 794 PHE cc_start: 0.8071 (m-10) cc_final: 0.7810 (m-10) REVERT: A 797 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6328 (mt) REVERT: A 802 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: A 804 LEU cc_start: 0.8838 (tp) cc_final: 0.8606 (mt) REVERT: A 897 ARG cc_start: 0.8693 (mtt180) cc_final: 0.7641 (mmt180) REVERT: A 950 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7950 (ttm170) REVERT: A 985 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7302 (mp) REVERT: A 988 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6285 (pm20) REVERT: A 1048 GLU cc_start: 0.7196 (pm20) cc_final: 0.6809 (mp0) REVERT: B 163 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8428 (ptpt) REVERT: B 294 ASN cc_start: 0.8050 (p0) cc_final: 0.7696 (p0) REVERT: B 330 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: B 364 ARG cc_start: 0.7240 (tpm170) cc_final: 0.6779 (ttm110) REVERT: B 402 GLU cc_start: 0.7711 (pp20) cc_final: 0.7478 (pp20) REVERT: B 457 ASP cc_start: 0.7454 (p0) cc_final: 0.7122 (p0) REVERT: B 459 GLN cc_start: 0.7016 (mp10) cc_final: 0.6566 (mm-40) REVERT: B 507 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7265 (tpm170) REVERT: B 627 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8595 (mt-10) REVERT: B 666 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8584 (mt0) REVERT: B 689 ASP cc_start: 0.7899 (p0) cc_final: 0.7580 (p0) REVERT: B 726 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7460 (m-10) REVERT: B 732 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7568 (p) REVERT: B 794 PHE cc_start: 0.8077 (m-10) cc_final: 0.7814 (m-10) REVERT: B 797 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6328 (mt) REVERT: B 802 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: B 804 LEU cc_start: 0.8842 (tp) cc_final: 0.8606 (mt) REVERT: B 897 ARG cc_start: 0.8691 (mtt180) cc_final: 0.7637 (mmt180) REVERT: B 950 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7956 (ttm170) REVERT: B 985 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7321 (mp) REVERT: B 988 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6295 (pm20) REVERT: B 1046 ARG cc_start: 0.7341 (ttm170) cc_final: 0.7048 (mtp85) REVERT: B 1047 ASN cc_start: 0.6563 (m-40) cc_final: 0.5851 (t0) REVERT: B 1048 GLU cc_start: 0.7222 (pm20) cc_final: 0.6689 (mp0) REVERT: C 163 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8425 (ptpt) REVERT: C 294 ASN cc_start: 0.8003 (p0) cc_final: 0.7643 (p0) REVERT: C 330 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: C 364 ARG cc_start: 0.7323 (tpm170) cc_final: 0.6840 (ttm110) REVERT: C 402 GLU cc_start: 0.7705 (pp20) cc_final: 0.7477 (pp20) REVERT: C 507 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7278 (tpm170) REVERT: C 627 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8583 (mt-10) REVERT: C 666 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8601 (mt0) REVERT: C 689 ASP cc_start: 0.7898 (p0) cc_final: 0.7565 (p0) REVERT: C 726 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7483 (m-10) REVERT: C 863 MET cc_start: 0.8716 (mmt) cc_final: 0.8355 (mmt) REVERT: C 897 ARG cc_start: 0.8720 (mtt180) cc_final: 0.7659 (mmt180) REVERT: C 950 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7948 (ttm170) REVERT: C 988 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: C 1045 PHE cc_start: 0.6681 (p90) cc_final: 0.6445 (p90) REVERT: C 1046 ARG cc_start: 0.7309 (ttm170) cc_final: 0.7055 (mtp85) REVERT: C 1047 ASN cc_start: 0.6550 (m-40) cc_final: 0.5839 (t0) REVERT: C 1048 GLU cc_start: 0.7229 (pm20) cc_final: 0.6650 (mp0) REVERT: D 123 ASP cc_start: 0.7179 (m-30) cc_final: 0.6893 (m-30) REVERT: D 163 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8407 (ptpt) REVERT: D 294 ASN cc_start: 0.7964 (p0) cc_final: 0.7586 (p0) REVERT: D 364 ARG cc_start: 0.7359 (tpm170) cc_final: 0.6976 (mmm-85) REVERT: D 402 GLU cc_start: 0.7715 (pp20) cc_final: 0.7474 (pp20) REVERT: D 457 ASP cc_start: 0.7444 (p0) cc_final: 0.7128 (p0) REVERT: D 459 GLN cc_start: 0.7021 (mp10) cc_final: 0.6558 (mm-40) REVERT: D 507 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7254 (tpm170) REVERT: D 627 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8596 (mt-10) REVERT: D 726 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7471 (m-10) REVERT: D 732 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7576 (p) REVERT: D 794 PHE cc_start: 0.8078 (m-10) cc_final: 0.7816 (m-10) REVERT: D 797 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6304 (mt) REVERT: D 802 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: D 804 LEU cc_start: 0.8840 (tp) cc_final: 0.8609 (mt) REVERT: D 863 MET cc_start: 0.8699 (mmt) cc_final: 0.8333 (mmt) REVERT: D 897 ARG cc_start: 0.8699 (mtt180) cc_final: 0.7644 (mmt180) REVERT: D 950 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7921 (ttm170) REVERT: D 988 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6420 (pm20) REVERT: D 1048 GLU cc_start: 0.7183 (pm20) cc_final: 0.6807 (mp0) outliers start: 151 outliers final: 60 residues processed: 451 average time/residue: 0.5700 time to fit residues: 306.1780 Evaluate side-chains 418 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 319 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 950 ARG Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 666 GLN Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 574 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 726 TYR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 950 ARG Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 726 TYR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 950 ARG Chi-restraints excluded: chain D residue 988 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 339 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 326 optimal weight: 0.5980 chunk 153 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 265 optimal weight: 0.6980 chunk 255 optimal weight: 0.9990 chunk 295 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.169467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123150 restraints weight = 47001.703| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.41 r_work: 0.3362 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31192 Z= 0.142 Angle : 0.653 14.227 42260 Z= 0.325 Chirality : 0.041 0.153 4708 Planarity : 0.004 0.042 5280 Dihedral : 5.184 51.669 4024 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.76 % Allowed : 19.50 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3656 helix: 1.28 (0.11), residues: 2456 sheet: -1.37 (0.38), residues: 188 loop : -2.05 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1079 TYR 0.042 0.002 TYR C 191 PHE 0.025 0.001 PHE C 807 TRP 0.032 0.002 TRP C 786 HIS 0.004 0.001 HIS A 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (31188) covalent geometry : angle 0.65182 / 0.32 (42252) SS BOND : bond 0.00500 / 0.23 ( 4) SS BOND : angle 2.41338 / 1.35 ( 8) hydrogen bonds : bond 0.04351 / 3.00 ( 1756) hydrogen bonds : angle 3.95594 / 2.76 ( 5232) *********************** 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 474 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 349 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7193 (m-30) cc_final: 0.6947 (m-30) REVERT: A 141 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7921 (p) REVERT: A 163 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8351 (ptmt) REVERT: A 294 ASN cc_start: 0.7895 (p0) cc_final: 0.7533 (p0) REVERT: A 330 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: A 353 MET cc_start: 0.7014 (mpp) cc_final: 0.6747 (pmm) REVERT: A 364 ARG cc_start: 0.7470 (tpm170) cc_final: 0.6961 (mmm-85) REVERT: A 402 GLU cc_start: 0.7737 (pp20) cc_final: 0.7477 (pp20) REVERT: A 451 ARG cc_start: 0.5956 (OUTLIER) cc_final: 0.5703 (ppt170) REVERT: A 457 ASP cc_start: 0.7448 (p0) cc_final: 0.7130 (p0) REVERT: A 459 GLN cc_start: 0.7035 (mp10) cc_final: 0.6585 (mm-40) REVERT: A 480 ASN cc_start: 0.7774 (m-40) cc_final: 0.7337 (m-40) REVERT: A 566 ILE cc_start: 0.8974 (mt) cc_final: 0.8713 (mp) REVERT: A 627 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8522 (mt-10) REVERT: A 689 ASP cc_start: 0.7893 (p0) cc_final: 0.7571 (p0) REVERT: A 726 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7455 (m-10) REVERT: A 758 MET cc_start: 0.9214 (mtp) cc_final: 0.9004 (mtm) REVERT: A 794 PHE cc_start: 0.8025 (m-10) cc_final: 0.7754 (m-10) REVERT: A 797 LEU cc_start: 0.7230 (pt) cc_final: 0.6543 (mt) REVERT: A 802 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: A 804 LEU cc_start: 0.8772 (tp) cc_final: 0.8523 (mt) REVERT: A 863 MET cc_start: 0.8688 (mmt) cc_final: 0.8379 (mmt) REVERT: A 897 ARG cc_start: 0.8604 (mtt180) cc_final: 0.7468 (mmt180) REVERT: A 950 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7879 (ttm170) REVERT: A 985 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7221 (mp) REVERT: A 988 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6120 (pm20) REVERT: A 1023 MET cc_start: 0.6339 (mmp) cc_final: 0.4517 (ttm) REVERT: A 1048 GLU cc_start: 0.7234 (pm20) cc_final: 0.6749 (mp0) REVERT: A 1051 GLU cc_start: 0.8207 (tp30) cc_final: 0.7892 (tp30) REVERT: B 123 ASP cc_start: 0.7195 (m-30) cc_final: 0.6949 (m-30) REVERT: B 141 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7910 (p) REVERT: B 163 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8310 (ptmt) REVERT: B 294 ASN cc_start: 0.7981 (p0) cc_final: 0.7600 (p0) REVERT: B 330 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: B 353 MET cc_start: 0.7004 (mpp) cc_final: 0.6733 (pmm) REVERT: B 364 ARG cc_start: 0.7187 (tpm170) cc_final: 0.6813 (ttm110) REVERT: B 402 GLU cc_start: 0.7731 (pp20) cc_final: 0.7439 (pp20) REVERT: B 457 ASP cc_start: 0.7391 (p0) cc_final: 0.7029 (p0) REVERT: B 459 GLN cc_start: 0.7009 (mp10) cc_final: 0.6570 (mm-40) REVERT: B 627 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8528 (mt-10) REVERT: B 689 ASP cc_start: 0.7879 (p0) cc_final: 0.7555 (p0) REVERT: B 726 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7461 (m-10) REVERT: B 758 MET cc_start: 0.9220 (mtp) cc_final: 0.9011 (mtm) REVERT: B 794 PHE cc_start: 0.8016 (m-10) cc_final: 0.7743 (m-10) REVERT: B 797 LEU cc_start: 0.7242 (pt) cc_final: 0.6552 (mt) REVERT: B 802 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: B 804 LEU cc_start: 0.8767 (tp) cc_final: 0.8519 (mt) REVERT: B 863 MET cc_start: 0.8675 (mmt) cc_final: 0.8368 (mmt) REVERT: B 897 ARG cc_start: 0.8614 (mtt180) cc_final: 0.7465 (mmt180) REVERT: B 950 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7877 (ttm170) REVERT: B 985 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7261 (mp) REVERT: B 988 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6149 (pm20) REVERT: B 1023 MET cc_start: 0.6336 (mmp) cc_final: 0.4512 (ttm) REVERT: B 1046 ARG cc_start: 0.7379 (ttm170) cc_final: 0.7067 (ttm-80) REVERT: B 1047 ASN cc_start: 0.6478 (m-40) cc_final: 0.5878 (t0) REVERT: B 1048 GLU cc_start: 0.7185 (pm20) cc_final: 0.6661 (mp0) REVERT: C 141 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7920 (p) REVERT: C 163 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8318 (ptmt) REVERT: C 294 ASN cc_start: 0.7848 (p0) cc_final: 0.7481 (p0) REVERT: C 330 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: C 353 MET cc_start: 0.7015 (mpp) cc_final: 0.6748 (pmm) REVERT: C 364 ARG cc_start: 0.7197 (tpm170) cc_final: 0.6816 (ttm110) REVERT: C 402 GLU cc_start: 0.7727 (pp20) cc_final: 0.7453 (pp20) REVERT: C 457 ASP cc_start: 0.7442 (p0) cc_final: 0.7119 (p0) REVERT: C 459 GLN cc_start: 0.6928 (mp10) cc_final: 0.6499 (mm-40) REVERT: C 627 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8511 (mt-10) REVERT: C 666 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8615 (mt0) REVERT: C 689 ASP cc_start: 0.7863 (p0) cc_final: 0.7542 (p0) REVERT: C 758 MET cc_start: 0.9221 (mtp) cc_final: 0.9010 (mtm) REVERT: C 797 LEU cc_start: 0.7224 (pt) cc_final: 0.6545 (mt) REVERT: C 897 ARG cc_start: 0.8633 (mtt180) cc_final: 0.7488 (mmt180) REVERT: C 950 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7896 (ttm170) REVERT: C 985 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7364 (mp) REVERT: C 988 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6421 (pm20) REVERT: C 1023 MET cc_start: 0.6338 (mmp) cc_final: 0.4525 (ttm) REVERT: C 1045 PHE cc_start: 0.6694 (p90) cc_final: 0.6471 (p90) REVERT: C 1046 ARG cc_start: 0.7397 (ttm170) cc_final: 0.7129 (mtp85) REVERT: C 1047 ASN cc_start: 0.6461 (m-40) cc_final: 0.5823 (t0) REVERT: C 1048 GLU cc_start: 0.7230 (pm20) cc_final: 0.6665 (mp0) REVERT: D 141 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7919 (p) REVERT: D 163 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8333 (ptmt) REVERT: D 294 ASN cc_start: 0.7896 (p0) cc_final: 0.7515 (p0) REVERT: D 353 MET cc_start: 0.6991 (mpp) cc_final: 0.6723 (pmm) REVERT: D 364 ARG cc_start: 0.7476 (tpm170) cc_final: 0.6967 (mmm-85) REVERT: D 402 GLU cc_start: 0.7728 (pp20) cc_final: 0.7489 (pp20) REVERT: D 457 ASP cc_start: 0.7403 (p0) cc_final: 0.7044 (p0) REVERT: D 459 GLN cc_start: 0.7021 (mp10) cc_final: 0.6565 (mm-40) REVERT: D 627 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8511 (mt-10) REVERT: D 666 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8394 (mt0) REVERT: D 758 MET cc_start: 0.9230 (mtp) cc_final: 0.9020 (mtm) REVERT: D 794 PHE cc_start: 0.8021 (m-10) cc_final: 0.7750 (m-10) REVERT: D 797 LEU cc_start: 0.7251 (pt) cc_final: 0.6580 (mt) REVERT: D 802 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7328 (m-30) REVERT: D 804 LEU cc_start: 0.8772 (tp) cc_final: 0.8524 (mt) REVERT: D 897 ARG cc_start: 0.8616 (mtt180) cc_final: 0.7470 (mmt180) REVERT: D 950 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7888 (ttm170) REVERT: D 985 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7370 (mp) REVERT: D 988 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6401 (pm20) REVERT: D 1023 MET cc_start: 0.6315 (mmp) cc_final: 0.4507 (ttm) REVERT: D 1048 GLU cc_start: 0.7217 (pm20) cc_final: 0.6783 (mp0) REVERT: D 1051 GLU cc_start: 0.8202 (tp30) cc_final: 0.7896 (tp30) outliers start: 125 outliers final: 61 residues processed: 449 average time/residue: 0.6088 time to fit residues: 325.8190 Evaluate side-chains 423 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 331 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 950 ARG Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 574 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 950 ARG Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 666 GLN Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 950 ARG Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 988 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 24 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 279 optimal weight: 20.0000 chunk 356 optimal weight: 5.9990 chunk 216 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1050 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN D1050 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.171344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125582 restraints weight = 47107.620| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.39 r_work: 0.3401 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31192 Z= 0.124 Angle : 0.641 15.237 42260 Z= 0.316 Chirality : 0.040 0.155 4708 Planarity : 0.004 0.039 5280 Dihedral : 4.988 58.853 4024 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.16 % Allowed : 20.64 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3656 helix: 1.41 (0.11), residues: 2464 sheet: -1.21 (0.39), residues: 188 loop : -2.19 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 167 TYR 0.031 0.001 TYR C 191 PHE 0.011 0.001 PHE B 165 TRP 0.034 0.001 TRP D 786 HIS 0.003 0.001 HIS A 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (31188) covalent geometry : angle 0.63994 / 0.32 (42252) SS BOND : bond 0.00451 / 0.21 ( 4) SS BOND : angle 2.08910 / 1.17 ( 8) hydrogen bonds : bond 0.03856 / 2.65 ( 1756) hydrogen bonds : angle 3.84290 / 2.69 ( 5232) *********************** 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 498 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 393 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7104 (m-30) cc_final: 0.6864 (m-30) REVERT: A 158 LYS cc_start: 0.6860 (mppt) cc_final: 0.5547 (pttp) REVERT: A 163 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8377 (ptmt) REVERT: A 164 ILE cc_start: 0.8186 (mt) cc_final: 0.7962 (mt) REVERT: A 189 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6564 (ttm) REVERT: A 294 ASN cc_start: 0.7885 (p0) cc_final: 0.7548 (p0) REVERT: A 330 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: A 353 MET cc_start: 0.7010 (mpp) cc_final: 0.6738 (pmm) REVERT: A 364 ARG cc_start: 0.7460 (tpm170) cc_final: 0.6967 (mmm-85) REVERT: A 402 GLU cc_start: 0.7703 (pp20) cc_final: 0.7428 (pp20) REVERT: A 457 ASP cc_start: 0.7536 (p0) cc_final: 0.7236 (p0) REVERT: A 459 GLN cc_start: 0.7192 (mp10) cc_final: 0.6756 (mm-40) REVERT: A 480 ASN cc_start: 0.7473 (m-40) cc_final: 0.7114 (m-40) REVERT: A 566 ILE cc_start: 0.8984 (mt) cc_final: 0.8713 (mp) REVERT: A 666 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8401 (mt0) REVERT: A 689 ASP cc_start: 0.7794 (p0) cc_final: 0.7502 (p0) REVERT: A 726 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7536 (m-10) REVERT: A 731 PHE cc_start: 0.7700 (m-80) cc_final: 0.6656 (t80) REVERT: A 794 PHE cc_start: 0.8004 (m-10) cc_final: 0.7698 (m-10) REVERT: A 797 LEU cc_start: 0.7214 (pt) cc_final: 0.6573 (mt) REVERT: A 804 LEU cc_start: 0.8747 (tp) cc_final: 0.8466 (mt) REVERT: A 863 MET cc_start: 0.8638 (mmt) cc_final: 0.8338 (mmt) REVERT: A 897 ARG cc_start: 0.8626 (mtt180) cc_final: 0.7505 (mmt180) REVERT: A 950 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7888 (ttm170) REVERT: A 1023 MET cc_start: 0.6269 (mmp) cc_final: 0.4359 (ttm) REVERT: A 1048 GLU cc_start: 0.7279 (pm20) cc_final: 0.6726 (mp0) REVERT: A 1051 GLU cc_start: 0.8186 (tp30) cc_final: 0.7852 (tp30) REVERT: A 1079 ARG cc_start: 0.7199 (ttp80) cc_final: 0.6815 (mtt90) REVERT: B 123 ASP cc_start: 0.7098 (m-30) cc_final: 0.6857 (m-30) REVERT: B 158 LYS cc_start: 0.6943 (mppt) cc_final: 0.5623 (pttp) REVERT: B 163 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8387 (ptmt) REVERT: B 164 ILE cc_start: 0.8177 (mt) cc_final: 0.7959 (mt) REVERT: B 189 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6578 (ttm) REVERT: B 294 ASN cc_start: 0.7882 (p0) cc_final: 0.7531 (p0) REVERT: B 330 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: B 353 MET cc_start: 0.6950 (mpp) cc_final: 0.6683 (pmm) REVERT: B 364 ARG cc_start: 0.7169 (tpm170) cc_final: 0.6917 (ttm170) REVERT: B 402 GLU cc_start: 0.7677 (pp20) cc_final: 0.7434 (pp20) REVERT: B 457 ASP cc_start: 0.7612 (p0) cc_final: 0.7253 (p0) REVERT: B 459 GLN cc_start: 0.7253 (mp10) cc_final: 0.6841 (mm-40) REVERT: B 480 ASN cc_start: 0.7827 (m-40) cc_final: 0.7386 (m-40) REVERT: B 574 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7976 (tppp) REVERT: B 627 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8488 (mt-10) REVERT: B 666 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: B 689 ASP cc_start: 0.7815 (p0) cc_final: 0.7500 (p0) REVERT: B 726 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7527 (m-10) REVERT: B 731 PHE cc_start: 0.7693 (m-80) cc_final: 0.6629 (t80) REVERT: B 794 PHE cc_start: 0.8002 (m-10) cc_final: 0.7695 (m-10) REVERT: B 797 LEU cc_start: 0.7221 (pt) cc_final: 0.6579 (mt) REVERT: B 804 LEU cc_start: 0.8744 (tp) cc_final: 0.8463 (mt) REVERT: B 863 MET cc_start: 0.8637 (mmt) cc_final: 0.8342 (mmt) REVERT: B 897 ARG cc_start: 0.8640 (mtt180) cc_final: 0.7506 (mmt180) REVERT: B 950 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7856 (ttm170) REVERT: B 1023 MET cc_start: 0.6256 (mmp) cc_final: 0.4345 (ttm) REVERT: B 1047 ASN cc_start: 0.6354 (m-40) cc_final: 0.5823 (t0) REVERT: B 1048 GLU cc_start: 0.7053 (pm20) cc_final: 0.6600 (mp0) REVERT: B 1051 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7856 (tp30) REVERT: B 1079 ARG cc_start: 0.7207 (ttp80) cc_final: 0.6866 (mtt90) REVERT: C 123 ASP cc_start: 0.7098 (m-30) cc_final: 0.6849 (m-30) REVERT: C 163 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8377 (ptmt) REVERT: C 164 ILE cc_start: 0.8171 (mt) cc_final: 0.7967 (mt) REVERT: C 189 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6567 (ttm) REVERT: C 294 ASN cc_start: 0.7861 (p0) cc_final: 0.7510 (p0) REVERT: C 353 MET cc_start: 0.6994 (mpp) cc_final: 0.6723 (pmm) REVERT: C 364 ARG cc_start: 0.7168 (tpm170) cc_final: 0.6908 (ttm170) REVERT: C 402 GLU cc_start: 0.7661 (pp20) cc_final: 0.7420 (pp20) REVERT: C 457 ASP cc_start: 0.7564 (p0) cc_final: 0.7251 (p0) REVERT: C 459 GLN cc_start: 0.6983 (mp10) cc_final: 0.6543 (mm-40) REVERT: C 480 ASN cc_start: 0.7829 (m-40) cc_final: 0.7386 (m-40) REVERT: C 627 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8461 (mt-10) REVERT: C 666 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8654 (mt0) REVERT: C 689 ASP cc_start: 0.7809 (p0) cc_final: 0.7491 (p0) REVERT: C 731 PHE cc_start: 0.7784 (m-80) cc_final: 0.6759 (t80) REVERT: C 758 MET cc_start: 0.9213 (mtp) cc_final: 0.9009 (mtm) REVERT: C 797 LEU cc_start: 0.7213 (pt) cc_final: 0.6607 (mt) REVERT: C 897 ARG cc_start: 0.8630 (mtt180) cc_final: 0.7511 (mmt180) REVERT: C 950 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7893 (ttm170) REVERT: C 985 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7499 (mp) REVERT: C 988 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6363 (pm20) REVERT: C 1023 MET cc_start: 0.6278 (mmp) cc_final: 0.4362 (ttm) REVERT: C 1046 ARG cc_start: 0.7435 (ttm170) cc_final: 0.6875 (mpt180) REVERT: C 1047 ASN cc_start: 0.6337 (m-40) cc_final: 0.5837 (t0) REVERT: C 1048 GLU cc_start: 0.7263 (pm20) cc_final: 0.6582 (mp0) REVERT: C 1051 GLU cc_start: 0.8175 (tp30) cc_final: 0.7880 (tp30) REVERT: C 1079 ARG cc_start: 0.7190 (ttp80) cc_final: 0.6890 (mtt90) REVERT: D 123 ASP cc_start: 0.7069 (m-30) cc_final: 0.6824 (m-30) REVERT: D 163 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8361 (ptmt) REVERT: D 189 MET cc_start: 0.6847 (mtm) cc_final: 0.6550 (ttm) REVERT: D 294 ASN cc_start: 0.7841 (p0) cc_final: 0.7487 (p0) REVERT: D 353 MET cc_start: 0.7020 (mpp) cc_final: 0.6750 (pmm) REVERT: D 364 ARG cc_start: 0.7433 (tpm170) cc_final: 0.6948 (mmm-85) REVERT: D 402 GLU cc_start: 0.7685 (pp20) cc_final: 0.7406 (pp20) REVERT: D 457 ASP cc_start: 0.7554 (p0) cc_final: 0.7201 (p0) REVERT: D 459 GLN cc_start: 0.7247 (mp10) cc_final: 0.6809 (mm-40) REVERT: D 480 ASN cc_start: 0.7746 (m-40) cc_final: 0.7373 (m-40) REVERT: D 731 PHE cc_start: 0.7689 (m-80) cc_final: 0.6651 (t80) REVERT: D 794 PHE cc_start: 0.7951 (m-10) cc_final: 0.7643 (m-10) REVERT: D 797 LEU cc_start: 0.7252 (pt) cc_final: 0.6606 (mt) REVERT: D 804 LEU cc_start: 0.8745 (tp) cc_final: 0.8468 (mt) REVERT: D 897 ARG cc_start: 0.8617 (mtt180) cc_final: 0.7493 (mmt180) REVERT: D 950 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7876 (ttm170) REVERT: D 985 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7492 (mp) REVERT: D 988 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6495 (pm20) REVERT: D 1023 MET cc_start: 0.6264 (mmp) cc_final: 0.4362 (ttm) REVERT: D 1048 GLU cc_start: 0.7179 (pm20) cc_final: 0.6725 (mp0) REVERT: D 1051 GLU cc_start: 0.8175 (tp30) cc_final: 0.7852 (tp30) REVERT: D 1079 ARG cc_start: 0.7188 (ttp80) cc_final: 0.6888 (mtt90) outliers start: 105 outliers final: 44 residues processed: 474 average time/residue: 0.6593 time to fit residues: 368.8837 Evaluate side-chains 418 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 353 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 950 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 666 GLN Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 1051 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 666 GLN 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 950 ARG Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 628 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 950 ARG Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 988 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 147 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 188 optimal weight: 0.9990 chunk 204 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 304 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 338 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 265 optimal weight: 0.5980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.168371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120580 restraints weight = 46917.497| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.48 r_work: 0.3337 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31192 Z= 0.173 Angle : 0.693 14.880 42260 Z= 0.344 Chirality : 0.042 0.190 4708 Planarity : 0.004 0.042 5280 Dihedral : 4.930 50.194 4024 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.52 % Allowed : 22.18 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3656 helix: 1.38 (0.11), residues: 2432 sheet: -1.22 (0.39), residues: 188 loop : -2.03 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 167 TYR 0.043 0.002 TYR A 646 PHE 0.018 0.001 PHE C1013 TRP 0.035 0.002 TRP C 786 HIS 0.006 0.001 HIS D 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 (31188) covalent geometry : angle 0.69225 / 0.34 (42252) SS BOND : bond 0.00522 / 0.24 ( 4) SS BOND : angle 2.44773 / 1.37 ( 8) hydrogen bonds : bond 0.04799 / 3.32 ( 1756) hydrogen bonds : angle 3.98039 / 2.78 ( 5232) ********************** 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 436 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 352 time to evaluate : 1.104 Fit side-chains REVERT: A 123 ASP cc_start: 0.7300 (m-30) cc_final: 0.7043 (m-30) REVERT: A 163 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8368 (ptmt) REVERT: A 189 MET cc_start: 0.6911 (mtm) cc_final: 0.6569 (ttm) REVERT: A 294 ASN cc_start: 0.7896 (p0) cc_final: 0.7539 (p0) REVERT: A 353 MET cc_start: 0.6971 (mpp) cc_final: 0.6685 (pmm) REVERT: A 364 ARG cc_start: 0.7287 (tpm170) cc_final: 0.6982 (mmm-85) REVERT: A 402 GLU cc_start: 0.7659 (pp20) cc_final: 0.7420 (pp20) REVERT: A 457 ASP cc_start: 0.7601 (p0) cc_final: 0.7269 (OUTLIER) REVERT: A 459 GLN cc_start: 0.7050 (mp10) cc_final: 0.6622 (mm-40) REVERT: A 480 ASN cc_start: 0.7648 (m-40) cc_final: 0.7369 (m-40) REVERT: A 566 ILE cc_start: 0.9015 (mt) cc_final: 0.8799 (mp) REVERT: A 666 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8489 (mt0) REVERT: A 689 ASP cc_start: 0.7914 (p0) cc_final: 0.7594 (p0) REVERT: A 726 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7479 (m-10) REVERT: A 794 PHE cc_start: 0.8027 (m-10) cc_final: 0.7753 (m-10) REVERT: A 797 LEU cc_start: 0.7226 (pt) cc_final: 0.6605 (mt) REVERT: A 804 LEU cc_start: 0.8791 (tp) cc_final: 0.8540 (mt) REVERT: A 847 PHE cc_start: 0.8013 (m-10) cc_final: 0.7747 (m-10) REVERT: A 863 MET cc_start: 0.8706 (mmt) cc_final: 0.8366 (mmt) REVERT: A 897 ARG cc_start: 0.8726 (mtt180) cc_final: 0.7650 (mmt180) REVERT: A 950 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7939 (ttm170) REVERT: A 1023 MET cc_start: 0.6400 (mmp) cc_final: 0.4474 (ttm) REVERT: A 1048 GLU cc_start: 0.7279 (pm20) cc_final: 0.6704 (mp0) REVERT: A 1051 GLU cc_start: 0.8203 (tp30) cc_final: 0.7898 (tp30) REVERT: B 123 ASP cc_start: 0.7291 (m-30) cc_final: 0.7033 (m-30) REVERT: B 163 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8383 (ptmt) REVERT: B 164 ILE cc_start: 0.8186 (mt) cc_final: 0.7984 (mt) REVERT: B 189 MET cc_start: 0.6900 (mtm) cc_final: 0.6548 (ttm) REVERT: B 294 ASN cc_start: 0.7906 (p0) cc_final: 0.7564 (p0) REVERT: B 353 MET cc_start: 0.6983 (mpp) cc_final: 0.6691 (pmm) REVERT: B 402 GLU cc_start: 0.7659 (pp20) cc_final: 0.7441 (pp20) REVERT: B 627 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8592 (mt-10) REVERT: B 666 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8477 (mt0) REVERT: B 689 ASP cc_start: 0.7892 (p0) cc_final: 0.7571 (p0) REVERT: B 726 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7485 (m-10) REVERT: B 794 PHE cc_start: 0.8022 (m-10) cc_final: 0.7745 (m-10) REVERT: B 797 LEU cc_start: 0.7226 (pt) cc_final: 0.6606 (mt) REVERT: B 804 LEU cc_start: 0.8795 (tp) cc_final: 0.8539 (mt) REVERT: B 863 MET cc_start: 0.8706 (mmt) cc_final: 0.8372 (mmt) REVERT: B 897 ARG cc_start: 0.8726 (mtt180) cc_final: 0.7591 (mmt180) REVERT: B 950 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7926 (ttm170) REVERT: B 1023 MET cc_start: 0.6384 (mmp) cc_final: 0.4451 (ttm) REVERT: B 1047 ASN cc_start: 0.6265 (m-40) cc_final: 0.5904 (t0) REVERT: B 1048 GLU cc_start: 0.7143 (pm20) cc_final: 0.6621 (mp0) REVERT: B 1051 GLU cc_start: 0.8170 (tp30) cc_final: 0.7837 (tp30) REVERT: C 123 ASP cc_start: 0.7310 (m-30) cc_final: 0.7051 (m-30) REVERT: C 163 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8365 (ptmt) REVERT: C 189 MET cc_start: 0.6920 (mtm) cc_final: 0.6573 (ttm) REVERT: C 294 ASN cc_start: 0.7915 (p0) cc_final: 0.7585 (p0) REVERT: C 353 MET cc_start: 0.6991 (mpp) cc_final: 0.6695 (pmm) REVERT: C 402 GLU cc_start: 0.7649 (pp20) cc_final: 0.7429 (pp20) REVERT: C 457 ASP cc_start: 0.7508 (p0) cc_final: 0.7164 (p0) REVERT: C 459 GLN cc_start: 0.7020 (mp10) cc_final: 0.6600 (mm-40) REVERT: C 627 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8582 (mt-10) REVERT: C 666 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8540 (mt0) REVERT: C 689 ASP cc_start: 0.7864 (p0) cc_final: 0.7543 (p0) REVERT: C 758 MET cc_start: 0.9235 (mtp) cc_final: 0.8995 (mtm) REVERT: C 797 LEU cc_start: 0.7172 (pt) cc_final: 0.6460 (mt) REVERT: C 897 ARG cc_start: 0.8718 (mtt180) cc_final: 0.7630 (mmt180) REVERT: C 950 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7948 (ttm170) REVERT: C 985 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7337 (mp) REVERT: C 988 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6398 (pm20) REVERT: C 1023 MET cc_start: 0.6388 (mmp) cc_final: 0.4472 (ttm) REVERT: C 1047 ASN cc_start: 0.6352 (m-40) cc_final: 0.5819 (t0) REVERT: C 1048 GLU cc_start: 0.7240 (pm20) cc_final: 0.6551 (mp0) REVERT: C 1051 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: D 123 ASP cc_start: 0.7278 (m-30) cc_final: 0.7032 (m-30) REVERT: D 163 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8352 (ptmt) REVERT: D 189 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6539 (ttm) REVERT: D 294 ASN cc_start: 0.7899 (p0) cc_final: 0.7553 (p0) REVERT: D 353 MET cc_start: 0.6988 (mpp) cc_final: 0.6694 (pmm) REVERT: D 364 ARG cc_start: 0.7286 (tpm170) cc_final: 0.6972 (mmm-85) REVERT: D 402 GLU cc_start: 0.7723 (pp20) cc_final: 0.7484 (pp20) REVERT: D 794 PHE cc_start: 0.8019 (m-10) cc_final: 0.7745 (m-10) REVERT: D 797 LEU cc_start: 0.7245 (pt) cc_final: 0.6619 (mt) REVERT: D 804 LEU cc_start: 0.8797 (tp) cc_final: 0.8536 (mt) REVERT: D 847 PHE cc_start: 0.8016 (m-10) cc_final: 0.7717 (m-10) REVERT: D 897 ARG cc_start: 0.8716 (mtt180) cc_final: 0.7631 (mmt180) REVERT: D 950 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7931 (ttm170) REVERT: D 988 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6384 (pm20) REVERT: D 1023 MET cc_start: 0.6392 (mmp) cc_final: 0.4464 (ttm) REVERT: D 1048 GLU cc_start: 0.7152 (pm20) cc_final: 0.6731 (mp0) REVERT: D 1051 GLU cc_start: 0.8169 (tp30) cc_final: 0.7870 (tp30) outliers start: 84 outliers final: 55 residues processed: 423 average time/residue: 0.6261 time to fit residues: 314.9750 Evaluate side-chains 415 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 345 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 950 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 666 GLN Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 763 VAL 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 950 ARG Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 763 VAL 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 950 ARG Chi-restraints excluded: chain D residue 988 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 167 optimal weight: 0.3980 chunk 325 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 353 optimal weight: 0.8980 chunk 364 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.172383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125998 restraints weight = 47442.018| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.43 r_work: 0.3409 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31192 Z= 0.125 Angle : 0.659 15.423 42260 Z= 0.326 Chirality : 0.040 0.177 4708 Planarity : 0.004 0.039 5280 Dihedral : 4.703 46.612 4024 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.61 % Allowed : 22.12 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3656 helix: 1.42 (0.11), residues: 2468 sheet: -1.09 (0.40), residues: 188 loop : -2.22 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 167 TYR 0.048 0.002 TYR B 646 PHE 0.026 0.001 PHE D 807 TRP 0.035 0.002 TRP C 786 HIS 0.003 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (31188) covalent geometry : angle 0.65864 / 0.33 (42252) SS BOND : bond 0.00393 / 0.18 ( 4) SS BOND : angle 2.00833 / 1.12 ( 8) hydrogen bonds : bond 0.03758 / 2.58 ( 1756) hydrogen bonds : angle 3.84461 / 2.69 ( 5232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12497.50 seconds wall clock time: 212 minutes 52.57 seconds (12772.57 seconds total)