Starting phenix.real_space_refine on Thu Jun 26 06:48:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrd_32723/06_2025/7wrd_32723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrd_32723/06_2025/7wrd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wrd_32723/06_2025/7wrd_32723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrd_32723/06_2025/7wrd_32723.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrd_32723/06_2025/7wrd_32723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrd_32723/06_2025/7wrd_32723.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 20.29, per 1000 atoms: 0.67 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 C 929 " - pdb=" SG CYS C 940 " distance=2.01 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 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: 7.57 Conformation dependent library (CDL) restraints added in 3.5 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: 3.18 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: 10.15 Time building geometry restraints manager: 8.86 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 66.570 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.740 ------------------------------------------------------------------------------- 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 : 5.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (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 TRP 0.028 0.004 TRP B 740 HIS 0.010 0.003 HIS A 845 PHE 0.037 0.004 PHE B 832 TYR 0.040 0.004 TYR A 772 ARG 0.009 0.001 ARG C 829 Details of bonding type rmsd hydrogen bonds : bond 0.14339 ( 1756) hydrogen bonds : angle 6.37465 ( 5232) SS BOND : bond 0.01778 ( 4) SS BOND : angle 5.22624 ( 8) covalent geometry : bond 0.00914 (31188) covalent geometry : angle 1.07922 (42252) *********************** 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 : 3.623 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: 0.7897 (ttmm) REVERT: A 277 LEU cc_start: 0.8180 (tp) cc_final: 0.7924 (tm) REVERT: A 464 THR cc_start: 0.8764 (m) cc_final: 0.8541 (p) 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: 0.7893 (ttmm) REVERT: B 277 LEU cc_start: 0.8178 (tp) cc_final: 0.7929 (tm) REVERT: B 464 THR cc_start: 0.8767 (m) cc_final: 0.8542 (p) REVERT: B 510 GLN cc_start: 0.7822 (mt0) cc_final: 0.7520 (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: 0.7895 (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 464 THR cc_start: 0.8768 (m) cc_final: 0.8543 (p) REVERT: C 510 GLN cc_start: 0.7818 (mt0) cc_final: 0.7513 (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: 0.7899 (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 464 THR cc_start: 0.8769 (m) cc_final: 0.8543 (p) 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: 1.5292 time to fit residues: 1381.2716 Evaluate side-chains 375 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.8980 chunk 281 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 291 optimal weight: 0.0370 chunk 112 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 217 optimal weight: 6.9990 chunk 337 optimal weight: 0.9980 overall best weight: 0.9862 ------------------------------------------------------------------------------- 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 671 GLN A 675 GLN A 861 GLN A 987 GLN A1050 ASN B 136 HIS B 199 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 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 671 GLN C 675 GLN C 861 GLN C 987 GLN C1050 ASN 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 671 GLN D 675 GLN D 861 GLN D 987 GLN D1050 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.174550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127530 restraints weight = 47884.367| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.44 r_work: 0.3444 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31192 Z= 0.134 Angle : 0.630 8.148 42260 Z= 0.329 Chirality : 0.040 0.141 4708 Planarity : 0.004 0.046 5280 Dihedral : 5.865 55.085 4024 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.88 % Allowed : 13.79 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 3656 helix: 0.01 (0.10), residues: 2472 sheet: -1.52 (0.34), residues: 200 loop : -2.73 (0.16), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 898 HIS 0.004 0.001 HIS A 765 PHE 0.018 0.001 PHE C 165 TYR 0.018 0.002 TYR D 191 ARG 0.007 0.001 ARG A 451 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 1756) hydrogen bonds : angle 4.31596 ( 5232) SS BOND : bond 0.00505 ( 4) SS BOND : angle 1.83708 ( 8) covalent geometry : bond 0.00297 (31188) covalent geometry : angle 0.62906 (42252) *********************** 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 581 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 485 time to evaluate : 3.181 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 189 MET cc_start: 0.7103 (mtm) cc_final: 0.6813 (mtm) REVERT: A 190 LYS cc_start: 0.8645 (ttmm) cc_final: 0.7999 (ttmm) REVERT: A 217 TRP cc_start: 0.7826 (t-100) cc_final: 0.7518 (t-100) REVERT: A 402 GLU cc_start: 0.7665 (pp20) cc_final: 0.7378 (pp20) REVERT: A 510 GLN cc_start: 0.7743 (mt0) cc_final: 0.7381 (mt0) REVERT: A 518 ASP cc_start: 0.7722 (t70) cc_final: 0.7477 (t70) REVERT: A 574 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8062 (tppt) REVERT: A 642 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7432 (mt0) REVERT: A 665 ASP cc_start: 0.8138 (t0) cc_final: 0.7931 (t0) REVERT: A 758 MET cc_start: 0.8987 (mtp) cc_final: 0.8748 (mtm) REVERT: A 797 LEU cc_start: 0.7120 (pt) cc_final: 0.6581 (mt) REVERT: A 989 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7410 (t0) REVERT: A 1023 MET cc_start: 0.6360 (mmm) cc_final: 0.4705 (ttt) REVERT: B 123 ASP cc_start: 0.6790 (m-30) cc_final: 0.5924 (p0) REVERT: B 189 MET cc_start: 0.7104 (mtm) cc_final: 0.6817 (mtm) REVERT: B 190 LYS cc_start: 0.8647 (ttmm) cc_final: 0.7998 (ttmm) REVERT: B 217 TRP cc_start: 0.7822 (t-100) cc_final: 0.7513 (t-100) REVERT: B 364 ARG cc_start: 0.7234 (tpm170) cc_final: 0.6999 (mmm-85) REVERT: B 402 GLU cc_start: 0.7631 (pp20) cc_final: 0.7353 (pp20) REVERT: B 510 GLN cc_start: 0.7751 (mt0) cc_final: 0.7388 (mt0) REVERT: B 518 ASP cc_start: 0.7700 (t70) cc_final: 0.7469 (t70) REVERT: B 574 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8097 (tppt) REVERT: B 642 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7416 (mt0) REVERT: B 665 ASP cc_start: 0.8138 (t0) cc_final: 0.7908 (t0) REVERT: B 758 MET cc_start: 0.8985 (mtp) cc_final: 0.8751 (mtm) REVERT: B 797 LEU cc_start: 0.7119 (pt) cc_final: 0.6575 (mt) REVERT: B 989 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7405 (t0) REVERT: B 1023 MET cc_start: 0.6365 (mmm) cc_final: 0.4706 (ttt) REVERT: C 189 MET cc_start: 0.7095 (mtm) cc_final: 0.6806 (mtm) REVERT: C 190 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8002 (ttmm) REVERT: C 217 TRP cc_start: 0.7817 (t-100) cc_final: 0.7510 (t-100) REVERT: C 364 ARG cc_start: 0.7273 (tpm170) cc_final: 0.7045 (mmm-85) REVERT: C 402 GLU cc_start: 0.7624 (pp20) cc_final: 0.7348 (pp20) REVERT: C 451 ARG cc_start: 0.5729 (pmt-80) cc_final: 0.5458 (ppt170) REVERT: C 510 GLN cc_start: 0.7771 (mt0) cc_final: 0.7398 (mt0) REVERT: C 574 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8098 (tppt) REVERT: C 642 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7413 (mt0) REVERT: C 665 ASP cc_start: 0.8192 (t0) cc_final: 0.7956 (t0) REVERT: C 758 MET cc_start: 0.8991 (mtp) cc_final: 0.8755 (mtm) REVERT: C 797 LEU cc_start: 0.7113 (pt) cc_final: 0.6568 (mt) REVERT: C 989 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7430 (t0) REVERT: C 1023 MET cc_start: 0.6366 (mmm) cc_final: 0.4707 (ttt) REVERT: D 189 MET cc_start: 0.7090 (mtm) cc_final: 0.6802 (mtm) REVERT: D 190 LYS cc_start: 0.8647 (ttmm) cc_final: 0.7998 (ttmm) REVERT: D 217 TRP cc_start: 0.7823 (t-100) cc_final: 0.7509 (t-100) REVERT: D 402 GLU cc_start: 0.7638 (pp20) cc_final: 0.7359 (pp20) REVERT: D 451 ARG cc_start: 0.5733 (pmt-80) cc_final: 0.5460 (ppt170) REVERT: D 510 GLN cc_start: 0.7763 (mt0) cc_final: 0.7407 (mt0) REVERT: D 518 ASP cc_start: 0.7732 (t70) cc_final: 0.7489 (t70) REVERT: D 574 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8113 (tppt) REVERT: D 642 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7423 (mt0) REVERT: D 665 ASP cc_start: 0.8111 (t0) cc_final: 0.7871 (t0) REVERT: D 758 MET cc_start: 0.8997 (mtp) cc_final: 0.8758 (mtm) REVERT: D 797 LEU cc_start: 0.7117 (pt) cc_final: 0.6570 (mt) REVERT: D 847 PHE cc_start: 0.7617 (m-10) cc_final: 0.7397 (m-10) REVERT: D 989 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7434 (t0) REVERT: D 1023 MET cc_start: 0.6354 (mmm) cc_final: 0.4704 (ttt) outliers start: 96 outliers final: 21 residues processed: 559 average time/residue: 1.4319 time to fit residues: 937.1721 Evaluate side-chains 390 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 361 time to evaluate : 3.119 ------------------------------------------------------------------------------- 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 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 628 LEU Chi-restraints excluded: chain B residue 671 GLN 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 628 LEU Chi-restraints excluded: chain C residue 671 GLN 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 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 81 optimal weight: 0.5980 chunk 209 optimal weight: 20.0000 chunk 263 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 328 optimal weight: 0.0970 chunk 96 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 overall best weight: 1.7182 ------------------------------------------------------------------------------- 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 A 818 HIS B 259 HIS ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN B 676 ASN B 741 ASN B 818 HIS C 259 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN C 676 ASN C 741 ASN C 818 HIS D 259 HIS ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN D 676 ASN D 741 ASN D 818 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.172552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124061 restraints weight = 47969.366| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.63 r_work: 0.3412 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31192 Z= 0.141 Angle : 0.614 7.950 42260 Z= 0.316 Chirality : 0.040 0.130 4708 Planarity : 0.004 0.040 5280 Dihedral : 5.530 53.257 4024 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.61 % Allowed : 14.42 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3656 helix: 0.84 (0.10), residues: 2452 sheet: -1.52 (0.37), residues: 188 loop : -2.42 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 786 HIS 0.004 0.001 HIS D 845 PHE 0.019 0.001 PHE B 752 TYR 0.015 0.002 TYR B 186 ARG 0.006 0.000 ARG B1079 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 1756) hydrogen bonds : angle 4.04075 ( 5232) SS BOND : bond 0.00552 ( 4) SS BOND : angle 2.93994 ( 8) covalent geometry : bond 0.00324 (31188) covalent geometry : angle 0.61290 (42252) *********************** 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 526 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 406 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.6890 (m-30) cc_final: 0.5921 (p0) REVERT: A 163 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8420 (ptmt) REVERT: A 189 MET cc_start: 0.7268 (mtm) cc_final: 0.6849 (mtm) REVERT: A 294 ASN cc_start: 0.7893 (p0) cc_final: 0.7516 (p0) REVERT: A 310 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6959 (mtp-110) REVERT: A 353 MET cc_start: 0.5368 (mpp) cc_final: 0.5099 (pmm) REVERT: A 402 GLU cc_start: 0.7878 (pp20) cc_final: 0.7633 (pp20) REVERT: A 464 THR cc_start: 0.9029 (m) cc_final: 0.8769 (p) REVERT: A 518 ASP cc_start: 0.7844 (t70) cc_final: 0.7545 (t70) REVERT: A 758 MET cc_start: 0.9175 (mtp) cc_final: 0.8936 (mtm) REVERT: A 797 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6543 (mt) REVERT: A 802 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7236 (m-30) REVERT: A 804 LEU cc_start: 0.8830 (tp) cc_final: 0.8541 (mt) REVERT: A 817 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8534 (mm) REVERT: A 897 ARG cc_start: 0.8766 (mtt180) cc_final: 0.7671 (mmt180) REVERT: A 988 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6554 (pm20) REVERT: A 989 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.7192 (t0) REVERT: B 123 ASP cc_start: 0.6881 (m-30) cc_final: 0.5917 (p0) REVERT: B 163 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8414 (ptmt) REVERT: B 189 MET cc_start: 0.7250 (mtm) cc_final: 0.6865 (mtm) REVERT: B 201 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7992 (tp) REVERT: B 294 ASN cc_start: 0.7887 (p0) cc_final: 0.7507 (p0) REVERT: B 310 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6988 (mtp-110) REVERT: B 353 MET cc_start: 0.5377 (mpp) cc_final: 0.5106 (pmm) REVERT: B 402 GLU cc_start: 0.7877 (pp20) cc_final: 0.7624 (pp20) REVERT: B 464 THR cc_start: 0.8983 (m) cc_final: 0.8722 (p) REVERT: B 518 ASP cc_start: 0.7834 (t70) cc_final: 0.7545 (t70) REVERT: B 726 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7495 (m-10) REVERT: B 758 MET cc_start: 0.9180 (mtp) cc_final: 0.8944 (mtm) REVERT: B 802 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: B 804 LEU cc_start: 0.8830 (tp) cc_final: 0.8542 (mt) REVERT: B 817 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8533 (mm) REVERT: B 897 ARG cc_start: 0.8760 (mtt180) cc_final: 0.7661 (mmt180) REVERT: B 988 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6563 (pm20) REVERT: B 989 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.7178 (t0) REVERT: C 123 ASP cc_start: 0.6893 (m-30) cc_final: 0.5927 (p0) REVERT: C 163 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8404 (ptmt) REVERT: C 189 MET cc_start: 0.7281 (mtm) cc_final: 0.6848 (mtm) REVERT: C 201 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.7996 (tp) REVERT: C 294 ASN cc_start: 0.7873 (p0) cc_final: 0.7495 (p0) REVERT: C 310 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6980 (mtp-110) REVERT: C 353 MET cc_start: 0.5355 (mpp) cc_final: 0.5086 (pmm) REVERT: C 402 GLU cc_start: 0.7872 (pp20) cc_final: 0.7620 (pp20) REVERT: C 464 THR cc_start: 0.9033 (m) cc_final: 0.8768 (p) REVERT: C 758 MET cc_start: 0.9178 (mtp) cc_final: 0.8943 (mtm) REVERT: C 802 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7281 (m-30) REVERT: C 804 LEU cc_start: 0.8824 (tp) cc_final: 0.8535 (mt) REVERT: C 817 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8532 (mm) REVERT: C 897 ARG cc_start: 0.8784 (mtt180) cc_final: 0.7671 (mmt180) REVERT: C 988 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6573 (pm20) REVERT: C 989 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.7195 (t0) REVERT: D 123 ASP cc_start: 0.6883 (m-30) cc_final: 0.5919 (p0) REVERT: D 163 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8411 (ptmt) REVERT: D 189 MET cc_start: 0.7263 (mtm) cc_final: 0.6844 (mtm) REVERT: D 294 ASN cc_start: 0.7857 (p0) cc_final: 0.7478 (p0) REVERT: D 310 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6962 (mtp-110) REVERT: D 353 MET cc_start: 0.5342 (mpp) cc_final: 0.5076 (pmm) REVERT: D 402 GLU cc_start: 0.7879 (pp20) cc_final: 0.7626 (pp20) REVERT: D 464 THR cc_start: 0.9033 (m) cc_final: 0.8770 (p) REVERT: D 518 ASP cc_start: 0.7829 (t70) cc_final: 0.7537 (t70) REVERT: D 758 MET cc_start: 0.9182 (mtp) cc_final: 0.8945 (mtm) REVERT: D 802 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: D 804 LEU cc_start: 0.8822 (tp) cc_final: 0.8535 (mt) REVERT: D 817 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8534 (mm) REVERT: D 897 ARG cc_start: 0.8771 (mtt180) cc_final: 0.7679 (mmt180) REVERT: D 988 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6579 (pm20) REVERT: D 989 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.7186 (t0) outliers start: 120 outliers final: 41 residues processed: 494 average time/residue: 1.3443 time to fit residues: 786.4435 Evaluate side-chains 421 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 356 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 807 PHE Chi-restraints excluded: chain A residue 817 LEU 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 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 726 TYR 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 817 LEU 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 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 488 LEU Chi-restraints excluded: chain C residue 574 LYS Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 807 PHE Chi-restraints excluded: chain C residue 817 LEU 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 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 488 LEU 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 791 VAL Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 807 PHE Chi-restraints excluded: chain D residue 817 LEU 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 335 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 334 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 347 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN B 666 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN C 666 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN D 666 GLN D 671 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.167391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121363 restraints weight = 48018.121| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.37 r_work: 0.3341 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 31192 Z= 0.223 Angle : 0.693 9.217 42260 Z= 0.357 Chirality : 0.044 0.132 4708 Planarity : 0.004 0.040 5280 Dihedral : 5.699 55.109 4024 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.39 % Allowed : 15.66 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3656 helix: 0.80 (0.10), residues: 2472 sheet: -1.63 (0.34), residues: 200 loop : -2.37 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 786 HIS 0.008 0.001 HIS C 765 PHE 0.029 0.002 PHE B 752 TYR 0.032 0.002 TYR B 191 ARG 0.004 0.001 ARG B 829 Details of bonding type rmsd hydrogen bonds : bond 0.05598 ( 1756) hydrogen bonds : angle 4.18192 ( 5232) SS BOND : bond 0.00544 ( 4) SS BOND : angle 2.89272 ( 8) covalent geometry : bond 0.00540 (31188) covalent geometry : angle 0.69146 (42252) *********************** 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 516 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 370 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7137 (m-30) cc_final: 0.6116 (p0) REVERT: A 163 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8434 (ptmt) REVERT: A 294 ASN cc_start: 0.8006 (p0) cc_final: 0.7617 (p0) REVERT: A 353 MET cc_start: 0.5505 (mpp) cc_final: 0.5198 (pmm) REVERT: A 364 ARG cc_start: 0.7591 (tpp-160) cc_final: 0.6853 (ttm110) REVERT: A 402 GLU cc_start: 0.7917 (pp20) cc_final: 0.7502 (pp20) REVERT: A 464 THR cc_start: 0.8970 (m) cc_final: 0.8709 (p) REVERT: A 574 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8248 (tppt) REVERT: A 689 ASP cc_start: 0.7948 (p0) cc_final: 0.7577 (p0) REVERT: A 726 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7408 (m-10) REVERT: A 732 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7962 (p) REVERT: A 758 MET cc_start: 0.9158 (mtp) cc_final: 0.8934 (mtm) REVERT: A 802 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: A 804 LEU cc_start: 0.8849 (tp) cc_final: 0.8629 (mt) REVERT: A 897 ARG cc_start: 0.8777 (mtt180) cc_final: 0.7773 (mmt-90) REVERT: A 988 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6339 (pm20) REVERT: A 989 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7335 (t0) REVERT: A 1023 MET cc_start: 0.6443 (mmp) cc_final: 0.4489 (ttt) REVERT: A 1046 ARG cc_start: 0.8038 (ttm170) cc_final: 0.7511 (mtp85) REVERT: B 123 ASP cc_start: 0.7096 (m-30) cc_final: 0.6074 (p0) REVERT: B 163 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8386 (ptmt) REVERT: B 294 ASN cc_start: 0.7992 (p0) cc_final: 0.7601 (p0) REVERT: B 353 MET cc_start: 0.5497 (mpp) cc_final: 0.5195 (pmm) REVERT: B 364 ARG cc_start: 0.7352 (tpm170) cc_final: 0.6790 (ttm110) REVERT: B 402 GLU cc_start: 0.7909 (pp20) cc_final: 0.7443 (pp20) REVERT: B 464 THR cc_start: 0.8984 (m) cc_final: 0.8720 (p) REVERT: B 574 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8337 (tppt) REVERT: B 616 GLU cc_start: 0.8264 (tp30) cc_final: 0.7988 (tt0) REVERT: B 689 ASP cc_start: 0.7930 (p0) cc_final: 0.7562 (p0) REVERT: B 726 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7443 (m-10) REVERT: B 732 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7962 (p) REVERT: B 758 MET cc_start: 0.9171 (mtp) cc_final: 0.8947 (mtm) REVERT: B 802 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: B 804 LEU cc_start: 0.8839 (tp) cc_final: 0.8622 (mt) REVERT: B 863 MET cc_start: 0.8636 (mmt) cc_final: 0.8296 (mmt) REVERT: B 897 ARG cc_start: 0.8776 (mtt180) cc_final: 0.7770 (mmt-90) REVERT: B 988 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6331 (pm20) REVERT: B 989 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7317 (t0) REVERT: B 1023 MET cc_start: 0.6436 (mmp) cc_final: 0.4487 (ttt) REVERT: B 1046 ARG cc_start: 0.8045 (ttm170) cc_final: 0.7518 (mtp85) REVERT: C 123 ASP cc_start: 0.7084 (m-30) cc_final: 0.6060 (p0) REVERT: C 163 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8372 (ptmt) REVERT: C 294 ASN cc_start: 0.8003 (p0) cc_final: 0.7611 (p0) REVERT: C 353 MET cc_start: 0.5501 (mpp) cc_final: 0.5198 (pmm) REVERT: C 364 ARG cc_start: 0.7352 (tpm170) cc_final: 0.6791 (ttm110) REVERT: C 402 GLU cc_start: 0.7913 (pp20) cc_final: 0.7447 (pp20) REVERT: C 464 THR cc_start: 0.8961 (m) cc_final: 0.8698 (p) REVERT: C 574 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8341 (tppt) REVERT: C 616 GLU cc_start: 0.8219 (tp30) cc_final: 0.7949 (tt0) REVERT: C 689 ASP cc_start: 0.7947 (p0) cc_final: 0.7544 (p0) REVERT: C 732 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7967 (p) REVERT: C 758 MET cc_start: 0.9164 (mtp) cc_final: 0.8940 (mtm) REVERT: C 802 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: C 804 LEU cc_start: 0.8837 (tp) cc_final: 0.8616 (mt) REVERT: C 897 ARG cc_start: 0.8785 (mtt180) cc_final: 0.7777 (mmt-90) REVERT: C 988 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6313 (pm20) REVERT: C 989 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7321 (t0) REVERT: C 1023 MET cc_start: 0.6453 (mmp) cc_final: 0.4493 (ttt) REVERT: C 1046 ARG cc_start: 0.8039 (ttm170) cc_final: 0.7509 (mtp85) REVERT: D 123 ASP cc_start: 0.7081 (m-30) cc_final: 0.6057 (p0) REVERT: D 163 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8377 (ptmt) REVERT: D 294 ASN cc_start: 0.7996 (p0) cc_final: 0.7607 (p0) REVERT: D 353 MET cc_start: 0.5490 (mpp) cc_final: 0.5188 (pmm) REVERT: D 364 ARG cc_start: 0.7511 (tpp-160) cc_final: 0.6839 (ttm110) REVERT: D 402 GLU cc_start: 0.7922 (pp20) cc_final: 0.7478 (pp20) REVERT: D 464 THR cc_start: 0.8972 (m) cc_final: 0.8712 (p) REVERT: D 574 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8336 (tppt) REVERT: D 616 GLU cc_start: 0.8253 (tp30) cc_final: 0.7978 (tt0) REVERT: D 689 ASP cc_start: 0.7971 (p0) cc_final: 0.7572 (p0) REVERT: D 732 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.7968 (p) REVERT: D 758 MET cc_start: 0.9163 (mtp) cc_final: 0.8938 (mtm) REVERT: D 802 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: D 804 LEU cc_start: 0.8841 (tp) cc_final: 0.8621 (mt) REVERT: D 897 ARG cc_start: 0.8779 (mtt180) cc_final: 0.7774 (mmt-90) REVERT: D 988 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6318 (pm20) REVERT: D 989 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7345 (t0) REVERT: D 1023 MET cc_start: 0.6447 (mmp) cc_final: 0.4492 (ttt) REVERT: D 1046 ARG cc_start: 0.8031 (ttm170) cc_final: 0.7507 (mtp85) outliers start: 146 outliers final: 46 residues processed: 484 average time/residue: 1.3736 time to fit residues: 783.7110 Evaluate side-chains 388 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 320 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 201 ILE 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 630 THR 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 802 ASP 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 201 ILE Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 859 MET 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 136 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 352 optimal weight: 4.9990 chunk 294 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 355 optimal weight: 10.0000 chunk 321 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 300 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 571 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.167137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120232 restraints weight = 47176.770| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.42 r_work: 0.3321 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31192 Z= 0.185 Angle : 0.655 8.065 42260 Z= 0.337 Chirality : 0.042 0.139 4708 Planarity : 0.004 0.038 5280 Dihedral : 5.509 51.798 4024 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.60 % Allowed : 16.50 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3656 helix: 0.98 (0.10), residues: 2468 sheet: -1.71 (0.35), residues: 188 loop : -2.22 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 786 HIS 0.006 0.001 HIS B 765 PHE 0.021 0.002 PHE C1013 TYR 0.020 0.002 TYR A 191 ARG 0.008 0.001 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 1756) hydrogen bonds : angle 4.07525 ( 5232) SS BOND : bond 0.00486 ( 4) SS BOND : angle 2.13181 ( 8) covalent geometry : bond 0.00446 (31188) covalent geometry : angle 0.65467 (42252) *********************** 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 503 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 350 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7187 (m-30) cc_final: 0.6094 (p0) REVERT: A 163 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8367 (ptmt) REVERT: A 294 ASN cc_start: 0.8020 (p0) cc_final: 0.7640 (p0) REVERT: A 353 MET cc_start: 0.6220 (mpp) cc_final: 0.5890 (pmm) REVERT: A 364 ARG cc_start: 0.7585 (tpp-160) cc_final: 0.7359 (mmm-85) REVERT: A 402 GLU cc_start: 0.7689 (pp20) cc_final: 0.7466 (pp20) REVERT: A 464 THR cc_start: 0.8971 (m) cc_final: 0.8716 (p) REVERT: A 507 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7249 (tpm170) REVERT: A 574 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8341 (tppt) REVERT: A 627 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8662 (mt-10) REVERT: A 689 ASP cc_start: 0.7951 (p0) cc_final: 0.7550 (p0) REVERT: A 726 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7396 (m-10) REVERT: A 732 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.7961 (p) REVERT: A 758 MET cc_start: 0.9202 (mtp) cc_final: 0.8996 (mtm) REVERT: A 802 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: A 804 LEU cc_start: 0.8819 (tp) cc_final: 0.8597 (mt) REVERT: A 863 MET cc_start: 0.8699 (mmt) cc_final: 0.8340 (mmt) REVERT: A 897 ARG cc_start: 0.8691 (mtt180) cc_final: 0.7570 (mmt180) REVERT: A 988 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6287 (pm20) REVERT: A 989 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7423 (t0) REVERT: A 1046 ARG cc_start: 0.7729 (ttm170) cc_final: 0.7430 (mtp85) REVERT: A 1047 ASN cc_start: 0.6713 (m-40) cc_final: 0.5964 (t0) REVERT: A 1048 GLU cc_start: 0.7222 (pm20) cc_final: 0.6842 (mp0) REVERT: A 1051 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7992 (tp30) REVERT: B 123 ASP cc_start: 0.7278 (m-30) cc_final: 0.6130 (p0) REVERT: B 163 LYS cc_start: 0.8716 (ttpt) cc_final: 0.8405 (ptmt) REVERT: B 294 ASN cc_start: 0.8013 (p0) cc_final: 0.7632 (p0) REVERT: B 353 MET cc_start: 0.6216 (mpp) cc_final: 0.5887 (pmm) REVERT: B 364 ARG cc_start: 0.7374 (tpm170) cc_final: 0.6881 (ttm110) REVERT: B 464 THR cc_start: 0.8976 (m) cc_final: 0.8726 (p) REVERT: B 507 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7269 (tpm170) REVERT: B 616 GLU cc_start: 0.8330 (tp30) cc_final: 0.8069 (tt0) REVERT: B 689 ASP cc_start: 0.7928 (p0) cc_final: 0.7527 (p0) REVERT: B 732 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.7969 (p) REVERT: B 758 MET cc_start: 0.9204 (mtp) cc_final: 0.8997 (mtm) REVERT: B 797 LEU cc_start: 0.7031 (pt) cc_final: 0.6340 (mt) REVERT: B 802 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: B 804 LEU cc_start: 0.8811 (tp) cc_final: 0.8591 (mt) REVERT: B 897 ARG cc_start: 0.8697 (mtt180) cc_final: 0.7571 (mmt180) REVERT: B 988 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6310 (pm20) REVERT: B 989 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7437 (t0) REVERT: B 1046 ARG cc_start: 0.7732 (ttm170) cc_final: 0.7439 (mtp85) REVERT: B 1047 ASN cc_start: 0.6729 (m-40) cc_final: 0.5978 (t0) REVERT: B 1048 GLU cc_start: 0.7199 (pm20) cc_final: 0.6820 (mp0) REVERT: B 1051 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7995 (tp30) REVERT: C 123 ASP cc_start: 0.7284 (m-30) cc_final: 0.6131 (p0) REVERT: C 163 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8404 (ptmt) REVERT: C 294 ASN cc_start: 0.8015 (p0) cc_final: 0.7636 (p0) REVERT: C 353 MET cc_start: 0.6198 (mpp) cc_final: 0.5871 (pmm) REVERT: C 364 ARG cc_start: 0.7372 (tpm170) cc_final: 0.6880 (ttm110) REVERT: C 402 GLU cc_start: 0.7652 (pp20) cc_final: 0.7451 (pp20) REVERT: C 464 THR cc_start: 0.8982 (m) cc_final: 0.8725 (p) REVERT: C 507 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7272 (tpm170) REVERT: C 616 GLU cc_start: 0.8319 (tp30) cc_final: 0.8055 (tt0) REVERT: C 689 ASP cc_start: 0.7930 (p0) cc_final: 0.7528 (p0) REVERT: C 726 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7405 (m-10) REVERT: C 732 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7965 (p) REVERT: C 758 MET cc_start: 0.9205 (mtp) cc_final: 0.8996 (mtm) REVERT: C 797 LEU cc_start: 0.7028 (pt) cc_final: 0.6337 (mt) REVERT: C 802 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: C 804 LEU cc_start: 0.8806 (tp) cc_final: 0.8587 (mt) REVERT: C 863 MET cc_start: 0.8704 (mmt) cc_final: 0.8334 (mmt) REVERT: C 897 ARG cc_start: 0.8699 (mtt180) cc_final: 0.7586 (mmt180) REVERT: C 988 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6308 (pm20) REVERT: C 989 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7438 (t0) REVERT: C 1046 ARG cc_start: 0.7733 (ttm170) cc_final: 0.7439 (mtp85) REVERT: C 1047 ASN cc_start: 0.6719 (m-40) cc_final: 0.5977 (t0) REVERT: C 1048 GLU cc_start: 0.7203 (pm20) cc_final: 0.6825 (mp0) REVERT: C 1051 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7999 (tp30) REVERT: D 123 ASP cc_start: 0.7276 (m-30) cc_final: 0.6109 (p0) REVERT: D 163 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8405 (ptmt) REVERT: D 294 ASN cc_start: 0.8031 (p0) cc_final: 0.7653 (p0) REVERT: D 364 ARG cc_start: 0.7566 (tpp-160) cc_final: 0.7145 (ttm110) REVERT: D 464 THR cc_start: 0.8980 (m) cc_final: 0.8725 (p) REVERT: D 507 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7261 (tpm170) REVERT: D 616 GLU cc_start: 0.8309 (tp30) cc_final: 0.8054 (tt0) REVERT: D 627 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8637 (mt-10) REVERT: D 689 ASP cc_start: 0.7945 (p0) cc_final: 0.7541 (p0) REVERT: D 726 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7395 (m-10) REVERT: D 732 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7953 (p) REVERT: D 758 MET cc_start: 0.9212 (mtp) cc_final: 0.9003 (mtm) REVERT: D 797 LEU cc_start: 0.7031 (pt) cc_final: 0.6344 (mt) REVERT: D 802 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: D 804 LEU cc_start: 0.8817 (tp) cc_final: 0.8598 (mt) REVERT: D 863 MET cc_start: 0.8700 (mmt) cc_final: 0.8333 (mmt) REVERT: D 897 ARG cc_start: 0.8701 (mtt180) cc_final: 0.7586 (mmt180) REVERT: D 988 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6245 (pm20) REVERT: D 989 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7435 (t0) REVERT: D 1046 ARG cc_start: 0.7732 (ttm170) cc_final: 0.7435 (mtp85) REVERT: D 1047 ASN cc_start: 0.6730 (m-40) cc_final: 0.5968 (t0) REVERT: D 1048 GLU cc_start: 0.7205 (pm20) cc_final: 0.6828 (mp0) REVERT: D 1051 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7999 (tp30) outliers start: 153 outliers final: 61 residues processed: 475 average time/residue: 1.2856 time to fit residues: 731.1949 Evaluate side-chains 411 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 320 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 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 A residue 1051 GLU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 ARG 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 702 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 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 B residue 1051 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 488 LEU 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 628 LEU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 726 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 726 TYR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 1051 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 74 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 229 optimal weight: 7.9990 chunk 153 optimal weight: 0.0170 chunk 83 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 286 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- 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 A 671 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN B 671 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN C 671 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.170837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124699 restraints weight = 47288.189| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.51 r_work: 0.3384 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31192 Z= 0.121 Angle : 0.600 10.383 42260 Z= 0.303 Chirality : 0.040 0.188 4708 Planarity : 0.004 0.039 5280 Dihedral : 5.151 56.887 4024 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.34 % Allowed : 18.72 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3656 helix: 1.32 (0.11), residues: 2464 sheet: -1.42 (0.37), residues: 188 loop : -2.06 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 786 HIS 0.003 0.001 HIS D 185 PHE 0.017 0.001 PHE C 807 TYR 0.039 0.001 TYR B 191 ARG 0.007 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 1756) hydrogen bonds : angle 3.85113 ( 5232) SS BOND : bond 0.00297 ( 4) SS BOND : angle 2.66323 ( 8) covalent geometry : bond 0.00273 (31188) covalent geometry : angle 0.59878 (42252) *********************** 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 468 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 357 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7080 (m-30) cc_final: 0.5995 (p0) REVERT: A 163 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8348 (ptmt) REVERT: A 294 ASN cc_start: 0.7973 (p0) cc_final: 0.7601 (p0) REVERT: A 353 MET cc_start: 0.6289 (mpp) cc_final: 0.5988 (pmm) REVERT: A 402 GLU cc_start: 0.7655 (pp20) cc_final: 0.7448 (pp20) REVERT: A 459 GLN cc_start: 0.6763 (mp10) cc_final: 0.6271 (mm-40) REVERT: A 464 THR cc_start: 0.8999 (m) cc_final: 0.8706 (p) REVERT: A 496 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7877 (mp) REVERT: A 574 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8287 (tppt) REVERT: A 666 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8530 (mt0) REVERT: A 689 ASP cc_start: 0.7807 (p0) cc_final: 0.7486 (p0) REVERT: A 758 MET cc_start: 0.9186 (mtp) cc_final: 0.8981 (mtm) REVERT: A 797 LEU cc_start: 0.7252 (pt) cc_final: 0.6672 (mt) REVERT: A 802 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: A 804 LEU cc_start: 0.8747 (tp) cc_final: 0.8500 (mt) REVERT: A 863 MET cc_start: 0.8615 (mmt) cc_final: 0.8298 (mmt) REVERT: A 897 ARG cc_start: 0.8606 (mtt180) cc_final: 0.7485 (mmt180) REVERT: A 944 ASP cc_start: 0.7592 (t0) cc_final: 0.6939 (p0) REVERT: A 985 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7311 (mp) REVERT: A 988 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6144 (pm20) REVERT: A 989 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.7246 (t0) REVERT: A 1023 MET cc_start: 0.6306 (mmp) cc_final: 0.4476 (ttm) REVERT: A 1046 ARG cc_start: 0.7550 (ttm170) cc_final: 0.7236 (ttm-80) REVERT: A 1047 ASN cc_start: 0.6475 (m-40) cc_final: 0.5795 (t0) REVERT: A 1048 GLU cc_start: 0.7094 (pm20) cc_final: 0.6718 (mp0) REVERT: B 123 ASP cc_start: 0.7212 (m-30) cc_final: 0.6068 (p0) REVERT: B 163 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8355 (ptmt) REVERT: B 294 ASN cc_start: 0.7974 (p0) cc_final: 0.7601 (p0) REVERT: B 353 MET cc_start: 0.6297 (mpp) cc_final: 0.5993 (pmm) REVERT: B 364 ARG cc_start: 0.7321 (tpm170) cc_final: 0.6903 (ttm170) REVERT: B 459 GLN cc_start: 0.6761 (mp10) cc_final: 0.6282 (mm-40) REVERT: B 464 THR cc_start: 0.8952 (m) cc_final: 0.8727 (p) REVERT: B 480 ASN cc_start: 0.7989 (m-40) cc_final: 0.7543 (m-40) REVERT: B 666 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8533 (mt0) REVERT: B 689 ASP cc_start: 0.7795 (p0) cc_final: 0.7479 (p0) REVERT: B 758 MET cc_start: 0.9201 (mtp) cc_final: 0.8997 (mtm) REVERT: B 797 LEU cc_start: 0.7223 (pt) cc_final: 0.6601 (mt) REVERT: B 802 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7251 (m-30) REVERT: B 804 LEU cc_start: 0.8747 (tp) cc_final: 0.8500 (mt) REVERT: B 863 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8280 (mmt) REVERT: B 897 ARG cc_start: 0.8614 (mtt180) cc_final: 0.7487 (mmt180) REVERT: B 944 ASP cc_start: 0.7589 (t0) cc_final: 0.6951 (p0) REVERT: B 985 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7313 (mp) REVERT: B 988 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6154 (pm20) REVERT: B 989 ASN cc_start: 0.7464 (OUTLIER) cc_final: 0.7263 (t0) REVERT: B 1023 MET cc_start: 0.6322 (mmp) cc_final: 0.4493 (ttm) REVERT: B 1046 ARG cc_start: 0.7546 (ttm170) cc_final: 0.7338 (mtp85) REVERT: B 1047 ASN cc_start: 0.6479 (m-40) cc_final: 0.5738 (t0) REVERT: B 1048 GLU cc_start: 0.7108 (pm20) cc_final: 0.6647 (mp0) REVERT: C 163 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8354 (ptmt) REVERT: C 294 ASN cc_start: 0.7972 (p0) cc_final: 0.7601 (p0) REVERT: C 353 MET cc_start: 0.6291 (mpp) cc_final: 0.5989 (pmm) REVERT: C 364 ARG cc_start: 0.7327 (tpm170) cc_final: 0.6900 (ttm170) REVERT: C 402 GLU cc_start: 0.7684 (pp20) cc_final: 0.7472 (pp20) REVERT: C 457 ASP cc_start: 0.7270 (p0) cc_final: 0.6909 (p0) REVERT: C 459 GLN cc_start: 0.6741 (mp10) cc_final: 0.6209 (mm-40) REVERT: C 464 THR cc_start: 0.9002 (m) cc_final: 0.8706 (p) REVERT: C 480 ASN cc_start: 0.7985 (m-40) cc_final: 0.7541 (m-40) REVERT: C 666 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: C 689 ASP cc_start: 0.7803 (p0) cc_final: 0.7463 (p0) REVERT: C 758 MET cc_start: 0.9198 (mtp) cc_final: 0.8991 (mtm) REVERT: C 797 LEU cc_start: 0.7258 (pt) cc_final: 0.6623 (mt) REVERT: C 802 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7265 (m-30) REVERT: C 804 LEU cc_start: 0.8740 (tp) cc_final: 0.8494 (mt) REVERT: C 863 MET cc_start: 0.8604 (mmt) cc_final: 0.8282 (mmt) REVERT: C 897 ARG cc_start: 0.8610 (mtt180) cc_final: 0.7490 (mmt180) REVERT: C 944 ASP cc_start: 0.7617 (t0) cc_final: 0.6973 (p0) REVERT: C 985 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7314 (mp) REVERT: C 988 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6152 (pm20) REVERT: C 989 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.7256 (t0) REVERT: C 1023 MET cc_start: 0.6302 (mmp) cc_final: 0.4498 (ttm) REVERT: C 1046 ARG cc_start: 0.7554 (ttm170) cc_final: 0.7241 (ttm-80) REVERT: C 1047 ASN cc_start: 0.6502 (m-40) cc_final: 0.5799 (t0) REVERT: C 1048 GLU cc_start: 0.7093 (pm20) cc_final: 0.6712 (mp0) REVERT: D 123 ASP cc_start: 0.7097 (m-30) cc_final: 0.6000 (p0) REVERT: D 163 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8356 (ptmt) REVERT: D 294 ASN cc_start: 0.7979 (p0) cc_final: 0.7610 (p0) REVERT: D 353 MET cc_start: 0.6569 (mpp) cc_final: 0.6341 (pmm) REVERT: D 464 THR cc_start: 0.9002 (m) cc_final: 0.8707 (p) REVERT: D 480 ASN cc_start: 0.7986 (m-40) cc_final: 0.7541 (m-40) REVERT: D 627 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8550 (mt-10) REVERT: D 666 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8540 (mt0) REVERT: D 689 ASP cc_start: 0.7837 (p0) cc_final: 0.7493 (p0) REVERT: D 758 MET cc_start: 0.9206 (mtp) cc_final: 0.8999 (mtm) REVERT: D 797 LEU cc_start: 0.7212 (pt) cc_final: 0.6593 (mt) REVERT: D 802 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7278 (m-30) REVERT: D 804 LEU cc_start: 0.8745 (tp) cc_final: 0.8499 (mt) REVERT: D 863 MET cc_start: 0.8623 (mmt) cc_final: 0.8305 (mmt) REVERT: D 897 ARG cc_start: 0.8613 (mtt180) cc_final: 0.7492 (mmt180) REVERT: D 944 ASP cc_start: 0.7638 (t0) cc_final: 0.6984 (p0) REVERT: D 985 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7343 (mp) REVERT: D 988 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6190 (pm20) REVERT: D 1023 MET cc_start: 0.6300 (mmp) cc_final: 0.4494 (ttm) REVERT: D 1046 ARG cc_start: 0.7553 (ttm170) cc_final: 0.7343 (mtp85) REVERT: D 1047 ASN cc_start: 0.6472 (m-40) cc_final: 0.5739 (t0) REVERT: D 1048 GLU cc_start: 0.7093 (pm20) cc_final: 0.6675 (mp0) outliers start: 111 outliers final: 41 residues processed: 447 average time/residue: 1.3469 time to fit residues: 711.8652 Evaluate side-chains 395 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 331 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER 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 496 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 666 GLN Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 849 VAL 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 A residue 989 ASN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 488 LEU 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 702 ILE Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 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 B residue 989 ASN Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 491 GLU 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 666 GLN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 849 VAL 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 C residue 989 ASN Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 666 GLN Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 849 VAL 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 23 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 293 optimal weight: 0.3980 chunk 334 optimal weight: 0.9980 chunk 286 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.167645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121234 restraints weight = 47301.271| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.43 r_work: 0.3330 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31192 Z= 0.182 Angle : 0.667 12.923 42260 Z= 0.334 Chirality : 0.042 0.152 4708 Planarity : 0.004 0.043 5280 Dihedral : 5.197 57.484 4024 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.12 % Allowed : 18.36 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3656 helix: 1.25 (0.11), residues: 2464 sheet: -1.45 (0.37), residues: 188 loop : -2.07 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 786 HIS 0.006 0.001 HIS B 765 PHE 0.018 0.001 PHE D1013 TYR 0.029 0.002 TYR C 191 ARG 0.007 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04838 ( 1756) hydrogen bonds : angle 3.99237 ( 5232) SS BOND : bond 0.00537 ( 4) SS BOND : angle 2.70141 ( 8) covalent geometry : bond 0.00441 (31188) covalent geometry : angle 0.66560 (42252) *********************** 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 471 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 334 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8393 (ptmt) REVERT: A 294 ASN cc_start: 0.7948 (p0) cc_final: 0.7577 (p0) REVERT: A 402 GLU cc_start: 0.7670 (pp20) cc_final: 0.7444 (pp20) REVERT: A 464 THR cc_start: 0.8944 (m) cc_final: 0.8705 (p) REVERT: A 496 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 507 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7242 (tpm170) REVERT: A 627 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8620 (mt-10) REVERT: A 689 ASP cc_start: 0.7924 (p0) cc_final: 0.7560 (p0) REVERT: A 726 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7478 (m-10) REVERT: A 732 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7592 (p) REVERT: A 758 MET cc_start: 0.9234 (mtp) cc_final: 0.9028 (mtm) REVERT: A 797 LEU cc_start: 0.7105 (pt) cc_final: 0.6410 (mt) REVERT: A 804 LEU cc_start: 0.8776 (tp) cc_final: 0.8544 (mt) REVERT: A 863 MET cc_start: 0.8711 (mmt) cc_final: 0.8375 (mmt) REVERT: A 897 ARG cc_start: 0.8718 (mtt180) cc_final: 0.7578 (mmt180) REVERT: A 942 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: A 944 ASP cc_start: 0.7785 (t0) cc_final: 0.6949 (p0) REVERT: A 1023 MET cc_start: 0.6180 (mmp) cc_final: 0.4282 (ttm) REVERT: A 1047 ASN cc_start: 0.6492 (m-40) cc_final: 0.5845 (t0) REVERT: A 1048 GLU cc_start: 0.7145 (pm20) cc_final: 0.6746 (mp0) REVERT: B 163 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8410 (ptpt) REVERT: B 294 ASN cc_start: 0.7954 (p0) cc_final: 0.7582 (p0) REVERT: B 364 ARG cc_start: 0.7282 (tpm170) cc_final: 0.6907 (ttm170) REVERT: B 464 THR cc_start: 0.8943 (m) cc_final: 0.8702 (p) REVERT: B 507 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7262 (tpm170) REVERT: B 689 ASP cc_start: 0.7914 (p0) cc_final: 0.7555 (p0) REVERT: B 732 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7581 (p) REVERT: B 758 MET cc_start: 0.9230 (mtp) cc_final: 0.9025 (mtm) REVERT: B 797 LEU cc_start: 0.7036 (pt) cc_final: 0.6334 (mt) REVERT: B 804 LEU cc_start: 0.8780 (tp) cc_final: 0.8547 (mt) REVERT: B 897 ARG cc_start: 0.8721 (mtt180) cc_final: 0.7577 (mmt180) REVERT: B 942 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: B 944 ASP cc_start: 0.7781 (t0) cc_final: 0.6938 (p0) REVERT: B 985 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7623 (mp) REVERT: B 1023 MET cc_start: 0.6192 (mmp) cc_final: 0.4340 (ttt) REVERT: B 1045 PHE cc_start: 0.6890 (p90) cc_final: 0.6689 (p90) REVERT: B 1046 ARG cc_start: 0.7566 (ttm170) cc_final: 0.7311 (mtp85) REVERT: B 1047 ASN cc_start: 0.6494 (m-40) cc_final: 0.5797 (t0) REVERT: B 1048 GLU cc_start: 0.7141 (pm20) cc_final: 0.6707 (mp0) REVERT: C 163 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8380 (ptmt) REVERT: C 294 ASN cc_start: 0.7959 (p0) cc_final: 0.7589 (p0) REVERT: C 364 ARG cc_start: 0.7358 (tpm170) cc_final: 0.6951 (ttm170) REVERT: C 402 GLU cc_start: 0.7713 (pp20) cc_final: 0.7501 (pp20) REVERT: C 464 THR cc_start: 0.8961 (m) cc_final: 0.8714 (p) REVERT: C 507 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7257 (tpm170) REVERT: C 689 ASP cc_start: 0.7882 (p0) cc_final: 0.7541 (p0) REVERT: C 726 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7438 (m-10) REVERT: C 732 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7609 (p) REVERT: C 758 MET cc_start: 0.9231 (mtp) cc_final: 0.9022 (mtm) REVERT: C 797 LEU cc_start: 0.7060 (pt) cc_final: 0.6339 (mt) REVERT: C 804 LEU cc_start: 0.8779 (tp) cc_final: 0.8545 (mt) REVERT: C 863 MET cc_start: 0.8686 (mmt) cc_final: 0.8329 (mmt) REVERT: C 897 ARG cc_start: 0.8719 (mtt180) cc_final: 0.7580 (mmt180) REVERT: C 942 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: C 944 ASP cc_start: 0.7793 (t0) cc_final: 0.6960 (p0) REVERT: C 1023 MET cc_start: 0.6182 (mmp) cc_final: 0.4334 (ttt) REVERT: C 1047 ASN cc_start: 0.6490 (m-40) cc_final: 0.5849 (t0) REVERT: C 1048 GLU cc_start: 0.7144 (pm20) cc_final: 0.6744 (mp0) REVERT: D 163 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8413 (ptpt) REVERT: D 294 ASN cc_start: 0.7961 (p0) cc_final: 0.7595 (p0) REVERT: D 353 MET cc_start: 0.6588 (mpp) cc_final: 0.6337 (pmm) REVERT: D 464 THR cc_start: 0.8949 (m) cc_final: 0.8723 (p) REVERT: D 507 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7253 (tpm170) REVERT: D 627 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8588 (mt-10) REVERT: D 666 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8543 (mt0) REVERT: D 689 ASP cc_start: 0.7917 (p0) cc_final: 0.7590 (p0) REVERT: D 726 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7426 (m-10) REVERT: D 732 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7565 (p) REVERT: D 758 MET cc_start: 0.9232 (mtp) cc_final: 0.9023 (mtm) REVERT: D 797 LEU cc_start: 0.7025 (pt) cc_final: 0.6325 (mt) REVERT: D 804 LEU cc_start: 0.8782 (tp) cc_final: 0.8545 (mt) REVERT: D 863 MET cc_start: 0.8694 (mmt) cc_final: 0.8347 (mmt) REVERT: D 897 ARG cc_start: 0.8707 (mtt180) cc_final: 0.7566 (mmt180) REVERT: D 942 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: D 944 ASP cc_start: 0.7798 (t0) cc_final: 0.6960 (p0) REVERT: D 1023 MET cc_start: 0.6186 (mmp) cc_final: 0.4292 (ttm) REVERT: D 1045 PHE cc_start: 0.6882 (p90) cc_final: 0.6674 (p90) REVERT: D 1046 ARG cc_start: 0.7570 (ttm170) cc_final: 0.7311 (mtp85) REVERT: D 1047 ASN cc_start: 0.6505 (m-40) cc_final: 0.5801 (t0) REVERT: D 1048 GLU cc_start: 0.7143 (pm20) cc_final: 0.6709 (mp0) outliers start: 137 outliers final: 55 residues processed: 448 average time/residue: 1.6916 time to fit residues: 905.6868 Evaluate side-chains 398 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 323 time to evaluate : 4.142 ------------------------------------------------------------------------------- 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 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 496 LEU 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 620 GLU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 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 929 CYS Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 ARG 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 702 ILE 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 929 CYS Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 491 GLU 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 628 LEU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 726 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 666 GLN Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 726 TYR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 849 VAL 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 34 optimal weight: 1.9990 chunk 1 optimal weight: 0.0060 chunk 29 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 309 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 185 optimal weight: 8.9990 chunk 286 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- 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 154 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.168033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121944 restraints weight = 47297.419| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.42 r_work: 0.3337 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31192 Z= 0.158 Angle : 0.653 14.304 42260 Z= 0.329 Chirality : 0.041 0.161 4708 Planarity : 0.004 0.044 5280 Dihedral : 5.153 54.010 4024 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.49 % Allowed : 19.56 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3656 helix: 1.28 (0.11), residues: 2464 sheet: -1.41 (0.37), residues: 188 loop : -2.06 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 786 HIS 0.004 0.001 HIS B 765 PHE 0.026 0.001 PHE A 807 TYR 0.041 0.002 TYR C 191 ARG 0.006 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 1756) hydrogen bonds : angle 3.97580 ( 5232) SS BOND : bond 0.00510 ( 4) SS BOND : angle 2.49584 ( 8) covalent geometry : bond 0.00380 (31188) covalent geometry : angle 0.65210 (42252) *********************** 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 454 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 338 time to evaluate : 3.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7078 (m-30) cc_final: 0.5944 (p0) REVERT: A 163 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8350 (ptmt) REVERT: A 189 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6689 (ttm) REVERT: A 294 ASN cc_start: 0.7869 (p0) cc_final: 0.7512 (p0) REVERT: A 353 MET cc_start: 0.6995 (mpp) cc_final: 0.6724 (pmm) REVERT: A 402 GLU cc_start: 0.7682 (pp20) cc_final: 0.7427 (pp20) REVERT: A 459 GLN cc_start: 0.6828 (mp10) cc_final: 0.6326 (mm-40) REVERT: A 464 THR cc_start: 0.8943 (m) cc_final: 0.8723 (p) REVERT: A 496 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7908 (mp) REVERT: A 627 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8578 (mt-10) REVERT: A 666 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: A 689 ASP cc_start: 0.7889 (p0) cc_final: 0.7559 (p0) REVERT: A 726 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7468 (m-10) REVERT: A 732 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7586 (p) REVERT: A 758 MET cc_start: 0.9222 (mtp) cc_final: 0.8984 (mtm) REVERT: A 797 LEU cc_start: 0.7179 (pt) cc_final: 0.6462 (mt) REVERT: A 804 LEU cc_start: 0.8758 (tp) cc_final: 0.8541 (mt) REVERT: A 897 ARG cc_start: 0.8686 (mtt180) cc_final: 0.7551 (mmt180) REVERT: A 942 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: A 944 ASP cc_start: 0.7730 (t0) cc_final: 0.7014 (p0) REVERT: A 1023 MET cc_start: 0.6172 (mmp) cc_final: 0.4320 (ttt) REVERT: A 1047 ASN cc_start: 0.6454 (m-40) cc_final: 0.5902 (t0) REVERT: A 1048 GLU cc_start: 0.7268 (pm20) cc_final: 0.6727 (mp0) REVERT: A 1051 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: B 123 ASP cc_start: 0.7261 (m-30) cc_final: 0.6085 (p0) REVERT: B 163 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8357 (ptmt) REVERT: B 189 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6698 (ttm) REVERT: B 294 ASN cc_start: 0.7950 (p0) cc_final: 0.7580 (p0) REVERT: B 353 MET cc_start: 0.6981 (mpp) cc_final: 0.6708 (pmm) REVERT: B 459 GLN cc_start: 0.6845 (mp10) cc_final: 0.6364 (mm-40) REVERT: B 464 THR cc_start: 0.8933 (m) cc_final: 0.8715 (p) REVERT: B 689 ASP cc_start: 0.7887 (p0) cc_final: 0.7563 (p0) REVERT: B 726 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7380 (m-10) REVERT: B 758 MET cc_start: 0.9226 (mtp) cc_final: 0.8989 (mtm) REVERT: B 797 LEU cc_start: 0.7016 (pt) cc_final: 0.6330 (mt) REVERT: B 804 LEU cc_start: 0.8757 (tp) cc_final: 0.8545 (mt) REVERT: B 863 MET cc_start: 0.8692 (mmt) cc_final: 0.8327 (mmt) REVERT: B 897 ARG cc_start: 0.8690 (mtt180) cc_final: 0.7551 (mmt180) REVERT: B 942 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: B 944 ASP cc_start: 0.7736 (t0) cc_final: 0.7014 (p0) REVERT: B 1023 MET cc_start: 0.6179 (mmp) cc_final: 0.4328 (ttt) REVERT: B 1046 ARG cc_start: 0.7537 (ttm170) cc_final: 0.7138 (mtp85) REVERT: B 1047 ASN cc_start: 0.6452 (m-40) cc_final: 0.5809 (t0) REVERT: B 1048 GLU cc_start: 0.7045 (pm20) cc_final: 0.6675 (mp0) REVERT: B 1051 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: C 123 ASP cc_start: 0.7252 (m-30) cc_final: 0.6059 (p0) REVERT: C 163 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8361 (ptmt) REVERT: C 189 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6692 (ttm) REVERT: C 294 ASN cc_start: 0.7889 (p0) cc_final: 0.7534 (p0) REVERT: C 353 MET cc_start: 0.6988 (mpp) cc_final: 0.6718 (pmm) REVERT: C 402 GLU cc_start: 0.7727 (pp20) cc_final: 0.7514 (pp20) REVERT: C 457 ASP cc_start: 0.7411 (p0) cc_final: 0.7054 (OUTLIER) REVERT: C 459 GLN cc_start: 0.6812 (mp10) cc_final: 0.6316 (mm-40) REVERT: C 464 THR cc_start: 0.8931 (m) cc_final: 0.8720 (p) REVERT: C 666 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8388 (mt0) REVERT: C 689 ASP cc_start: 0.7880 (p0) cc_final: 0.7554 (p0) REVERT: C 726 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7432 (m-10) REVERT: C 732 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7600 (p) REVERT: C 758 MET cc_start: 0.9235 (mtp) cc_final: 0.8998 (mtm) REVERT: C 797 LEU cc_start: 0.7028 (pt) cc_final: 0.6349 (mt) REVERT: C 804 LEU cc_start: 0.8753 (tp) cc_final: 0.8541 (mt) REVERT: C 897 ARG cc_start: 0.8698 (mtt180) cc_final: 0.7563 (mmt180) REVERT: C 942 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: C 944 ASP cc_start: 0.7740 (t0) cc_final: 0.7026 (p0) REVERT: C 1023 MET cc_start: 0.6195 (mmp) cc_final: 0.4331 (ttt) REVERT: C 1047 ASN cc_start: 0.6405 (m-40) cc_final: 0.5870 (t0) REVERT: C 1048 GLU cc_start: 0.7257 (pm20) cc_final: 0.6719 (mp0) REVERT: C 1051 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7873 (tp30) REVERT: D 123 ASP cc_start: 0.7138 (m-30) cc_final: 0.5988 (p0) REVERT: D 163 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8372 (ptmt) REVERT: D 189 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6691 (ttm) REVERT: D 294 ASN cc_start: 0.7975 (p0) cc_final: 0.7581 (p0) REVERT: D 353 MET cc_start: 0.6677 (mpp) cc_final: 0.6411 (pmm) REVERT: D 464 THR cc_start: 0.8948 (m) cc_final: 0.8692 (p) REVERT: D 507 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7198 (tpm170) REVERT: D 627 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8600 (mt-10) REVERT: D 689 ASP cc_start: 0.7891 (p0) cc_final: 0.7569 (p0) REVERT: D 726 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7427 (m-10) REVERT: D 732 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7587 (p) REVERT: D 758 MET cc_start: 0.9226 (mtp) cc_final: 0.8985 (mtm) REVERT: D 797 LEU cc_start: 0.7008 (pt) cc_final: 0.6325 (mt) REVERT: D 804 LEU cc_start: 0.8756 (tp) cc_final: 0.8539 (mt) REVERT: D 897 ARG cc_start: 0.8691 (mtt180) cc_final: 0.7560 (mmt180) REVERT: D 942 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: D 944 ASP cc_start: 0.7747 (t0) cc_final: 0.7031 (p0) REVERT: D 1023 MET cc_start: 0.6181 (mmp) cc_final: 0.4327 (ttt) REVERT: D 1046 ARG cc_start: 0.7536 (ttm170) cc_final: 0.7134 (mtp85) REVERT: D 1047 ASN cc_start: 0.6476 (m-40) cc_final: 0.5818 (t0) REVERT: D 1048 GLU cc_start: 0.7049 (pm20) cc_final: 0.6678 (mp0) REVERT: D 1051 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7915 (tp30) outliers start: 116 outliers final: 63 residues processed: 436 average time/residue: 1.4222 time to fit residues: 735.5067 Evaluate side-chains 403 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 316 time to evaluate : 3.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 189 MET 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 405 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 807 PHE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 488 LEU 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 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 807 PHE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 1051 GLU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 491 GLU 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 666 GLN Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 726 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 807 PHE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain D residue 148 VAL 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 323 LYS Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 726 TYR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 807 PHE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 1051 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 176 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 260 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 186 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN ** 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 = 0.4118 r_free = 0.4118 target = 0.169790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123434 restraints weight = 47299.329| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.33 r_work: 0.3367 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31192 Z= 0.133 Angle : 0.653 15.336 42260 Z= 0.324 Chirality : 0.040 0.154 4708 Planarity : 0.004 0.043 5280 Dihedral : 5.012 50.104 4024 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.25 % Allowed : 19.77 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3656 helix: 1.37 (0.11), residues: 2460 sheet: -1.32 (0.38), residues: 188 loop : -2.04 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 786 HIS 0.003 0.001 HIS A 500 PHE 0.023 0.001 PHE B 807 TYR 0.048 0.002 TYR C 646 ARG 0.008 0.000 ARG C1079 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 1756) hydrogen bonds : angle 3.91827 ( 5232) SS BOND : bond 0.00471 ( 4) SS BOND : angle 2.21345 ( 8) covalent geometry : bond 0.00312 (31188) covalent geometry : angle 0.65216 (42252) *********************** 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 461 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 353 time to evaluate : 6.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8354 (ptmt) REVERT: A 189 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6854 (ttm) REVERT: A 294 ASN cc_start: 0.7825 (p0) cc_final: 0.7501 (p0) REVERT: A 330 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: A 353 MET cc_start: 0.7057 (mpp) cc_final: 0.6772 (pmm) REVERT: A 364 ARG cc_start: 0.7112 (ttp-110) cc_final: 0.6644 (tmt-80) REVERT: A 402 GLU cc_start: 0.7682 (pp20) cc_final: 0.7458 (pp20) REVERT: A 459 GLN cc_start: 0.6830 (mp10) cc_final: 0.6357 (mm-40) REVERT: A 464 THR cc_start: 0.8924 (m) cc_final: 0.8670 (p) REVERT: A 496 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7943 (mp) REVERT: A 507 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7111 (tpm170) REVERT: A 574 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8151 (tppt) REVERT: A 627 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: A 689 ASP cc_start: 0.7848 (p0) cc_final: 0.7523 (p0) REVERT: A 758 MET cc_start: 0.9201 (mtp) cc_final: 0.8988 (mtm) REVERT: A 797 LEU cc_start: 0.7315 (pt) cc_final: 0.6647 (mt) REVERT: A 863 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8255 (mmt) REVERT: A 897 ARG cc_start: 0.8638 (mtt180) cc_final: 0.7532 (mmt180) REVERT: A 942 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: A 944 ASP cc_start: 0.7612 (t0) cc_final: 0.7002 (p0) REVERT: A 1023 MET cc_start: 0.6224 (mmp) cc_final: 0.4359 (ttt) REVERT: A 1046 ARG cc_start: 0.5533 (ttm-80) cc_final: 0.5048 (mtp85) REVERT: A 1047 ASN cc_start: 0.6269 (m-40) cc_final: 0.5776 (t0) REVERT: A 1048 GLU cc_start: 0.7174 (pm20) cc_final: 0.6615 (mp0) REVERT: A 1051 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: B 144 LEU cc_start: 0.8281 (tt) cc_final: 0.7871 (mp) REVERT: B 163 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8322 (ptmt) REVERT: B 189 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6843 (ttm) REVERT: B 294 ASN cc_start: 0.7825 (p0) cc_final: 0.7489 (p0) REVERT: B 330 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: B 353 MET cc_start: 0.7048 (mpp) cc_final: 0.6762 (pmm) REVERT: B 364 ARG cc_start: 0.7411 (tpm170) cc_final: 0.7073 (mmm-85) REVERT: B 459 GLN cc_start: 0.6825 (mp10) cc_final: 0.6369 (mm-40) REVERT: B 464 THR cc_start: 0.8920 (m) cc_final: 0.8707 (p) REVERT: B 480 ASN cc_start: 0.8002 (m-40) cc_final: 0.7555 (m-40) REVERT: B 616 GLU cc_start: 0.7928 (tt0) cc_final: 0.7658 (tp30) REVERT: B 689 ASP cc_start: 0.7864 (p0) cc_final: 0.7538 (p0) REVERT: B 726 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7405 (m-10) REVERT: B 758 MET cc_start: 0.9216 (mtp) cc_final: 0.9005 (mtm) REVERT: B 797 LEU cc_start: 0.7320 (pt) cc_final: 0.6617 (mt) REVERT: B 863 MET cc_start: 0.8667 (mmt) cc_final: 0.8289 (mmt) REVERT: B 897 ARG cc_start: 0.8646 (mtt180) cc_final: 0.7531 (mmt180) REVERT: B 942 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: B 944 ASP cc_start: 0.7605 (t0) cc_final: 0.6996 (p0) REVERT: B 1023 MET cc_start: 0.6239 (mmp) cc_final: 0.4366 (ttt) REVERT: B 1047 ASN cc_start: 0.6287 (m-40) cc_final: 0.5727 (t0) REVERT: B 1048 GLU cc_start: 0.6911 (pm20) cc_final: 0.6541 (mp0) REVERT: B 1051 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7869 (tp30) REVERT: C 163 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8343 (ptmt) REVERT: C 189 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6851 (ttm) REVERT: C 294 ASN cc_start: 0.7834 (p0) cc_final: 0.7510 (p0) REVERT: C 330 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: C 353 MET cc_start: 0.7017 (mpp) cc_final: 0.6736 (pmm) REVERT: C 364 ARG cc_start: 0.7392 (tpm170) cc_final: 0.7047 (mmm-85) REVERT: C 402 GLU cc_start: 0.7709 (pp20) cc_final: 0.7473 (pp20) REVERT: C 457 ASP cc_start: 0.7446 (p0) cc_final: 0.7108 (p0) REVERT: C 459 GLN cc_start: 0.6800 (mp10) cc_final: 0.6341 (mm-40) REVERT: C 464 THR cc_start: 0.8917 (m) cc_final: 0.8677 (p) REVERT: C 480 ASN cc_start: 0.7944 (m-40) cc_final: 0.7510 (m-40) REVERT: C 689 ASP cc_start: 0.7837 (p0) cc_final: 0.7519 (p0) REVERT: C 726 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.7493 (m-10) REVERT: C 758 MET cc_start: 0.9208 (mtp) cc_final: 0.8993 (mtm) REVERT: C 797 LEU cc_start: 0.7321 (pt) cc_final: 0.6615 (mt) REVERT: C 863 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8243 (mmt) REVERT: C 897 ARG cc_start: 0.8646 (mtt180) cc_final: 0.7545 (mmt180) REVERT: C 942 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: C 944 ASP cc_start: 0.7616 (t0) cc_final: 0.7004 (p0) REVERT: C 1023 MET cc_start: 0.6224 (mmp) cc_final: 0.4352 (ttt) REVERT: C 1046 ARG cc_start: 0.5538 (ttm-80) cc_final: 0.5046 (mtp85) REVERT: C 1047 ASN cc_start: 0.6282 (m-40) cc_final: 0.5786 (t0) REVERT: C 1048 GLU cc_start: 0.7179 (pm20) cc_final: 0.6614 (mp0) REVERT: C 1051 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7877 (tp30) REVERT: D 163 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8327 (ptmt) REVERT: D 189 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6849 (ttm) REVERT: D 294 ASN cc_start: 0.7844 (p0) cc_final: 0.7516 (p0) REVERT: D 353 MET cc_start: 0.6801 (mpp) cc_final: 0.6529 (pmm) REVERT: D 364 ARG cc_start: 0.7098 (ttp-110) cc_final: 0.6646 (tmt-80) REVERT: D 459 GLN cc_start: 0.6739 (mp10) cc_final: 0.6264 (mm-40) REVERT: D 464 THR cc_start: 0.8939 (m) cc_final: 0.8686 (p) REVERT: D 480 ASN cc_start: 0.7994 (m-40) cc_final: 0.7549 (m-40) REVERT: D 616 GLU cc_start: 0.7968 (tt0) cc_final: 0.7682 (tp30) REVERT: D 689 ASP cc_start: 0.7842 (p0) cc_final: 0.7519 (p0) REVERT: D 726 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7466 (m-10) REVERT: D 758 MET cc_start: 0.9201 (mtp) cc_final: 0.8982 (mtm) REVERT: D 797 LEU cc_start: 0.7313 (pt) cc_final: 0.6612 (mt) REVERT: D 863 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8275 (mmt) REVERT: D 897 ARG cc_start: 0.8649 (mtt180) cc_final: 0.7548 (mmt180) REVERT: D 942 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: D 944 ASP cc_start: 0.7628 (t0) cc_final: 0.6992 (p0) REVERT: D 1023 MET cc_start: 0.6212 (mmp) cc_final: 0.4352 (ttt) REVERT: D 1047 ASN cc_start: 0.6293 (m-40) cc_final: 0.5737 (t0) REVERT: D 1048 GLU cc_start: 0.6910 (pm20) cc_final: 0.6543 (mp0) REVERT: D 1051 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7873 (tp30) outliers start: 108 outliers final: 47 residues processed: 433 average time/residue: 1.6909 time to fit residues: 871.9129 Evaluate side-chains 410 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 338 time to evaluate : 5.598 ------------------------------------------------------------------------------- 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 189 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 496 LEU 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 702 ILE 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 863 MET Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 588 THR 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 791 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 1051 GLU 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 323 LYS Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 491 GLU 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 702 ILE Chi-restraints excluded: chain C residue 726 TYR Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 849 VAL 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 C residue 1051 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 488 LEU 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 702 ILE 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 863 MET Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 942 GLU Chi-restraints excluded: chain D residue 1051 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 140 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 167 optimal weight: 0.4980 chunk 352 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 306 optimal weight: 4.9990 chunk 371 optimal weight: 0.0270 chunk 173 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- 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 973 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.171820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.125126 restraints weight = 47194.587| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.54 r_work: 0.3395 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31192 Z= 0.123 Angle : 0.639 15.286 42260 Z= 0.317 Chirality : 0.039 0.166 4708 Planarity : 0.004 0.040 5280 Dihedral : 4.794 50.733 4024 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.58 % Allowed : 20.49 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3656 helix: 1.46 (0.11), residues: 2472 sheet: -1.18 (0.38), residues: 188 loop : -2.09 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 786 HIS 0.004 0.001 HIS C 845 PHE 0.010 0.001 PHE C 847 TYR 0.036 0.002 TYR B 191 ARG 0.010 0.000 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 1756) hydrogen bonds : angle 3.81300 ( 5232) SS BOND : bond 0.00484 ( 4) SS BOND : angle 2.02297 ( 8) covalent geometry : bond 0.00286 (31188) covalent geometry : angle 0.63796 (42252) ********************** 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 479 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 393 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7082 (m-30) cc_final: 0.6012 (p0) REVERT: A 163 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8390 (ptmt) REVERT: A 189 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6836 (ttm) REVERT: A 294 ASN cc_start: 0.7837 (p0) cc_final: 0.7456 (p0) REVERT: A 353 MET cc_start: 0.7018 (mpp) cc_final: 0.6738 (pmm) REVERT: A 402 GLU cc_start: 0.7676 (pp20) cc_final: 0.7448 (pp20) REVERT: A 459 GLN cc_start: 0.6840 (mp10) cc_final: 0.6441 (mm-40) REVERT: A 464 THR cc_start: 0.8919 (m) cc_final: 0.8638 (p) REVERT: A 496 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7626 (mp) REVERT: A 507 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7115 (tpm170) REVERT: A 627 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8558 (mt-10) REVERT: A 666 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8437 (mt0) REVERT: A 689 ASP cc_start: 0.7802 (p0) cc_final: 0.7519 (p0) REVERT: A 797 LEU cc_start: 0.7405 (pt) cc_final: 0.6784 (mp) REVERT: A 863 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8294 (mmt) REVERT: A 897 ARG cc_start: 0.8633 (mtt180) cc_final: 0.7503 (mmt180) REVERT: A 944 ASP cc_start: 0.7478 (t0) cc_final: 0.7182 (p0) REVERT: A 950 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7940 (ttm170) REVERT: A 1023 MET cc_start: 0.6159 (mmp) cc_final: 0.4298 (ttm) REVERT: A 1046 ARG cc_start: 0.5575 (ttm-80) cc_final: 0.5138 (mtp85) REVERT: A 1047 ASN cc_start: 0.6325 (m-40) cc_final: 0.5815 (t0) REVERT: A 1048 GLU cc_start: 0.7120 (pm20) cc_final: 0.6618 (mp0) REVERT: A 1051 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7802 (tp30) REVERT: A 1079 ARG cc_start: 0.7242 (ttp80) cc_final: 0.6855 (mtt90) REVERT: B 123 ASP cc_start: 0.7081 (m-30) cc_final: 0.5982 (p0) REVERT: B 144 LEU cc_start: 0.8283 (tt) cc_final: 0.7871 (mp) REVERT: B 163 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8342 (ptmt) REVERT: B 189 MET cc_start: 0.7075 (mtm) cc_final: 0.6827 (ttm) REVERT: B 294 ASN cc_start: 0.7840 (p0) cc_final: 0.7470 (p0) REVERT: B 353 MET cc_start: 0.6998 (mpp) cc_final: 0.6719 (pmm) REVERT: B 364 ARG cc_start: 0.7358 (tpm170) cc_final: 0.7035 (mmm-85) REVERT: B 402 GLU cc_start: 0.7456 (pp20) cc_final: 0.7247 (pp20) REVERT: B 459 GLN cc_start: 0.6894 (mp10) cc_final: 0.6470 (mm-40) REVERT: B 464 THR cc_start: 0.8915 (m) cc_final: 0.8692 (p) REVERT: B 480 ASN cc_start: 0.7744 (m-40) cc_final: 0.7365 (m-40) REVERT: B 689 ASP cc_start: 0.7824 (p0) cc_final: 0.7543 (p0) REVERT: B 726 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7504 (m-10) REVERT: B 731 PHE cc_start: 0.7788 (m-80) cc_final: 0.6758 (t80) REVERT: B 797 LEU cc_start: 0.7387 (pt) cc_final: 0.6764 (mt) REVERT: B 863 MET cc_start: 0.8649 (mmt) cc_final: 0.8319 (mmt) REVERT: B 897 ARG cc_start: 0.8637 (mtt180) cc_final: 0.7496 (mmt180) REVERT: B 944 ASP cc_start: 0.7446 (t0) cc_final: 0.7176 (p0) REVERT: B 950 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7954 (ttm170) REVERT: B 1023 MET cc_start: 0.6157 (mmp) cc_final: 0.4330 (ttt) REVERT: B 1047 ASN cc_start: 0.6221 (m-40) cc_final: 0.5793 (t0) REVERT: B 1048 GLU cc_start: 0.7102 (pm20) cc_final: 0.6604 (mp0) REVERT: B 1051 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7795 (tp30) REVERT: B 1079 ARG cc_start: 0.7235 (ttp80) cc_final: 0.6855 (mtt90) REVERT: C 123 ASP cc_start: 0.7081 (m-30) cc_final: 0.5982 (p0) REVERT: C 144 LEU cc_start: 0.8247 (tt) cc_final: 0.7805 (mp) REVERT: C 163 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8359 (ptmt) REVERT: C 189 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6828 (ttm) REVERT: C 294 ASN cc_start: 0.7870 (p0) cc_final: 0.7488 (p0) REVERT: C 353 MET cc_start: 0.7017 (mpp) cc_final: 0.6734 (pmm) REVERT: C 364 ARG cc_start: 0.7360 (tpm170) cc_final: 0.7026 (mmm-85) REVERT: C 396 MET cc_start: 0.6415 (mpm) cc_final: 0.6201 (mpp) REVERT: C 402 GLU cc_start: 0.7701 (pp20) cc_final: 0.7475 (pp20) REVERT: C 457 ASP cc_start: 0.7525 (p0) cc_final: 0.7177 (p0) REVERT: C 459 GLN cc_start: 0.6870 (mp10) cc_final: 0.6437 (mm-40) REVERT: C 464 THR cc_start: 0.8959 (m) cc_final: 0.8680 (p) REVERT: C 480 ASN cc_start: 0.7727 (m-40) cc_final: 0.7348 (m-40) REVERT: C 507 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7133 (tpm170) REVERT: C 666 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: C 689 ASP cc_start: 0.7811 (p0) cc_final: 0.7529 (p0) REVERT: C 731 PHE cc_start: 0.7695 (m-80) cc_final: 0.6686 (t80) REVERT: C 797 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6763 (mt) REVERT: C 897 ARG cc_start: 0.8647 (mtt180) cc_final: 0.7513 (mmt180) REVERT: C 944 ASP cc_start: 0.7469 (t0) cc_final: 0.7220 (p0) REVERT: C 950 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7969 (ttm170) REVERT: C 1023 MET cc_start: 0.6159 (mmp) cc_final: 0.4321 (ttt) REVERT: C 1046 ARG cc_start: 0.5588 (ttm-80) cc_final: 0.5155 (mtp85) REVERT: C 1047 ASN cc_start: 0.6303 (m-40) cc_final: 0.5816 (t0) REVERT: C 1048 GLU cc_start: 0.7113 (pm20) cc_final: 0.6603 (mp0) REVERT: C 1051 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7797 (tp30) REVERT: C 1079 ARG cc_start: 0.7240 (ttp80) cc_final: 0.6853 (mtt90) REVERT: D 123 ASP cc_start: 0.7098 (m-30) cc_final: 0.6029 (p0) REVERT: D 144 LEU cc_start: 0.8252 (tt) cc_final: 0.7823 (mp) REVERT: D 163 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8354 (ptmt) REVERT: D 189 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6843 (ttm) REVERT: D 294 ASN cc_start: 0.7779 (p0) cc_final: 0.7418 (p0) REVERT: D 353 MET cc_start: 0.6962 (mpp) cc_final: 0.6699 (pmm) REVERT: D 402 GLU cc_start: 0.7532 (pp20) cc_final: 0.7224 (pp20) REVERT: D 459 GLN cc_start: 0.6675 (mp10) cc_final: 0.6251 (mm-40) REVERT: D 464 THR cc_start: 0.8939 (m) cc_final: 0.8675 (p) REVERT: D 480 ASN cc_start: 0.7746 (m-40) cc_final: 0.7368 (m-40) REVERT: D 666 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: D 689 ASP cc_start: 0.7778 (p0) cc_final: 0.7490 (p0) REVERT: D 731 PHE cc_start: 0.7653 (m-80) cc_final: 0.6578 (t80) REVERT: D 797 LEU cc_start: 0.7380 (pt) cc_final: 0.6761 (mt) REVERT: D 863 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8297 (mmt) REVERT: D 897 ARG cc_start: 0.8644 (mtt180) cc_final: 0.7515 (mmt180) REVERT: D 944 ASP cc_start: 0.7473 (t0) cc_final: 0.7189 (p0) REVERT: D 950 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7962 (ttm170) REVERT: D 1023 MET cc_start: 0.6152 (mmp) cc_final: 0.4320 (ttt) REVERT: D 1047 ASN cc_start: 0.6236 (m-40) cc_final: 0.5797 (t0) REVERT: D 1048 GLU cc_start: 0.7097 (pm20) cc_final: 0.6599 (mp0) REVERT: D 1051 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7803 (tp30) REVERT: D 1079 ARG cc_start: 0.7238 (ttp80) cc_final: 0.6852 (mtt90) outliers start: 86 outliers final: 41 residues processed: 453 average time/residue: 1.3457 time to fit residues: 721.8658 Evaluate side-chains 413 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 350 time to evaluate : 3.235 ------------------------------------------------------------------------------- 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 189 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 496 LEU 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 783 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 A residue 1051 GLU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 148 VAL 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 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 950 ARG Chi-restraints excluded: chain B residue 1051 GLU 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 488 LEU Chi-restraints excluded: chain C residue 491 GLU 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 628 LEU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 929 CYS Chi-restraints excluded: chain C residue 950 ARG Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain D residue 148 VAL 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 488 LEU 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 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 Chi-restraints excluded: chain D residue 950 ARG Chi-restraints excluded: chain D residue 1051 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 104 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 317 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 350 optimal weight: 4.9990 chunk 328 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 A 973 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.167085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120652 restraints weight = 47257.130| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.44 r_work: 0.3333 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 31192 Z= 0.201 Angle : 0.717 14.831 42260 Z= 0.358 Chirality : 0.044 0.189 4708 Planarity : 0.004 0.044 5280 Dihedral : 5.049 52.343 4024 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.49 % Allowed : 21.75 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3656 helix: 1.28 (0.11), residues: 2460 sheet: -1.24 (0.38), residues: 188 loop : -1.97 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 786 HIS 0.006 0.001 HIS D 765 PHE 0.024 0.002 PHE C 165 TYR 0.039 0.002 TYR D 191 ARG 0.010 0.001 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 1756) hydrogen bonds : angle 4.03314 ( 5232) SS BOND : bond 0.00520 ( 4) SS BOND : angle 2.57457 ( 8) covalent geometry : bond 0.00493 (31188) covalent geometry : angle 0.71612 (42252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29770.44 seconds wall clock time: 523 minutes 43.85 seconds (31423.85 seconds total)