Starting phenix.real_space_refine on Sat Feb 7 03:51:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrd_32723/02_2026/7wrd_32723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrd_32723/02_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_32723/02_2026/7wrd_32723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrd_32723/02_2026/7wrd_32723.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wrd_32723/02_2026/7wrd_32723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrd_32723/02_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 8.00, per 1000 atoms: 0.26 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: 2.55 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: 0.97 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: 6.49 Time building geometry restraints manager: 3.32 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 28.800 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 covalent geometry : bond 0.00914 (31188) covalent geometry : angle 1.07922 (42252) SS BOND : bond 0.01778 ( 4) SS BOND : angle 5.22624 ( 8) hydrogen bonds : bond 0.14339 ( 1756) hydrogen bonds : angle 6.37465 ( 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 : 1.116 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: 0.7431 time to fit residues: 666.3560 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 : 1.221 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4160 r_free = 0.4160 target = 0.172845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123947 restraints weight = 47947.918| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.58 r_work: 0.3416 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31192 Z= 0.148 Angle : 0.643 7.967 42260 Z= 0.336 Chirality : 0.041 0.141 4708 Planarity : 0.005 0.045 5280 Dihedral : 5.918 55.972 4024 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.19 % Allowed : 13.31 % 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: -1.32 (0.13), residues: 3656 helix: -0.03 (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 0.000 ARG C 167 TYR 0.018 0.002 TYR A 191 PHE 0.020 0.001 PHE A 165 TRP 0.017 0.002 TRP D 798 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00336 (31188) covalent geometry : angle 0.64252 (42252) SS BOND : bond 0.00495 ( 4) SS BOND : angle 2.07585 ( 8) hydrogen bonds : bond 0.04958 ( 1756) hydrogen bonds : angle 4.33816 ( 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 580 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 474 time to evaluate : 1.141 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: 0.7120 (mtm) cc_final: 0.6816 (mtm) REVERT: A 190 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8266 (ptmt) REVERT: A 217 TRP cc_start: 0.7842 (t-100) cc_final: 0.7502 (t-100) REVERT: A 353 MET cc_start: 0.5352 (mpp) cc_final: 0.5108 (pmm) REVERT: A 402 GLU cc_start: 0.7748 (pp20) cc_final: 0.7511 (pp20) REVERT: A 510 GLN cc_start: 0.7732 (mt0) cc_final: 0.7358 (mt0) REVERT: A 518 ASP cc_start: 0.7775 (t70) cc_final: 0.7522 (t70) REVERT: A 574 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8092 (tppt) REVERT: A 665 ASP cc_start: 0.8219 (t0) cc_final: 0.7965 (t0) REVERT: A 758 MET cc_start: 0.9038 (mtp) cc_final: 0.8752 (mtm) REVERT: A 989 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7501 (t0) REVERT: A 1026 LYS cc_start: 0.4209 (tmmt) cc_final: 0.4009 (mptm) REVERT: B 123 ASP cc_start: 0.6779 (m-30) cc_final: 0.5959 (p0) REVERT: B 189 MET cc_start: 0.7118 (mtm) cc_final: 0.6816 (mtm) REVERT: B 190 LYS cc_start: 0.8621 (ttmm) cc_final: 0.8264 (ptmt) REVERT: B 217 TRP cc_start: 0.7839 (t-100) cc_final: 0.7501 (t-100) REVERT: B 353 MET cc_start: 0.5364 (mpp) cc_final: 0.5116 (pmm) REVERT: B 402 GLU cc_start: 0.7746 (pp20) cc_final: 0.7510 (pp20) REVERT: B 451 ARG cc_start: 0.5795 (pmt-80) cc_final: 0.5490 (ppt170) REVERT: B 510 GLN cc_start: 0.7755 (mt0) cc_final: 0.7382 (mt0) REVERT: B 518 ASP cc_start: 0.7738 (t70) cc_final: 0.7512 (t70) REVERT: B 574 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8140 (tppt) REVERT: B 665 ASP cc_start: 0.8218 (t0) cc_final: 0.7961 (t0) REVERT: B 758 MET cc_start: 0.9031 (mtp) cc_final: 0.8746 (mtm) REVERT: B 989 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7498 (t0) REVERT: B 1026 LYS cc_start: 0.4219 (tmmt) cc_final: 0.4016 (mptm) REVERT: C 189 MET cc_start: 0.7109 (mtm) cc_final: 0.6805 (mtm) REVERT: C 190 LYS cc_start: 0.8621 (ttmm) cc_final: 0.8310 (ptmt) REVERT: C 217 TRP cc_start: 0.7833 (t-100) cc_final: 0.7495 (t-100) REVERT: C 353 MET cc_start: 0.5346 (mpp) cc_final: 0.5103 (pmm) REVERT: C 402 GLU cc_start: 0.7733 (pp20) cc_final: 0.7493 (pp20) REVERT: C 510 GLN cc_start: 0.7766 (mt0) cc_final: 0.7391 (mt0) REVERT: C 574 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8141 (tppt) REVERT: C 665 ASP cc_start: 0.8220 (t0) cc_final: 0.7948 (t0) REVERT: C 758 MET cc_start: 0.9050 (mtp) cc_final: 0.8835 (mtm) REVERT: C 989 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7502 (t0) REVERT: D 189 MET cc_start: 0.7102 (mtm) cc_final: 0.6797 (mtm) REVERT: D 190 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8307 (ptmt) REVERT: D 217 TRP cc_start: 0.7839 (t-100) cc_final: 0.7493 (t-100) REVERT: D 353 MET cc_start: 0.5345 (mpp) cc_final: 0.5103 (pmm) REVERT: D 402 GLU cc_start: 0.7734 (pp20) cc_final: 0.7493 (pp20) REVERT: D 510 GLN cc_start: 0.7760 (mt0) cc_final: 0.7402 (mt0) REVERT: D 518 ASP cc_start: 0.7784 (t70) cc_final: 0.7535 (t70) REVERT: D 574 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8135 (tppt) REVERT: D 665 ASP cc_start: 0.8208 (t0) cc_final: 0.7951 (t0) REVERT: D 758 MET cc_start: 0.9043 (mtp) cc_final: 0.8828 (mtm) REVERT: D 847 PHE cc_start: 0.7721 (m-10) cc_final: 0.7499 (m-10) REVERT: D 989 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7506 (t0) REVERT: D 1026 LYS cc_start: 0.4213 (tmmt) cc_final: 0.4009 (mptm) outliers start: 106 outliers final: 23 residues processed: 554 average time/residue: 0.7140 time to fit residues: 460.4346 Evaluate side-chains 402 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 371 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 63 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 278 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.172308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126121 restraints weight = 48012.731| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.48 r_work: 0.3402 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31192 Z= 0.142 Angle : 0.617 7.963 42260 Z= 0.317 Chirality : 0.040 0.128 4708 Planarity : 0.004 0.045 5280 Dihedral : 5.520 57.371 4024 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.31 % Allowed : 14.33 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.31 (0.14), residues: 3656 helix: 0.81 (0.10), residues: 2456 sheet: -1.48 (0.35), residues: 200 loop : -2.46 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1079 TYR 0.015 0.002 TYR B 186 PHE 0.018 0.001 PHE B 752 TRP 0.020 0.002 TRP B 786 HIS 0.004 0.001 HIS C 765 Details of bonding type rmsd covalent geometry : bond 0.00326 (31188) covalent geometry : angle 0.61557 (42252) SS BOND : bond 0.00625 ( 4) SS BOND : angle 2.79210 ( 8) hydrogen bonds : bond 0.04646 ( 1756) hydrogen bonds : angle 4.04156 ( 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 527 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 417 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.6963 (m-30) cc_final: 0.5989 (p0) REVERT: A 163 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8418 (ptmt) REVERT: A 186 TYR cc_start: 0.7105 (m-10) cc_final: 0.6897 (m-10) REVERT: A 189 MET cc_start: 0.7303 (mtm) cc_final: 0.6878 (mtm) REVERT: A 190 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8481 (ptmt) REVERT: A 294 ASN cc_start: 0.7964 (p0) cc_final: 0.7609 (p0) REVERT: A 310 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6949 (mtp-110) REVERT: A 396 MET cc_start: 0.6655 (mpm) cc_final: 0.6404 (mpp) REVERT: A 402 GLU cc_start: 0.7959 (pp20) cc_final: 0.7719 (pp20) REVERT: A 480 ASN cc_start: 0.7928 (m-40) cc_final: 0.7552 (m-40) REVERT: A 518 ASP cc_start: 0.7891 (t70) cc_final: 0.7607 (t70) REVERT: A 758 MET cc_start: 0.9183 (mtp) cc_final: 0.8942 (mtm) REVERT: A 797 LEU cc_start: 0.6980 (pt) cc_final: 0.6371 (mt) REVERT: A 802 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: A 804 LEU cc_start: 0.8794 (tp) cc_final: 0.8536 (mt) REVERT: A 897 ARG cc_start: 0.8762 (mtt180) cc_final: 0.7676 (mmt180) REVERT: A 988 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6396 (pm20) REVERT: A 989 ASN cc_start: 0.7419 (OUTLIER) cc_final: 0.7216 (t0) REVERT: A 1023 MET cc_start: 0.6071 (mmp) cc_final: 0.4414 (ttm) REVERT: A 1047 ASN cc_start: 0.6841 (m-40) cc_final: 0.6326 (t0) REVERT: B 123 ASP cc_start: 0.6950 (m-30) cc_final: 0.5976 (p0) REVERT: B 163 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8414 (ptmt) REVERT: B 186 TYR cc_start: 0.7105 (m-10) cc_final: 0.6894 (m-10) REVERT: B 189 MET cc_start: 0.7294 (mtm) cc_final: 0.6879 (mtm) REVERT: B 190 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8479 (ptmt) REVERT: B 294 ASN cc_start: 0.7956 (p0) cc_final: 0.7598 (p0) REVERT: B 310 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6960 (mtp-110) REVERT: B 364 ARG cc_start: 0.7265 (tpm170) cc_final: 0.6730 (ttm110) REVERT: B 402 GLU cc_start: 0.7956 (pp20) cc_final: 0.7716 (pp20) REVERT: B 518 ASP cc_start: 0.7881 (t70) cc_final: 0.7635 (t70) REVERT: B 758 MET cc_start: 0.9180 (mtp) cc_final: 0.8939 (mtm) REVERT: B 797 LEU cc_start: 0.6983 (pt) cc_final: 0.6371 (mt) REVERT: B 802 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: B 804 LEU cc_start: 0.8791 (tp) cc_final: 0.8534 (mt) REVERT: B 897 ARG cc_start: 0.8761 (mtt180) cc_final: 0.7673 (mmt180) REVERT: B 988 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6393 (pm20) REVERT: B 989 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.7201 (t0) REVERT: B 1023 MET cc_start: 0.6073 (mmp) cc_final: 0.4419 (ttm) REVERT: B 1047 ASN cc_start: 0.6851 (m-40) cc_final: 0.6325 (t0) REVERT: C 123 ASP cc_start: 0.6945 (m-30) cc_final: 0.5976 (p0) REVERT: C 163 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8412 (ptmt) REVERT: C 186 TYR cc_start: 0.7111 (m-10) cc_final: 0.6899 (m-10) REVERT: C 189 MET cc_start: 0.7236 (mtm) cc_final: 0.6819 (mtm) REVERT: C 294 ASN cc_start: 0.7958 (p0) cc_final: 0.7625 (p0) REVERT: C 310 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6957 (mtp-110) REVERT: C 364 ARG cc_start: 0.7273 (tpm170) cc_final: 0.6731 (ttm110) REVERT: C 402 GLU cc_start: 0.7946 (pp20) cc_final: 0.7710 (pp20) REVERT: C 726 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: C 758 MET cc_start: 0.9168 (mtp) cc_final: 0.8925 (mtm) REVERT: C 797 LEU cc_start: 0.6929 (pt) cc_final: 0.6325 (mt) REVERT: C 804 LEU cc_start: 0.8775 (tp) cc_final: 0.8537 (mt) REVERT: C 897 ARG cc_start: 0.8775 (mtt180) cc_final: 0.7686 (mmt180) REVERT: C 988 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6393 (pm20) REVERT: C 989 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7258 (t0) REVERT: C 1023 MET cc_start: 0.6243 (mmp) cc_final: 0.4435 (ttm) REVERT: C 1047 ASN cc_start: 0.6825 (m-40) cc_final: 0.6324 (t0) REVERT: D 123 ASP cc_start: 0.6946 (m-30) cc_final: 0.5974 (p0) REVERT: D 163 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8411 (ptmt) REVERT: D 186 TYR cc_start: 0.7092 (m-10) cc_final: 0.6891 (m-10) REVERT: D 189 MET cc_start: 0.7288 (mtm) cc_final: 0.6867 (mtm) REVERT: D 294 ASN cc_start: 0.7929 (p0) cc_final: 0.7585 (p0) REVERT: D 310 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6960 (mtp-110) REVERT: D 364 ARG cc_start: 0.7318 (tpm170) cc_final: 0.6760 (ttm110) REVERT: D 402 GLU cc_start: 0.7952 (pp20) cc_final: 0.7715 (pp20) REVERT: D 518 ASP cc_start: 0.7909 (t70) cc_final: 0.7631 (t70) REVERT: D 726 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7480 (m-10) REVERT: D 758 MET cc_start: 0.9178 (mtp) cc_final: 0.8936 (mtm) REVERT: D 797 LEU cc_start: 0.6971 (pt) cc_final: 0.6366 (mt) REVERT: D 802 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7207 (m-30) REVERT: D 804 LEU cc_start: 0.8787 (tp) cc_final: 0.8529 (mt) REVERT: D 897 ARG cc_start: 0.8773 (mtt180) cc_final: 0.7686 (mmt180) REVERT: D 988 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6388 (pm20) REVERT: D 989 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.7215 (t0) REVERT: D 1023 MET cc_start: 0.6059 (mmp) cc_final: 0.4410 (ttm) REVERT: D 1047 ASN cc_start: 0.6829 (m-40) cc_final: 0.6320 (t0) outliers start: 110 outliers final: 51 residues processed: 499 average time/residue: 0.6106 time to fit residues: 358.4483 Evaluate side-chains 412 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 344 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 310 ARG Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 488 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 628 LEU Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 807 PHE 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 310 ARG 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 802 ASP Chi-restraints excluded: chain B residue 807 PHE 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 310 ARG 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 726 TYR Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 807 PHE Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 310 ARG 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 802 ASP Chi-restraints excluded: chain D residue 807 PHE Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 13 optimal weight: 6.9990 chunk 371 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 333 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 chunk 297 optimal weight: 8.9990 chunk 223 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 666 GLN A 671 GLN A 818 HIS ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN B 671 GLN B 818 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN C 671 GLN C 741 ASN C 818 HIS ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN D 671 GLN D 818 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.168862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123192 restraints weight = 47285.393| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.46 r_work: 0.3368 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31192 Z= 0.178 Angle : 0.643 8.065 42260 Z= 0.330 Chirality : 0.042 0.130 4708 Planarity : 0.004 0.038 5280 Dihedral : 5.518 52.900 4024 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.45 % Allowed : 15.50 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3656 helix: 0.96 (0.10), residues: 2464 sheet: -1.70 (0.36), residues: 188 loop : -2.33 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 364 TYR 0.032 0.002 TYR B 191 PHE 0.022 0.002 PHE C 752 TRP 0.022 0.002 TRP D 786 HIS 0.006 0.001 HIS B 765 Details of bonding type rmsd covalent geometry : bond 0.00428 (31188) covalent geometry : angle 0.64235 (42252) SS BOND : bond 0.00545 ( 4) SS BOND : angle 2.65967 ( 8) hydrogen bonds : bond 0.05034 ( 1756) hydrogen bonds : angle 4.05466 ( 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 534 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 386 time to evaluate : 1.114 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 146 ILE cc_start: 0.8731 (mt) cc_final: 0.8491 (tt) REVERT: A 163 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8382 (ptmt) REVERT: A 294 ASN cc_start: 0.8002 (p0) cc_final: 0.7652 (p0) REVERT: A 353 MET cc_start: 0.6099 (mpp) cc_final: 0.5808 (pmm) REVERT: A 402 GLU cc_start: 0.7971 (pp20) cc_final: 0.7564 (pp20) REVERT: A 627 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8547 (mt-10) REVERT: A 689 ASP cc_start: 0.7893 (p0) cc_final: 0.7521 (p0) REVERT: A 732 THR cc_start: 0.8239 (m) cc_final: 0.7956 (p) REVERT: A 758 MET cc_start: 0.9196 (mtp) cc_final: 0.8968 (mtm) REVERT: A 804 LEU cc_start: 0.8841 (tp) cc_final: 0.8595 (mt) REVERT: A 817 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8487 (mm) REVERT: A 863 MET cc_start: 0.8639 (mmt) cc_final: 0.8298 (mmt) REVERT: A 897 ARG cc_start: 0.8777 (mtt180) cc_final: 0.7690 (mmt180) REVERT: A 988 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6334 (pm20) REVERT: A 989 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.7320 (t0) REVERT: A 1047 ASN cc_start: 0.6710 (m-40) cc_final: 0.6301 (t0) REVERT: B 123 ASP cc_start: 0.7071 (m-30) cc_final: 0.6039 (p0) REVERT: B 163 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8376 (ptmt) REVERT: B 294 ASN cc_start: 0.8007 (p0) cc_final: 0.7658 (p0) REVERT: B 353 MET cc_start: 0.6121 (mpp) cc_final: 0.5825 (pmm) REVERT: B 364 ARG cc_start: 0.7327 (tpm170) cc_final: 0.6771 (ttm170) REVERT: B 402 GLU cc_start: 0.7960 (pp20) cc_final: 0.7554 (pp20) REVERT: B 574 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8327 (tppt) REVERT: B 616 GLU cc_start: 0.8211 (tp30) cc_final: 0.7959 (tt0) REVERT: B 627 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8533 (mt-10) REVERT: B 689 ASP cc_start: 0.7864 (p0) cc_final: 0.7489 (p0) REVERT: B 732 THR cc_start: 0.8234 (m) cc_final: 0.7944 (p) REVERT: B 758 MET cc_start: 0.9188 (mtp) cc_final: 0.8961 (mtm) REVERT: B 804 LEU cc_start: 0.8840 (tp) cc_final: 0.8592 (mt) REVERT: B 817 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8509 (mm) REVERT: B 863 MET cc_start: 0.8639 (mmt) cc_final: 0.8301 (mmt) REVERT: B 897 ARG cc_start: 0.8768 (mtt180) cc_final: 0.7677 (mmt180) REVERT: B 988 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6278 (pm20) REVERT: B 989 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.7306 (t0) REVERT: B 1047 ASN cc_start: 0.6737 (m-40) cc_final: 0.6305 (t0) REVERT: C 146 ILE cc_start: 0.8728 (mt) cc_final: 0.8488 (tt) REVERT: C 163 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8371 (ptmt) REVERT: C 294 ASN cc_start: 0.8014 (p0) cc_final: 0.7638 (p0) REVERT: C 353 MET cc_start: 0.6111 (mpp) cc_final: 0.5819 (pmm) REVERT: C 364 ARG cc_start: 0.7361 (tpm170) cc_final: 0.6811 (ttm170) REVERT: C 402 GLU cc_start: 0.7965 (pp20) cc_final: 0.7556 (pp20) REVERT: C 574 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8329 (tppt) REVERT: C 616 GLU cc_start: 0.8183 (tp30) cc_final: 0.7944 (tt0) REVERT: C 627 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8541 (mt-10) REVERT: C 689 ASP cc_start: 0.7885 (p0) cc_final: 0.7509 (p0) REVERT: C 732 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7926 (p) REVERT: C 758 MET cc_start: 0.9176 (mtp) cc_final: 0.8945 (mtm) REVERT: C 804 LEU cc_start: 0.8818 (tp) cc_final: 0.8592 (mt) REVERT: C 817 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8491 (mm) REVERT: C 863 MET cc_start: 0.8639 (mmt) cc_final: 0.8300 (mmt) REVERT: C 897 ARG cc_start: 0.8778 (mtt180) cc_final: 0.7688 (mmt180) REVERT: C 988 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6266 (pm20) REVERT: C 989 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.7304 (t0) REVERT: C 1047 ASN cc_start: 0.6704 (m-40) cc_final: 0.6302 (t0) REVERT: D 123 ASP cc_start: 0.7042 (m-30) cc_final: 0.6013 (p0) REVERT: D 163 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8379 (ptmt) REVERT: D 294 ASN cc_start: 0.8009 (p0) cc_final: 0.7653 (p0) REVERT: D 353 MET cc_start: 0.6106 (mpp) cc_final: 0.5814 (pmm) REVERT: D 364 ARG cc_start: 0.7336 (tpm170) cc_final: 0.6781 (ttm170) REVERT: D 402 GLU cc_start: 0.7963 (pp20) cc_final: 0.7554 (pp20) REVERT: D 574 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8333 (tppt) REVERT: D 616 GLU cc_start: 0.8182 (tp30) cc_final: 0.7939 (tt0) REVERT: D 689 ASP cc_start: 0.7889 (p0) cc_final: 0.7517 (p0) REVERT: D 732 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7934 (p) REVERT: D 758 MET cc_start: 0.9189 (mtp) cc_final: 0.8961 (mtm) REVERT: D 804 LEU cc_start: 0.8830 (tp) cc_final: 0.8582 (mt) REVERT: D 817 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8487 (mm) REVERT: D 897 ARG cc_start: 0.8769 (mtt180) cc_final: 0.7680 (mmt180) REVERT: D 988 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6314 (pm20) REVERT: D 989 ASN cc_start: 0.7568 (OUTLIER) cc_final: 0.7324 (t0) REVERT: D 1047 ASN cc_start: 0.6707 (m-40) cc_final: 0.6294 (t0) outliers start: 148 outliers final: 48 residues processed: 496 average time/residue: 0.6355 time to fit residues: 371.9991 Evaluate side-chains 398 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 330 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 488 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 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 817 LEU 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 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 817 LEU 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 201 ILE 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 732 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 817 LEU 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 C residue 989 ASN 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 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 732 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 134 optimal weight: 0.6980 chunk 349 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 348 optimal weight: 1.9990 chunk 340 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 336 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4123 r_free = 0.4123 target = 0.170173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123913 restraints weight = 47515.220| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.38 r_work: 0.3365 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3833 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= 0.138 Angle : 0.626 13.482 42260 Z= 0.315 Chirality : 0.041 0.196 4708 Planarity : 0.004 0.038 5280 Dihedral : 5.170 57.261 4024 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.06 % Allowed : 16.89 % Favored : 79.06 % 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: 0.20 (0.14), residues: 3656 helix: 1.21 (0.11), residues: 2464 sheet: -1.45 (0.35), residues: 200 loop : -2.29 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 167 TYR 0.019 0.001 TYR B 191 PHE 0.015 0.001 PHE A 165 TRP 0.025 0.002 TRP C 786 HIS 0.004 0.001 HIS B 765 Details of bonding type rmsd covalent geometry : bond 0.00322 (31188) covalent geometry : angle 0.62554 (42252) SS BOND : bond 0.00433 ( 4) SS BOND : angle 1.79027 ( 8) hydrogen bonds : bond 0.04360 ( 1756) hydrogen bonds : angle 3.89683 ( 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 505 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 370 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7116 (m-30) cc_final: 0.5976 (p0) REVERT: A 163 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8370 (ptmt) REVERT: A 294 ASN cc_start: 0.8001 (p0) cc_final: 0.7641 (p0) REVERT: A 353 MET cc_start: 0.6198 (mpp) cc_final: 0.5893 (pmm) REVERT: A 364 ARG cc_start: 0.7533 (tpp-160) cc_final: 0.7092 (mmm-85) REVERT: A 402 GLU cc_start: 0.7745 (pp20) cc_final: 0.7538 (pp20) REVERT: A 480 ASN cc_start: 0.7756 (m-40) cc_final: 0.7293 (m-40) REVERT: A 507 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7173 (tpm170) REVERT: A 627 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8518 (mt-10) REVERT: A 689 ASP cc_start: 0.7849 (p0) cc_final: 0.7471 (p0) REVERT: A 726 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7459 (m-10) REVERT: A 732 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7912 (p) REVERT: A 758 MET cc_start: 0.9212 (mtp) cc_final: 0.8971 (mtm) REVERT: A 797 LEU cc_start: 0.7065 (pt) cc_final: 0.6431 (mt) REVERT: A 804 LEU cc_start: 0.8738 (tp) cc_final: 0.8513 (mt) REVERT: A 897 ARG cc_start: 0.8637 (mtt180) cc_final: 0.7518 (mmt180) REVERT: A 988 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6265 (pm20) REVERT: A 989 ASN cc_start: 0.7534 (OUTLIER) cc_final: 0.7324 (t0) REVERT: A 1023 MET cc_start: 0.6256 (mmp) cc_final: 0.4361 (ttm) REVERT: A 1047 ASN cc_start: 0.6733 (m-40) cc_final: 0.6274 (t0) REVERT: A 1051 GLU cc_start: 0.8172 (tp30) cc_final: 0.7959 (tp30) REVERT: B 123 ASP cc_start: 0.7117 (m-30) cc_final: 0.5981 (p0) REVERT: B 163 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8363 (ptmt) REVERT: B 294 ASN cc_start: 0.7998 (p0) cc_final: 0.7639 (p0) REVERT: B 353 MET cc_start: 0.6241 (mpp) cc_final: 0.5941 (pmm) REVERT: B 402 GLU cc_start: 0.7747 (pp20) cc_final: 0.7542 (pp20) REVERT: B 507 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7179 (tpm170) REVERT: B 627 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8538 (mt-10) REVERT: B 689 ASP cc_start: 0.7841 (p0) cc_final: 0.7463 (p0) REVERT: B 726 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7430 (m-10) REVERT: B 732 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7916 (p) REVERT: B 758 MET cc_start: 0.9201 (mtp) cc_final: 0.8958 (mtm) REVERT: B 797 LEU cc_start: 0.7077 (pt) cc_final: 0.6434 (mt) REVERT: B 804 LEU cc_start: 0.8735 (tp) cc_final: 0.8508 (mt) REVERT: B 897 ARG cc_start: 0.8634 (mtt180) cc_final: 0.7502 (mmt180) REVERT: B 988 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6256 (pm20) REVERT: B 989 ASN cc_start: 0.7534 (OUTLIER) cc_final: 0.7326 (t0) REVERT: B 1023 MET cc_start: 0.6271 (mmp) cc_final: 0.4376 (ttm) REVERT: B 1047 ASN cc_start: 0.6794 (m-40) cc_final: 0.6328 (t0) REVERT: B 1051 GLU cc_start: 0.8193 (tp30) cc_final: 0.7986 (tp30) REVERT: C 123 ASP cc_start: 0.7117 (m-30) cc_final: 0.5979 (p0) REVERT: C 163 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8379 (ptmt) REVERT: C 294 ASN cc_start: 0.7983 (p0) cc_final: 0.7635 (p0) REVERT: C 353 MET cc_start: 0.6305 (mpp) cc_final: 0.6003 (pmm) REVERT: C 402 GLU cc_start: 0.7750 (pp20) cc_final: 0.7536 (pp20) REVERT: C 507 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7142 (tpm170) REVERT: C 627 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8539 (mt-10) REVERT: C 689 ASP cc_start: 0.7835 (p0) cc_final: 0.7459 (p0) REVERT: C 726 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7456 (m-10) REVERT: C 732 THR cc_start: 0.8184 (m) cc_final: 0.7902 (p) REVERT: C 758 MET cc_start: 0.9196 (mtp) cc_final: 0.8953 (mtm) REVERT: C 797 LEU cc_start: 0.7090 (pt) cc_final: 0.6420 (mt) REVERT: C 804 LEU cc_start: 0.8724 (tp) cc_final: 0.8509 (mt) REVERT: C 897 ARG cc_start: 0.8639 (mtt180) cc_final: 0.7515 (mmt180) REVERT: C 988 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6273 (pm20) REVERT: C 989 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.7332 (t0) REVERT: C 1023 MET cc_start: 0.6244 (mmp) cc_final: 0.4379 (ttm) REVERT: C 1047 ASN cc_start: 0.6771 (m-40) cc_final: 0.6296 (t0) REVERT: C 1051 GLU cc_start: 0.8195 (tp30) cc_final: 0.7989 (tp30) REVERT: D 123 ASP cc_start: 0.7120 (m-30) cc_final: 0.5977 (p0) REVERT: D 153 LYS cc_start: 0.5316 (mmmt) cc_final: 0.5115 (pmtt) REVERT: D 163 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8382 (ptmt) REVERT: D 294 ASN cc_start: 0.7992 (p0) cc_final: 0.7634 (p0) REVERT: D 353 MET cc_start: 0.6194 (mpp) cc_final: 0.5892 (pmm) REVERT: D 402 GLU cc_start: 0.7762 (pp20) cc_final: 0.7550 (pp20) REVERT: D 507 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7181 (tpm170) REVERT: D 627 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8541 (mt-10) REVERT: D 689 ASP cc_start: 0.7841 (p0) cc_final: 0.7466 (p0) REVERT: D 726 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7443 (m-10) REVERT: D 732 THR cc_start: 0.8193 (m) cc_final: 0.7911 (p) REVERT: D 758 MET cc_start: 0.9214 (mtp) cc_final: 0.8971 (mtm) REVERT: D 797 LEU cc_start: 0.7070 (pt) cc_final: 0.6432 (mt) REVERT: D 804 LEU cc_start: 0.8738 (tp) cc_final: 0.8510 (mt) REVERT: D 897 ARG cc_start: 0.8652 (mtt180) cc_final: 0.7524 (mmt180) REVERT: D 988 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6274 (pm20) REVERT: D 989 ASN cc_start: 0.7528 (OUTLIER) cc_final: 0.7318 (t0) REVERT: D 1023 MET cc_start: 0.6257 (mmp) cc_final: 0.4384 (ttm) REVERT: D 1047 ASN cc_start: 0.6758 (m-40) cc_final: 0.6287 (t0) REVERT: D 1051 GLU cc_start: 0.8172 (tp30) cc_final: 0.7963 (tp30) outliers start: 135 outliers final: 56 residues processed: 467 average time/residue: 0.6232 time to fit residues: 345.9890 Evaluate side-chains 412 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 334 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 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 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 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 323 LYS 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 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 323 LYS 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 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 859 MET 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 C residue 989 ASN 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 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 726 TYR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 323 optimal weight: 1.9990 chunk 344 optimal weight: 6.9990 chunk 182 optimal weight: 0.2980 chunk 117 optimal weight: 0.4980 chunk 303 optimal weight: 1.9990 chunk 360 optimal weight: 0.8980 chunk 187 optimal weight: 20.0000 chunk 214 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 98 optimal weight: 0.4980 chunk 239 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 GLN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.172766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125819 restraints weight = 47172.496| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.43 r_work: 0.3401 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31192 Z= 0.117 Angle : 0.605 13.651 42260 Z= 0.304 Chirality : 0.040 0.133 4708 Planarity : 0.004 0.038 5280 Dihedral : 4.925 50.209 4024 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.88 % Allowed : 17.91 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.44 (0.14), residues: 3656 helix: 1.39 (0.11), residues: 2476 sheet: -1.43 (0.38), residues: 188 loop : -2.22 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 167 TYR 0.039 0.001 TYR D 191 PHE 0.012 0.001 PHE A 165 TRP 0.027 0.001 TRP B 786 HIS 0.003 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00263 (31188) covalent geometry : angle 0.60349 (42252) SS BOND : bond 0.00346 ( 4) SS BOND : angle 2.63120 ( 8) hydrogen bonds : bond 0.03866 ( 1756) hydrogen bonds : angle 3.79846 ( 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 472 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 343 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7104 (m-30) cc_final: 0.6010 (p0) REVERT: A 163 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8382 (ptmt) REVERT: A 294 ASN cc_start: 0.7952 (p0) cc_final: 0.7596 (p0) REVERT: A 353 MET cc_start: 0.6219 (mpp) cc_final: 0.5906 (pmm) REVERT: A 364 ARG cc_start: 0.7472 (tpp-160) cc_final: 0.7105 (ttm170) REVERT: A 402 GLU cc_start: 0.7786 (pp20) cc_final: 0.7565 (pp20) REVERT: A 457 ASP cc_start: 0.7428 (p0) cc_final: 0.7099 (p0) REVERT: A 459 GLN cc_start: 0.6760 (mp10) cc_final: 0.6352 (mm-40) REVERT: A 480 ASN cc_start: 0.7553 (m-40) cc_final: 0.7128 (m-40) REVERT: A 627 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8495 (mt-10) REVERT: A 666 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8562 (mt0) REVERT: A 689 ASP cc_start: 0.7784 (p0) cc_final: 0.7466 (p0) REVERT: A 726 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7534 (m-10) REVERT: A 732 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7826 (p) REVERT: A 758 MET cc_start: 0.9199 (mtp) cc_final: 0.8991 (mtm) REVERT: A 797 LEU cc_start: 0.7281 (pt) cc_final: 0.6648 (mt) REVERT: A 804 LEU cc_start: 0.8709 (tp) cc_final: 0.8471 (mt) REVERT: A 863 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8307 (mmt) REVERT: A 897 ARG cc_start: 0.8625 (mtt180) cc_final: 0.7488 (mmt180) REVERT: A 953 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8196 (mt-10) REVERT: A 985 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7312 (mp) REVERT: A 988 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6193 (pm20) REVERT: A 1023 MET cc_start: 0.6269 (mmp) cc_final: 0.4352 (ttm) REVERT: A 1047 ASN cc_start: 0.6680 (m-40) cc_final: 0.6281 (t0) REVERT: A 1051 GLU cc_start: 0.8144 (tp30) cc_final: 0.7885 (tp30) REVERT: B 123 ASP cc_start: 0.7051 (m-30) cc_final: 0.5950 (p0) REVERT: B 163 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8350 (ptmt) REVERT: B 294 ASN cc_start: 0.7934 (p0) cc_final: 0.7575 (p0) REVERT: B 353 MET cc_start: 0.6206 (mpp) cc_final: 0.5894 (pmm) REVERT: B 364 ARG cc_start: 0.7354 (tpm170) cc_final: 0.6761 (ttm110) REVERT: B 402 GLU cc_start: 0.7788 (pp20) cc_final: 0.7567 (pp20) REVERT: B 457 ASP cc_start: 0.7385 (p0) cc_final: 0.7032 (p0) REVERT: B 459 GLN cc_start: 0.6771 (mp10) cc_final: 0.6372 (mm-40) REVERT: B 480 ASN cc_start: 0.7861 (m-40) cc_final: 0.7357 (m-40) REVERT: B 496 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7625 (mp) REVERT: B 627 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: B 666 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8556 (mt0) REVERT: B 689 ASP cc_start: 0.7788 (p0) cc_final: 0.7473 (p0) REVERT: B 726 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7523 (m-10) REVERT: B 732 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7843 (p) REVERT: B 758 MET cc_start: 0.9204 (mtp) cc_final: 0.8997 (mtm) REVERT: B 797 LEU cc_start: 0.7292 (pt) cc_final: 0.6653 (mt) REVERT: B 804 LEU cc_start: 0.8699 (tp) cc_final: 0.8451 (mt) REVERT: B 863 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8293 (mmt) REVERT: B 897 ARG cc_start: 0.8615 (mtt180) cc_final: 0.7472 (mmt180) REVERT: B 953 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8207 (mt-10) REVERT: B 985 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7311 (mp) REVERT: B 988 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6187 (pm20) REVERT: B 1023 MET cc_start: 0.6280 (mmp) cc_final: 0.4367 (ttm) REVERT: B 1047 ASN cc_start: 0.6726 (m-40) cc_final: 0.6300 (t0) REVERT: B 1051 GLU cc_start: 0.8100 (tp30) cc_final: 0.7845 (tp30) REVERT: C 163 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8366 (ptmt) REVERT: C 294 ASN cc_start: 0.7935 (p0) cc_final: 0.7591 (p0) REVERT: C 353 MET cc_start: 0.6221 (mpp) cc_final: 0.5908 (pmm) REVERT: C 364 ARG cc_start: 0.7369 (tpm170) cc_final: 0.6772 (ttm110) REVERT: C 402 GLU cc_start: 0.7775 (pp20) cc_final: 0.7548 (pp20) REVERT: C 457 ASP cc_start: 0.7210 (p0) cc_final: 0.6861 (p0) REVERT: C 459 GLN cc_start: 0.6775 (mp10) cc_final: 0.6370 (mm-40) REVERT: C 480 ASN cc_start: 0.7830 (m-40) cc_final: 0.7318 (m-40) REVERT: C 627 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: C 666 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8561 (mt0) REVERT: C 689 ASP cc_start: 0.7783 (p0) cc_final: 0.7467 (p0) REVERT: C 726 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7529 (m-10) REVERT: C 758 MET cc_start: 0.9190 (mtp) cc_final: 0.8982 (mtm) REVERT: C 797 LEU cc_start: 0.7216 (pt) cc_final: 0.6597 (mt) REVERT: C 804 LEU cc_start: 0.8694 (tp) cc_final: 0.8467 (mt) REVERT: C 863 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8307 (mmt) REVERT: C 897 ARG cc_start: 0.8628 (mtt180) cc_final: 0.7488 (mmt180) REVERT: C 985 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7309 (mp) REVERT: C 988 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6204 (pm20) REVERT: C 1023 MET cc_start: 0.6263 (mmp) cc_final: 0.4350 (ttm) REVERT: C 1047 ASN cc_start: 0.6710 (m-40) cc_final: 0.6317 (t0) REVERT: C 1051 GLU cc_start: 0.8147 (tp30) cc_final: 0.7890 (tp30) REVERT: D 123 ASP cc_start: 0.7035 (m-30) cc_final: 0.5909 (p0) REVERT: D 163 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8364 (ptmt) REVERT: D 186 TYR cc_start: 0.7108 (m-80) cc_final: 0.6769 (m-80) REVERT: D 294 ASN cc_start: 0.7946 (p0) cc_final: 0.7594 (p0) REVERT: D 353 MET cc_start: 0.6198 (mpp) cc_final: 0.5891 (pmm) REVERT: D 364 ARG cc_start: 0.7359 (tpm170) cc_final: 0.6757 (ttm110) REVERT: D 402 GLU cc_start: 0.7778 (pp20) cc_final: 0.7548 (pp20) REVERT: D 457 ASP cc_start: 0.7199 (p0) cc_final: 0.6844 (p0) REVERT: D 459 GLN cc_start: 0.6784 (mp10) cc_final: 0.6332 (mm-40) REVERT: D 480 ASN cc_start: 0.7830 (m-40) cc_final: 0.7318 (m-40) REVERT: D 666 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8554 (mt0) REVERT: D 689 ASP cc_start: 0.7794 (p0) cc_final: 0.7478 (p0) REVERT: D 726 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7523 (m-10) REVERT: D 758 MET cc_start: 0.9200 (mtp) cc_final: 0.8990 (mtm) REVERT: D 797 LEU cc_start: 0.7275 (pt) cc_final: 0.6640 (mt) REVERT: D 804 LEU cc_start: 0.8703 (tp) cc_final: 0.8459 (mt) REVERT: D 863 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8306 (mmt) REVERT: D 897 ARG cc_start: 0.8638 (mtt180) cc_final: 0.7491 (mmt180) REVERT: D 985 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7345 (mp) REVERT: D 988 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6193 (pm20) REVERT: D 1023 MET cc_start: 0.6261 (mmp) cc_final: 0.4357 (ttm) REVERT: D 1047 ASN cc_start: 0.6696 (m-40) cc_final: 0.6283 (t0) REVERT: D 1051 GLU cc_start: 0.8137 (tp30) cc_final: 0.7878 (tp30) outliers start: 129 outliers final: 33 residues processed: 431 average time/residue: 0.6712 time to fit residues: 341.4755 Evaluate side-chains 391 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 332 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 GLU 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 732 THR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 496 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 732 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 146 ILE 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 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 726 TYR Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 988 GLU 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 491 GLU 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 666 GLN Chi-restraints excluded: chain D residue 726 TYR Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 929 CYS 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: 4.9990 chunk 44 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 351 optimal weight: 0.5980 chunk 246 optimal weight: 2.9990 chunk 341 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 51 optimal weight: 0.0470 chunk 11 optimal weight: 6.9990 chunk 242 optimal weight: 0.9980 chunk 295 optimal weight: 0.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** 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 = 0.4145 r_free = 0.4145 target = 0.172603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125790 restraints weight = 47117.517| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.37 r_work: 0.3398 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31192 Z= 0.124 Angle : 0.612 14.394 42260 Z= 0.306 Chirality : 0.040 0.148 4708 Planarity : 0.003 0.040 5280 Dihedral : 4.835 50.034 4024 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.16 % Allowed : 18.81 % Favored : 78.03 % 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: 0.66 (0.14), residues: 3656 helix: 1.58 (0.11), residues: 2436 sheet: -1.36 (0.38), residues: 188 loop : -2.04 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1079 TYR 0.028 0.001 TYR C 191 PHE 0.013 0.001 PHE C 165 TRP 0.029 0.001 TRP C 786 HIS 0.004 0.001 HIS D 500 Details of bonding type rmsd covalent geometry : bond 0.00286 (31188) covalent geometry : angle 0.61150 (42252) SS BOND : bond 0.00471 ( 4) SS BOND : angle 2.44007 ( 8) hydrogen bonds : bond 0.03928 ( 1756) hydrogen bonds : angle 3.79680 ( 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 495 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 390 time to evaluate : 1.219 Fit side-chains REVERT: A 123 ASP cc_start: 0.7034 (m-30) cc_final: 0.6000 (p0) REVERT: A 163 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8383 (ptmt) REVERT: A 189 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6427 (ttm) REVERT: A 294 ASN cc_start: 0.7956 (p0) cc_final: 0.7598 (p0) REVERT: A 353 MET cc_start: 0.6246 (mpp) cc_final: 0.5940 (pmm) REVERT: A 402 GLU cc_start: 0.7745 (pp20) cc_final: 0.7502 (pp20) REVERT: A 457 ASP cc_start: 0.7345 (p0) cc_final: 0.6991 (p0) REVERT: A 459 GLN cc_start: 0.6780 (mp10) cc_final: 0.6357 (mm-40) REVERT: A 480 ASN cc_start: 0.7474 (m-40) cc_final: 0.7130 (m-40) REVERT: A 616 GLU cc_start: 0.8223 (tt0) cc_final: 0.8003 (tm-30) REVERT: A 666 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8492 (mt0) REVERT: A 689 ASP cc_start: 0.7779 (p0) cc_final: 0.7462 (p0) REVERT: A 726 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7553 (m-10) REVERT: A 732 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7524 (p) REVERT: A 758 MET cc_start: 0.9214 (mtp) cc_final: 0.9010 (mtm) REVERT: A 797 LEU cc_start: 0.7238 (pt) cc_final: 0.6600 (mt) REVERT: A 804 LEU cc_start: 0.8699 (tp) cc_final: 0.8462 (mt) REVERT: A 863 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8293 (mmt) REVERT: A 897 ARG cc_start: 0.8629 (mtt180) cc_final: 0.7506 (mmt180) REVERT: A 950 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7922 (ttm170) REVERT: A 1023 MET cc_start: 0.6197 (mmp) cc_final: 0.4308 (ttt) REVERT: A 1046 ARG cc_start: 0.7842 (ttm170) cc_final: 0.7263 (mtp85) REVERT: A 1051 GLU cc_start: 0.8151 (tp30) cc_final: 0.7856 (tp30) REVERT: B 123 ASP cc_start: 0.7106 (m-30) cc_final: 0.6068 (p0) REVERT: B 163 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8386 (ptmt) REVERT: B 189 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6396 (ttm) REVERT: B 294 ASN cc_start: 0.7939 (p0) cc_final: 0.7582 (p0) REVERT: B 353 MET cc_start: 0.6241 (mpp) cc_final: 0.5935 (pmm) REVERT: B 364 ARG cc_start: 0.7358 (tpm170) cc_final: 0.6711 (ttp-110) REVERT: B 402 GLU cc_start: 0.7756 (pp20) cc_final: 0.7523 (pp20) REVERT: B 457 ASP cc_start: 0.7346 (p0) cc_final: 0.6972 (p0) REVERT: B 459 GLN cc_start: 0.6818 (mp10) cc_final: 0.6480 (mm-40) REVERT: B 480 ASN cc_start: 0.7798 (m-40) cc_final: 0.7370 (m-40) REVERT: B 616 GLU cc_start: 0.8246 (tt0) cc_final: 0.8015 (tm-30) REVERT: B 666 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8499 (mt0) REVERT: B 689 ASP cc_start: 0.7791 (p0) cc_final: 0.7479 (p0) REVERT: B 726 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7541 (m-10) REVERT: B 732 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7531 (p) REVERT: B 797 LEU cc_start: 0.7243 (pt) cc_final: 0.6602 (mt) REVERT: B 804 LEU cc_start: 0.8698 (tp) cc_final: 0.8457 (mt) REVERT: B 863 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8274 (mmt) REVERT: B 897 ARG cc_start: 0.8634 (mtt180) cc_final: 0.7504 (mmt180) REVERT: B 942 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: B 1023 MET cc_start: 0.6212 (mmp) cc_final: 0.4321 (ttt) REVERT: B 1047 ASN cc_start: 0.6655 (m-40) cc_final: 0.6245 (t0) REVERT: B 1051 GLU cc_start: 0.8145 (tp30) cc_final: 0.7918 (tp30) REVERT: C 123 ASP cc_start: 0.7073 (m-30) cc_final: 0.6088 (p0) REVERT: C 163 LYS cc_start: 0.8674 (ttpt) cc_final: 0.8360 (ptmt) REVERT: C 189 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6446 (ttm) REVERT: C 294 ASN cc_start: 0.7935 (p0) cc_final: 0.7593 (p0) REVERT: C 353 MET cc_start: 0.6256 (mpp) cc_final: 0.5949 (pmm) REVERT: C 364 ARG cc_start: 0.7329 (tpm170) cc_final: 0.6674 (ttp-110) REVERT: C 402 GLU cc_start: 0.7734 (pp20) cc_final: 0.7511 (pp20) REVERT: C 457 ASP cc_start: 0.7345 (p0) cc_final: 0.6977 (p0) REVERT: C 459 GLN cc_start: 0.6830 (mp10) cc_final: 0.6449 (mm-40) REVERT: C 480 ASN cc_start: 0.7790 (m-40) cc_final: 0.7355 (m-40) REVERT: C 627 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8513 (mt-10) REVERT: C 666 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8394 (mt0) REVERT: C 689 ASP cc_start: 0.7780 (p0) cc_final: 0.7468 (p0) REVERT: C 726 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.7546 (m-10) REVERT: C 732 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7581 (p) REVERT: C 758 MET cc_start: 0.9205 (mtp) cc_final: 0.9002 (mtm) REVERT: C 797 LEU cc_start: 0.7227 (pt) cc_final: 0.6585 (mt) REVERT: C 804 LEU cc_start: 0.8696 (tp) cc_final: 0.8467 (mt) REVERT: C 863 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8282 (mmt) REVERT: C 897 ARG cc_start: 0.8648 (mtt180) cc_final: 0.7528 (mmt180) REVERT: C 942 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: C 1023 MET cc_start: 0.6201 (mmp) cc_final: 0.4304 (ttt) REVERT: C 1047 ASN cc_start: 0.6642 (m-40) cc_final: 0.6247 (t0) REVERT: C 1051 GLU cc_start: 0.8164 (tp30) cc_final: 0.7937 (tp30) REVERT: D 123 ASP cc_start: 0.7016 (m-30) cc_final: 0.5985 (p0) REVERT: D 163 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8417 (ptmt) REVERT: D 186 TYR cc_start: 0.7027 (m-80) cc_final: 0.6734 (m-80) REVERT: D 294 ASN cc_start: 0.7931 (p0) cc_final: 0.7566 (p0) REVERT: D 353 MET cc_start: 0.6236 (mpp) cc_final: 0.5932 (pmm) REVERT: D 364 ARG cc_start: 0.7360 (tpm170) cc_final: 0.6708 (ttp-110) REVERT: D 402 GLU cc_start: 0.7752 (pp20) cc_final: 0.7529 (pp20) REVERT: D 457 ASP cc_start: 0.7360 (p0) cc_final: 0.7032 (p0) REVERT: D 459 GLN cc_start: 0.6828 (mp10) cc_final: 0.6463 (mm-40) REVERT: D 480 ASN cc_start: 0.7790 (m-40) cc_final: 0.7355 (m-40) REVERT: D 616 GLU cc_start: 0.8191 (tt0) cc_final: 0.7971 (tm-30) REVERT: D 627 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8539 (mt-10) REVERT: D 666 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8487 (mt0) REVERT: D 689 ASP cc_start: 0.7796 (p0) cc_final: 0.7487 (p0) REVERT: D 726 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7545 (m-10) REVERT: D 732 THR cc_start: 0.7936 (OUTLIER) cc_final: 0.7571 (p) REVERT: D 758 MET cc_start: 0.9219 (mtp) cc_final: 0.9015 (mtm) REVERT: D 797 LEU cc_start: 0.7232 (pt) cc_final: 0.6593 (mt) REVERT: D 804 LEU cc_start: 0.8700 (tp) cc_final: 0.8453 (mt) REVERT: D 863 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8271 (mmt) REVERT: D 897 ARG cc_start: 0.8656 (mtt180) cc_final: 0.7531 (mmt180) REVERT: D 942 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: D 1023 MET cc_start: 0.6185 (mmp) cc_final: 0.4307 (ttt) REVERT: D 1046 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7256 (mtp85) REVERT: D 1051 GLU cc_start: 0.8153 (tp30) cc_final: 0.7925 (tp30) outliers start: 105 outliers final: 43 residues processed: 467 average time/residue: 0.6275 time to fit residues: 348.5435 Evaluate side-chains 404 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 336 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 405 SER Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 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 732 THR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 950 ARG Chi-restraints excluded: chain B residue 148 VAL 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 405 SER 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 666 GLN Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain C residue 148 VAL 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 338 VAL 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 726 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL 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 405 SER 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 726 TYR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 942 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 339 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 326 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 78 optimal weight: 0.0870 chunk 28 optimal weight: 10.0000 chunk 265 optimal weight: 0.7980 chunk 255 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 overall best weight: 2.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4108 r_free = 0.4108 target = 0.168649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122370 restraints weight = 47324.988| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.40 r_work: 0.3333 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31192 Z= 0.182 Angle : 0.681 14.278 42260 Z= 0.342 Chirality : 0.043 0.284 4708 Planarity : 0.004 0.047 5280 Dihedral : 5.054 51.280 4024 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.52 % Allowed : 19.38 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3656 helix: 1.40 (0.11), residues: 2432 sheet: -1.40 (0.37), residues: 188 loop : -2.02 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1079 TYR 0.042 0.002 TYR D 191 PHE 0.019 0.001 PHE A1013 TRP 0.032 0.002 TRP C 786 HIS 0.005 0.001 HIS C 765 Details of bonding type rmsd covalent geometry : bond 0.00444 (31188) covalent geometry : angle 0.68047 (42252) SS BOND : bond 0.00509 ( 4) SS BOND : angle 2.72857 ( 8) hydrogen bonds : bond 0.04924 ( 1756) hydrogen bonds : angle 3.99083 ( 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 459 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 342 time to evaluate : 1.192 Fit side-chains REVERT: A 163 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8448 (ptmt) REVERT: A 294 ASN cc_start: 0.7968 (p0) cc_final: 0.7594 (p0) REVERT: A 353 MET cc_start: 0.6395 (mpp) cc_final: 0.6073 (pmm) REVERT: A 364 ARG cc_start: 0.7460 (tpp-160) cc_final: 0.7226 (mmm-85) REVERT: A 402 GLU cc_start: 0.7761 (pp20) cc_final: 0.7480 (pp20) REVERT: A 480 ASN cc_start: 0.7825 (m-40) cc_final: 0.7435 (m-40) REVERT: A 507 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7228 (tpm170) REVERT: A 627 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8611 (mt-10) REVERT: A 666 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8489 (mt0) REVERT: A 689 ASP cc_start: 0.7867 (p0) cc_final: 0.7549 (p0) REVERT: A 726 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7482 (m-10) REVERT: A 758 MET cc_start: 0.9229 (mtp) cc_final: 0.9009 (mtm) REVERT: A 804 LEU cc_start: 0.8786 (tp) cc_final: 0.8558 (mt) REVERT: A 897 ARG cc_start: 0.8725 (mtt180) cc_final: 0.7642 (mmt180) REVERT: A 950 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7950 (ttm170) REVERT: A 1051 GLU cc_start: 0.8170 (tp30) cc_final: 0.7915 (tp30) REVERT: B 163 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8404 (ptmt) REVERT: B 189 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6593 (ttm) REVERT: B 294 ASN cc_start: 0.7962 (p0) cc_final: 0.7588 (p0) REVERT: B 353 MET cc_start: 0.6411 (mpp) cc_final: 0.6089 (pmm) REVERT: B 364 ARG cc_start: 0.7551 (tpm170) cc_final: 0.6916 (ttp-110) REVERT: B 402 GLU cc_start: 0.7740 (pp20) cc_final: 0.7426 (pp20) REVERT: B 507 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7231 (tpm170) REVERT: B 574 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8148 (tppt) REVERT: B 616 GLU cc_start: 0.8368 (tt0) cc_final: 0.8143 (tm-30) REVERT: B 627 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8597 (mt-10) REVERT: B 666 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8510 (mt0) REVERT: B 689 ASP cc_start: 0.7871 (p0) cc_final: 0.7556 (p0) REVERT: B 726 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7478 (m-10) REVERT: B 804 LEU cc_start: 0.8784 (tp) cc_final: 0.8558 (mt) REVERT: B 897 ARG cc_start: 0.8708 (mtt180) cc_final: 0.7591 (mmt180) REVERT: B 950 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7960 (ttm170) REVERT: B 1046 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7162 (mtp85) REVERT: B 1051 GLU cc_start: 0.8153 (tp30) cc_final: 0.7894 (tp30) REVERT: C 146 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8274 (tt) REVERT: C 163 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8311 (ptmt) REVERT: C 294 ASN cc_start: 0.7963 (p0) cc_final: 0.7599 (p0) REVERT: C 353 MET cc_start: 0.6331 (mpp) cc_final: 0.6007 (pmm) REVERT: C 364 ARG cc_start: 0.7565 (tpm170) cc_final: 0.6925 (ttp-110) REVERT: C 402 GLU cc_start: 0.7696 (pp20) cc_final: 0.7425 (pp20) REVERT: C 507 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7236 (tpm170) REVERT: C 627 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8614 (mt-10) REVERT: C 666 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8422 (mt0) REVERT: C 689 ASP cc_start: 0.7867 (p0) cc_final: 0.7523 (p0) REVERT: C 726 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: C 758 MET cc_start: 0.9221 (mtp) cc_final: 0.9000 (mtm) REVERT: C 797 LEU cc_start: 0.7060 (pt) cc_final: 0.6304 (mt) REVERT: C 804 LEU cc_start: 0.8757 (tp) cc_final: 0.8535 (mt) REVERT: C 897 ARG cc_start: 0.8716 (mtt180) cc_final: 0.7594 (mmt180) REVERT: C 950 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7954 (ttm170) REVERT: C 1046 ARG cc_start: 0.7784 (ttm170) cc_final: 0.7137 (mtp85) REVERT: C 1051 GLU cc_start: 0.8162 (tp30) cc_final: 0.7904 (tp30) REVERT: D 163 LYS cc_start: 0.8716 (ttpt) cc_final: 0.8396 (ptmt) REVERT: D 189 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6492 (ttm) REVERT: D 294 ASN cc_start: 0.7989 (p0) cc_final: 0.7645 (p0) REVERT: D 353 MET cc_start: 0.6313 (mpp) cc_final: 0.5991 (pmm) REVERT: D 364 ARG cc_start: 0.7533 (tpm170) cc_final: 0.6897 (ttp-110) REVERT: D 402 GLU cc_start: 0.7734 (pp20) cc_final: 0.7467 (pp20) REVERT: D 507 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7239 (tpm170) REVERT: D 574 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8132 (tppt) REVERT: D 616 GLU cc_start: 0.8294 (tt0) cc_final: 0.8090 (tm-30) REVERT: D 627 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8620 (mt-10) REVERT: D 666 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8487 (mt0) REVERT: D 689 ASP cc_start: 0.7852 (p0) cc_final: 0.7536 (p0) REVERT: D 726 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7468 (m-10) REVERT: D 758 MET cc_start: 0.9222 (mtp) cc_final: 0.9003 (mtm) REVERT: D 804 LEU cc_start: 0.8770 (tp) cc_final: 0.8548 (mt) REVERT: D 897 ARG cc_start: 0.8718 (mtt180) cc_final: 0.7600 (mmt180) REVERT: D 950 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7962 (ttm170) REVERT: D 1051 GLU cc_start: 0.8191 (tp30) cc_final: 0.7941 (tp30) outliers start: 117 outliers final: 52 residues processed: 435 average time/residue: 0.6262 time to fit residues: 323.0622 Evaluate side-chains 402 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 325 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER 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 507 ARG 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 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 849 VAL 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 405 SER 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 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 849 VAL 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 146 ILE 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 507 ARG 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 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 859 MET Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 950 ARG Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 405 SER 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 666 GLN 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 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 950 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 24 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 279 optimal weight: 20.0000 chunk 356 optimal weight: 0.6980 chunk 216 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 227 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN A1050 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN D1050 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.171953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124897 restraints weight = 47285.229| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.37 r_work: 0.3388 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 31192 Z= 0.129 Angle : 0.648 15.123 42260 Z= 0.325 Chirality : 0.041 0.240 4708 Planarity : 0.004 0.044 5280 Dihedral : 4.864 49.286 4024 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.64 % Allowed : 20.88 % Favored : 76.47 % 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: 0.50 (0.14), residues: 3656 helix: 1.41 (0.11), residues: 2460 sheet: -1.23 (0.39), residues: 188 loop : -2.11 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 167 TYR 0.040 0.001 TYR D 191 PHE 0.018 0.001 PHE A 165 TRP 0.034 0.001 TRP C 786 HIS 0.003 0.001 HIS D 500 Details of bonding type rmsd covalent geometry : bond 0.00305 (31188) covalent geometry : angle 0.64701 (42252) SS BOND : bond 0.00446 ( 4) SS BOND : angle 2.27166 ( 8) hydrogen bonds : bond 0.03941 ( 1756) hydrogen bonds : angle 3.89450 ( 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 439 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 351 time to evaluate : 1.109 Fit side-chains REVERT: A 123 ASP cc_start: 0.7040 (m-30) cc_final: 0.5991 (p0) REVERT: A 146 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8269 (tt) REVERT: A 163 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8334 (ptmt) REVERT: A 189 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6442 (ttm) REVERT: A 294 ASN cc_start: 0.7934 (p0) cc_final: 0.7568 (p0) REVERT: A 353 MET cc_start: 0.6553 (mpp) cc_final: 0.6226 (pmm) REVERT: A 364 ARG cc_start: 0.7626 (tpp-160) cc_final: 0.7044 (ttp-110) REVERT: A 402 GLU cc_start: 0.7838 (pp20) cc_final: 0.7574 (pp20) REVERT: A 457 ASP cc_start: 0.7503 (p0) cc_final: 0.7154 (p0) REVERT: A 459 GLN cc_start: 0.6762 (mp10) cc_final: 0.6309 (mm-40) REVERT: A 480 ASN cc_start: 0.7633 (m-40) cc_final: 0.7201 (m-40) REVERT: A 627 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8521 (mt-10) REVERT: A 689 ASP cc_start: 0.7778 (p0) cc_final: 0.7466 (p0) REVERT: A 726 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7520 (m-10) REVERT: A 758 MET cc_start: 0.9214 (mtp) cc_final: 0.8999 (mtm) REVERT: A 797 LEU cc_start: 0.7062 (pt) cc_final: 0.6389 (mt) REVERT: A 804 LEU cc_start: 0.8685 (tp) cc_final: 0.8440 (mt) REVERT: A 863 MET cc_start: 0.8648 (mmt) cc_final: 0.8312 (mmt) REVERT: A 897 ARG cc_start: 0.8657 (mtt180) cc_final: 0.7498 (mmt180) REVERT: A 950 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7952 (ttm170) REVERT: A 953 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8217 (mt-10) REVERT: A 1023 MET cc_start: 0.6316 (mmp) cc_final: 0.4548 (ttm) REVERT: A 1051 GLU cc_start: 0.8103 (tp30) cc_final: 0.7810 (tp30) REVERT: A 1079 ARG cc_start: 0.7268 (ttp80) cc_final: 0.7025 (ttm-80) REVERT: B 123 ASP cc_start: 0.7046 (m-30) cc_final: 0.6005 (p0) REVERT: B 163 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8321 (ptmt) REVERT: B 189 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6593 (ttm) REVERT: B 294 ASN cc_start: 0.7925 (p0) cc_final: 0.7560 (p0) REVERT: B 353 MET cc_start: 0.6536 (mpp) cc_final: 0.6205 (pmm) REVERT: B 364 ARG cc_start: 0.7390 (tpm170) cc_final: 0.6822 (ttm110) REVERT: B 396 MET cc_start: 0.6323 (mpm) cc_final: 0.6101 (mpp) REVERT: B 402 GLU cc_start: 0.7797 (pp20) cc_final: 0.7544 (pp20) REVERT: B 457 ASP cc_start: 0.7560 (p0) cc_final: 0.7221 (p0) REVERT: B 459 GLN cc_start: 0.6826 (mp10) cc_final: 0.6390 (mm-40) REVERT: B 480 ASN cc_start: 0.7541 (m-40) cc_final: 0.7129 (m-40) REVERT: B 574 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7810 (tppp) REVERT: B 627 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8507 (mt-10) REVERT: B 689 ASP cc_start: 0.7805 (p0) cc_final: 0.7494 (p0) REVERT: B 726 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7516 (m-10) REVERT: B 797 LEU cc_start: 0.7075 (pt) cc_final: 0.6402 (mt) REVERT: B 804 LEU cc_start: 0.8684 (tp) cc_final: 0.8443 (mt) REVERT: B 863 MET cc_start: 0.8666 (mmt) cc_final: 0.8332 (mmt) REVERT: B 897 ARG cc_start: 0.8655 (mtt180) cc_final: 0.7504 (mmt180) REVERT: B 953 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 1023 MET cc_start: 0.6346 (mmp) cc_final: 0.4578 (ttm) REVERT: B 1051 GLU cc_start: 0.8128 (tp30) cc_final: 0.7821 (tp30) REVERT: B 1079 ARG cc_start: 0.7412 (ttp80) cc_final: 0.7023 (ttm-80) REVERT: C 123 ASP cc_start: 0.7047 (m-30) cc_final: 0.5985 (p0) REVERT: C 158 LYS cc_start: 0.7033 (mppt) cc_final: 0.5680 (pttp) REVERT: C 163 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8371 (ptmt) REVERT: C 189 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6623 (ttm) REVERT: C 294 ASN cc_start: 0.7905 (p0) cc_final: 0.7577 (p0) REVERT: C 353 MET cc_start: 0.6570 (mpp) cc_final: 0.6236 (pmm) REVERT: C 364 ARG cc_start: 0.7400 (tpm170) cc_final: 0.6868 (ttp-110) REVERT: C 402 GLU cc_start: 0.7682 (pp20) cc_final: 0.7450 (pp20) REVERT: C 457 ASP cc_start: 0.7553 (p0) cc_final: 0.7222 (p0) REVERT: C 459 GLN cc_start: 0.6857 (mp10) cc_final: 0.6391 (mm-40) REVERT: C 480 ASN cc_start: 0.7675 (m-40) cc_final: 0.7327 (m-40) REVERT: C 627 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8512 (mt-10) REVERT: C 689 ASP cc_start: 0.7777 (p0) cc_final: 0.7472 (p0) REVERT: C 758 MET cc_start: 0.9200 (mtp) cc_final: 0.8984 (mtm) REVERT: C 797 LEU cc_start: 0.7023 (pt) cc_final: 0.6348 (mt) REVERT: C 804 LEU cc_start: 0.8672 (tp) cc_final: 0.8454 (mt) REVERT: C 863 MET cc_start: 0.8659 (mmt) cc_final: 0.8323 (mmt) REVERT: C 897 ARG cc_start: 0.8659 (mtt180) cc_final: 0.7519 (mmt180) REVERT: C 1023 MET cc_start: 0.6308 (mmp) cc_final: 0.4533 (ttm) REVERT: C 1051 GLU cc_start: 0.8149 (tp30) cc_final: 0.7833 (tp30) REVERT: D 123 ASP cc_start: 0.7023 (m-30) cc_final: 0.5964 (p0) REVERT: D 163 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8315 (ptmt) REVERT: D 189 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6398 (ttm) REVERT: D 294 ASN cc_start: 0.7830 (p0) cc_final: 0.7473 (p0) REVERT: D 353 MET cc_start: 0.6563 (mpp) cc_final: 0.6240 (pmm) REVERT: D 364 ARG cc_start: 0.7394 (tpm170) cc_final: 0.6856 (ttp-110) REVERT: D 402 GLU cc_start: 0.7791 (pp20) cc_final: 0.7541 (pp20) REVERT: D 457 ASP cc_start: 0.7333 (p0) cc_final: 0.6969 (p0) REVERT: D 459 GLN cc_start: 0.6778 (mp10) cc_final: 0.6338 (mm-40) REVERT: D 480 ASN cc_start: 0.7667 (m-40) cc_final: 0.7308 (m-40) REVERT: D 574 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7818 (tppp) REVERT: D 627 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8532 (mt-10) REVERT: D 689 ASP cc_start: 0.7767 (p0) cc_final: 0.7458 (p0) REVERT: D 758 MET cc_start: 0.9212 (mtp) cc_final: 0.8994 (mtm) REVERT: D 797 LEU cc_start: 0.7291 (pt) cc_final: 0.6635 (mt) REVERT: D 804 LEU cc_start: 0.8690 (tp) cc_final: 0.8459 (mt) REVERT: D 863 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8328 (mmt) REVERT: D 897 ARG cc_start: 0.8677 (mtt180) cc_final: 0.7528 (mmt180) REVERT: D 1023 MET cc_start: 0.6304 (mmp) cc_final: 0.4562 (ttm) REVERT: D 1051 GLU cc_start: 0.8104 (tp30) cc_final: 0.7812 (tp30) REVERT: D 1079 ARG cc_start: 0.7411 (ttp80) cc_final: 0.6960 (ttm-80) outliers start: 88 outliers final: 42 residues processed: 416 average time/residue: 0.6297 time to fit residues: 309.8095 Evaluate side-chains 388 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 333 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 146 ILE 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 584 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 628 LEU 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 929 CYS Chi-restraints excluded: chain A residue 950 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 148 VAL 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 405 SER 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 702 ILE Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 VAL 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 588 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 584 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 849 VAL Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 929 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 147 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 304 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 338 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 265 optimal weight: 0.0670 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.169335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122056 restraints weight = 46997.131| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.24 r_work: 0.3350 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4378 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= 0.172 Angle : 0.689 15.046 42260 Z= 0.346 Chirality : 0.043 0.202 4708 Planarity : 0.004 0.044 5280 Dihedral : 4.951 51.156 4024 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.25 % Allowed : 21.88 % Favored : 75.87 % 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: 0.48 (0.14), residues: 3656 helix: 1.39 (0.11), residues: 2432 sheet: -1.30 (0.38), residues: 188 loop : -1.98 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 167 TYR 0.041 0.002 TYR D 191 PHE 0.026 0.002 PHE C 807 TRP 0.036 0.002 TRP A 786 HIS 0.006 0.001 HIS C 500 Details of bonding type rmsd covalent geometry : bond 0.00423 (31188) covalent geometry : angle 0.68851 (42252) SS BOND : bond 0.00515 ( 4) SS BOND : angle 2.64511 ( 8) hydrogen bonds : bond 0.04728 ( 1756) hydrogen bonds : angle 4.01362 ( 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 409 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 334 time to evaluate : 1.153 Fit side-chains REVERT: A 189 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6620 (ttm) REVERT: A 294 ASN cc_start: 0.7968 (p0) cc_final: 0.7624 (p0) REVERT: A 353 MET cc_start: 0.6703 (mpp) cc_final: 0.6359 (pmm) REVERT: A 364 ARG cc_start: 0.7534 (tpp-160) cc_final: 0.7070 (ttp-110) REVERT: A 402 GLU cc_start: 0.7774 (pp20) cc_final: 0.7485 (pp20) REVERT: A 457 ASP cc_start: 0.7613 (p0) cc_final: 0.7240 (OUTLIER) REVERT: A 459 GLN cc_start: 0.6808 (mp10) cc_final: 0.6351 (mm-40) REVERT: A 480 ASN cc_start: 0.7821 (m-40) cc_final: 0.7403 (m-40) REVERT: A 627 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8595 (mt-10) REVERT: A 666 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8545 (pt0) REVERT: A 689 ASP cc_start: 0.7844 (p0) cc_final: 0.7547 (p0) REVERT: A 726 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7493 (m-10) REVERT: A 758 MET cc_start: 0.9215 (mtp) cc_final: 0.8967 (mtm) REVERT: A 804 LEU cc_start: 0.8768 (tp) cc_final: 0.8530 (mt) REVERT: A 897 ARG cc_start: 0.8733 (mtt180) cc_final: 0.7632 (mmt180) REVERT: A 950 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7982 (ttm170) REVERT: A 1023 MET cc_start: 0.6393 (mmp) cc_final: 0.4476 (ttm) REVERT: A 1051 GLU cc_start: 0.8152 (tp30) cc_final: 0.7867 (tp30) REVERT: B 123 ASP cc_start: 0.7095 (m-30) cc_final: 0.6019 (p0) REVERT: B 294 ASN cc_start: 0.7961 (p0) cc_final: 0.7620 (p0) REVERT: B 353 MET cc_start: 0.6694 (mpp) cc_final: 0.6347 (pmm) REVERT: B 364 ARG cc_start: 0.7344 (tpm170) cc_final: 0.6918 (ttm110) REVERT: B 396 MET cc_start: 0.6298 (mpm) cc_final: 0.6082 (mpp) REVERT: B 402 GLU cc_start: 0.7729 (pp20) cc_final: 0.7479 (pp20) REVERT: B 457 ASP cc_start: 0.7688 (p0) cc_final: 0.7380 (p0) REVERT: B 459 GLN cc_start: 0.6843 (mp10) cc_final: 0.6320 (mm-40) REVERT: B 627 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8611 (mt-10) REVERT: B 666 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8523 (pt0) REVERT: B 689 ASP cc_start: 0.7833 (p0) cc_final: 0.7539 (p0) REVERT: B 726 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7489 (m-10) REVERT: B 804 LEU cc_start: 0.8769 (tp) cc_final: 0.8534 (mt) REVERT: B 897 ARG cc_start: 0.8726 (mtt180) cc_final: 0.7628 (mmt180) REVERT: B 1023 MET cc_start: 0.6411 (mmp) cc_final: 0.4479 (ttm) REVERT: B 1051 GLU cc_start: 0.8132 (tp30) cc_final: 0.7837 (tp30) REVERT: C 123 ASP cc_start: 0.7066 (m-30) cc_final: 0.5989 (p0) REVERT: C 146 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8382 (tt) REVERT: C 163 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8390 (ptmt) REVERT: C 189 MET cc_start: 0.7076 (mtm) cc_final: 0.6814 (ttm) REVERT: C 294 ASN cc_start: 0.7925 (p0) cc_final: 0.7585 (p0) REVERT: C 353 MET cc_start: 0.6643 (mpp) cc_final: 0.6300 (pmm) REVERT: C 364 ARG cc_start: 0.7348 (tpm170) cc_final: 0.6797 (ttm110) REVERT: C 402 GLU cc_start: 0.7694 (pp20) cc_final: 0.7440 (pp20) REVERT: C 457 ASP cc_start: 0.7671 (p0) cc_final: 0.7337 (p0) REVERT: C 459 GLN cc_start: 0.6864 (mp10) cc_final: 0.6391 (mm-40) REVERT: C 627 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8617 (mt-10) REVERT: C 666 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8493 (pt0) REVERT: C 689 ASP cc_start: 0.7823 (p0) cc_final: 0.7527 (p0) REVERT: C 758 MET cc_start: 0.9219 (mtp) cc_final: 0.8968 (mtm) REVERT: C 804 LEU cc_start: 0.8749 (tp) cc_final: 0.8528 (mt) REVERT: C 897 ARG cc_start: 0.8729 (mtt180) cc_final: 0.7635 (mmt180) REVERT: C 1023 MET cc_start: 0.6402 (mmp) cc_final: 0.4484 (ttm) REVERT: C 1051 GLU cc_start: 0.8151 (tp30) cc_final: 0.7858 (tp30) REVERT: D 123 ASP cc_start: 0.7089 (m-30) cc_final: 0.6010 (p0) REVERT: D 189 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6555 (ttm) REVERT: D 294 ASN cc_start: 0.7987 (p0) cc_final: 0.7648 (p0) REVERT: D 353 MET cc_start: 0.6683 (mpp) cc_final: 0.6338 (pmm) REVERT: D 402 GLU cc_start: 0.7736 (pp20) cc_final: 0.7483 (pp20) REVERT: D 457 ASP cc_start: 0.7484 (p0) cc_final: 0.7108 (p0) REVERT: D 459 GLN cc_start: 0.6797 (mp10) cc_final: 0.6318 (mm-40) REVERT: D 507 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7242 (tpm170) REVERT: D 627 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8624 (mt-10) REVERT: D 666 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8555 (pt0) REVERT: D 689 ASP cc_start: 0.7833 (p0) cc_final: 0.7538 (p0) REVERT: D 758 MET cc_start: 0.9208 (mtp) cc_final: 0.8957 (mtm) REVERT: D 797 LEU cc_start: 0.7170 (pt) cc_final: 0.6460 (mt) REVERT: D 804 LEU cc_start: 0.8766 (tp) cc_final: 0.8530 (mt) REVERT: D 897 ARG cc_start: 0.8734 (mtt180) cc_final: 0.7634 (mmt180) REVERT: D 1023 MET cc_start: 0.6393 (mmp) cc_final: 0.4475 (ttm) REVERT: D 1051 GLU cc_start: 0.8152 (tp30) cc_final: 0.7868 (tp30) outliers start: 75 outliers final: 50 residues processed: 395 average time/residue: 0.6262 time to fit residues: 294.1174 Evaluate side-chains 389 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 325 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER 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 405 SER Chi-restraints excluded: chain A residue 584 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 783 VAL Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 950 ARG Chi-restraints excluded: chain B residue 121 SER 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 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 702 ILE 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 929 CYS Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 148 VAL 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 702 ILE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 VAL 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 405 SER Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 584 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 783 VAL Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 939 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 167 optimal weight: 1.9990 chunk 325 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 353 optimal weight: 0.8980 chunk 364 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 144 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1050 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.171927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125364 restraints weight = 47268.346| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.28 r_work: 0.3390 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31192 Z= 0.132 Angle : 0.663 15.243 42260 Z= 0.331 Chirality : 0.041 0.238 4708 Planarity : 0.004 0.041 5280 Dihedral : 4.820 47.799 4024 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.89 % Allowed : 22.24 % Favored : 75.87 % 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: 0.55 (0.14), residues: 3656 helix: 1.42 (0.11), residues: 2452 sheet: -1.20 (0.39), residues: 188 loop : -1.98 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 167 TYR 0.036 0.001 TYR C 191 PHE 0.018 0.001 PHE B 165 TRP 0.036 0.002 TRP B 786 HIS 0.004 0.001 HIS C 500 Details of bonding type rmsd covalent geometry : bond 0.00311 (31188) covalent geometry : angle 0.66203 (42252) SS BOND : bond 0.00445 ( 4) SS BOND : angle 2.22717 ( 8) hydrogen bonds : bond 0.04018 ( 1756) hydrogen bonds : angle 3.92739 ( 5232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13363.29 seconds wall clock time: 227 minutes 39.61 seconds (13659.61 seconds total)