Starting phenix.real_space_refine on Thu Mar 5 18:25:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fb1_31512/03_2026/7fb1_31512.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fb1_31512/03_2026/7fb1_31512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fb1_31512/03_2026/7fb1_31512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fb1_31512/03_2026/7fb1_31512.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fb1_31512/03_2026/7fb1_31512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fb1_31512/03_2026/7fb1_31512.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.070 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 15437 2.51 5 N 4020 2.21 5 O 4599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24168 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8039 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 50, 'TRANS': 978} Chain breaks: 7 Chain: "B" Number of atoms: 8091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8091 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 52, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8038 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 52, 'TRANS': 976} Chain breaks: 8 Time building chain proxies: 5.33, per 1000 atoms: 0.22 Number of scatterers: 24168 At special positions: 0 Unit cell: (138.72, 136, 195.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 4599 8.00 N 4020 7.00 C 15437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 999.2 milliseconds 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 48 sheets defined 24.2% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.219A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.721A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.710A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.623A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 7.122A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.963A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.933A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.630A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.140A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.566A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.696A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.924A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.530A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.680A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.697A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.626A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.780A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.897A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.533A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.823A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 857 removed outlier: 4.037A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY C 857 " --> pdb=" O LYS C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.592A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.518A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 966 removed outlier: 3.656A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.804A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.056A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.081A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 197 removed outlier: 3.569A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.600A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.596A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 552 through 554 removed outlier: 4.011A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.854A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 719 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 718 through 719 current: chain 'A' and resid 1059 through 1069 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 735 removed outlier: 3.701A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.665A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.775A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.762A pdb=" N VAL A1104 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.144A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 50 through 55 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.065A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 317 removed outlier: 6.398A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 356 through 357 removed outlier: 4.826A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.705A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.503A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 643 through 645 removed outlier: 3.619A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.796A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 720 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 720 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.758A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD5, first strand: chain 'B' and resid 1087 through 1090 removed outlier: 4.036A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B1121 " --> pdb=" O PHE B1089 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.996A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.803A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD9, first strand: chain 'C' and resid 166 through 170 removed outlier: 3.545A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 188 through 197 removed outlier: 3.840A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.570A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 357 removed outlier: 4.821A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.579A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 553 through 554 removed outlier: 3.511A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 642 through 645 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.748A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 722 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 712 through 722 current: chain 'C' and resid 1059 through 1075 No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.086A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AF3, first strand: chain 'C' and resid 1095 through 1096 778 hydrogen bonds defined for protein. 2088 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: 4.78 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7829 1.35 - 1.47: 6317 1.47 - 1.60: 10427 1.60 - 1.73: 0 1.73 - 1.85: 140 Bond restraints: 24713 Sorted by residual: bond pdb=" C ALA A 609 " pdb=" N VAL A 610 " ideal model delta sigma weight residual 1.334 1.299 0.034 1.24e-02 6.50e+03 7.66e+00 bond pdb=" CA LEU B1034 " pdb=" C LEU B1034 " ideal model delta sigma weight residual 1.522 1.476 0.045 1.72e-02 3.38e+03 6.94e+00 bond pdb=" N SER C 940 " pdb=" CA SER C 940 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.16e-02 7.43e+03 6.23e+00 bond pdb=" C THR A 599 " pdb=" N PRO A 600 " ideal model delta sigma weight residual 1.332 1.311 0.022 8.90e-03 1.26e+04 5.89e+00 bond pdb=" CA TYR A 917 " pdb=" C TYR A 917 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.72e-02 3.38e+03 5.85e+00 ... (remaining 24708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 33427 3.65 - 7.31: 184 7.31 - 10.96: 9 10.96 - 14.61: 1 14.61 - 18.27: 1 Bond angle restraints: 33622 Sorted by residual: angle pdb=" C VAL B 83 " pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta sigma weight residual 120.67 138.94 -18.27 1.34e+00 5.57e-01 1.86e+02 angle pdb=" N PHE B 79 " pdb=" CA PHE B 79 " pdb=" C PHE B 79 " ideal model delta sigma weight residual 112.72 105.49 7.23 1.36e+00 5.41e-01 2.83e+01 angle pdb=" N VAL B 483 " pdb=" CA VAL B 483 " pdb=" C VAL B 483 " ideal model delta sigma weight residual 113.71 109.24 4.47 9.50e-01 1.11e+00 2.21e+01 angle pdb=" C LEU B 335 " pdb=" N CYS B 336 " pdb=" CA CYS B 336 " ideal model delta sigma weight residual 120.94 112.71 8.23 1.90e+00 2.77e-01 1.88e+01 angle pdb=" C ARG B 328 " pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 121.80 132.26 -10.46 2.44e+00 1.68e-01 1.84e+01 ... (remaining 33617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13267 17.92 - 35.84: 1243 35.84 - 53.76: 173 53.76 - 71.68: 35 71.68 - 89.61: 34 Dihedral angle restraints: 14752 sinusoidal: 5745 harmonic: 9007 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -174.09 88.09 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -5.53 -80.47 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CA PHE B 329 " pdb=" C PHE B 329 " pdb=" N PRO B 330 " pdb=" CA PRO B 330 " ideal model delta harmonic sigma weight residual 180.00 136.75 43.25 0 5.00e+00 4.00e-02 7.48e+01 ... (remaining 14749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2657 0.043 - 0.086: 874 0.086 - 0.129: 273 0.129 - 0.172: 26 0.172 - 0.215: 1 Chirality restraints: 3831 Sorted by residual: chirality pdb=" CA PHE B 329 " pdb=" N PHE B 329 " pdb=" C PHE B 329 " pdb=" CB PHE B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB VAL B 213 " pdb=" CA VAL B 213 " pdb=" CG1 VAL B 213 " pdb=" CG2 VAL B 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CB ILE C 896 " pdb=" CA ILE C 896 " pdb=" CG1 ILE C 896 " pdb=" CG2 ILE C 896 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 3828 not shown) Planarity restraints: 4365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 329 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO B 330 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 425 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO A 426 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 426 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 426 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO A 330 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.029 5.00e-02 4.00e+02 ... (remaining 4362 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 815 2.65 - 3.21: 26029 3.21 - 3.78: 38419 3.78 - 4.34: 50900 4.34 - 4.90: 80155 Nonbonded interactions: 196318 Sorted by model distance: nonbonded pdb=" OG1 THR B 393 " pdb=" O GLU B 516 " model vdw 2.091 3.040 nonbonded pdb=" O THR A 108 " pdb=" OG1 THR A 236 " model vdw 2.103 3.040 nonbonded pdb=" O PHE B 106 " pdb=" OG SER B 116 " model vdw 2.120 3.040 nonbonded pdb=" ND2 ASN B 81 " pdb=" O THR B 240 " model vdw 2.129 3.120 nonbonded pdb=" O THR C 109 " pdb=" NH2 ARG C 237 " model vdw 2.137 3.120 ... (remaining 196313 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 141 or resid 156 through 244 or resid 260 throu \ gh 827 or resid 851 through 1146)) selection = (chain 'B' and (resid 26 through 68 or resid 78 through 141 or resid 156 through \ 244 or resid 260 through 620 or resid 641 through 827 or resid 851 through 1146 \ )) selection = (chain 'C' and (resid 26 through 68 or resid 78 through 244 or resid 260 through \ 1146)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.040 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 : 0.007 0.093 24750 Z= 0.331 Angle : 0.834 18.266 33696 Z= 0.479 Chirality : 0.046 0.215 3831 Planarity : 0.004 0.061 4365 Dihedral : 14.192 89.606 8835 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.53 % Favored : 86.47 % Rotamer: Outliers : 0.07 % Allowed : 9.51 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.12), residues: 3045 helix: -1.59 (0.18), residues: 657 sheet: -3.49 (0.18), residues: 538 loop : -3.85 (0.11), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 102 TYR 0.021 0.002 TYR A 170 PHE 0.024 0.002 PHE B 329 TRP 0.015 0.002 TRP B 886 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00682 (24713) covalent geometry : angle 0.83035 (33622) SS BOND : bond 0.00576 ( 37) SS BOND : angle 1.87855 ( 74) hydrogen bonds : bond 0.19580 ( 778) hydrogen bonds : angle 8.98236 ( 2088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASN cc_start: 0.6809 (OUTLIER) cc_final: 0.5637 (p0) REVERT: A 177 MET cc_start: 0.8241 (mmt) cc_final: 0.7959 (ptp) REVERT: A 191 GLU cc_start: 0.6814 (pm20) cc_final: 0.6373 (pm20) REVERT: A 353 TRP cc_start: 0.8499 (p-90) cc_final: 0.8215 (p-90) REVERT: A 369 TYR cc_start: 0.7583 (m-10) cc_final: 0.7335 (m-10) REVERT: A 426 PRO cc_start: 0.8616 (Cg_exo) cc_final: 0.8392 (Cg_endo) REVERT: A 456 PHE cc_start: 0.8795 (m-80) cc_final: 0.8368 (m-80) REVERT: A 731 MET cc_start: 0.9204 (ptm) cc_final: 0.8911 (ptp) REVERT: A 855 PHE cc_start: 0.8240 (m-10) cc_final: 0.7949 (m-80) REVERT: A 869 MET cc_start: 0.9045 (mtt) cc_final: 0.8710 (mtt) REVERT: A 1050 MET cc_start: 0.9187 (ptp) cc_final: 0.8846 (ptm) REVERT: A 1138 TYR cc_start: 0.8328 (t80) cc_final: 0.7579 (t80) REVERT: B 858 LEU cc_start: 0.9750 (mp) cc_final: 0.9525 (mp) REVERT: B 900 MET cc_start: 0.8520 (mtp) cc_final: 0.8315 (mtt) REVERT: B 954 GLN cc_start: 0.9167 (mt0) cc_final: 0.8869 (mt0) REVERT: B 995 ARG cc_start: 0.9219 (mtt180) cc_final: 0.8892 (mmm-85) REVERT: B 1029 MET cc_start: 0.9682 (tpp) cc_final: 0.9460 (tpp) REVERT: C 52 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8341 (pp30) REVERT: C 489 TYR cc_start: 0.8547 (m-10) cc_final: 0.8115 (m-80) REVERT: C 740 MET cc_start: 0.9240 (tpp) cc_final: 0.9031 (tpp) REVERT: C 759 PHE cc_start: 0.8630 (m-80) cc_final: 0.8092 (m-80) REVERT: C 780 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7945 (mt-10) REVERT: C 869 MET cc_start: 0.9219 (mtt) cc_final: 0.8995 (mtm) REVERT: C 1002 GLN cc_start: 0.9203 (tp40) cc_final: 0.8745 (tm-30) REVERT: C 1005 GLN cc_start: 0.9493 (tp-100) cc_final: 0.9123 (tp40) REVERT: C 1017 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8583 (tp30) REVERT: C 1029 MET cc_start: 0.9600 (tpp) cc_final: 0.8873 (tpp) outliers start: 2 outliers final: 0 residues processed: 142 average time/residue: 0.1579 time to fit residues: 36.2981 Evaluate side-chains 92 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 314 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 487 ASN A 519 HIS A 536 ASN A 564 GLN A 580 GLN A 657 ASN A 690 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 953 ASN A 969 ASN A 978 ASN A1036 GLN A1083 HIS B 115 GLN B 218 GLN B 317 ASN B 388 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 657 ASN B 751 ASN B 755 GLN B 787 GLN B 949 GLN B 953 ASN B 954 GLN B1010 GLN B1071 GLN B1088 HIS C 61 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 317 ASN C 321 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 536 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 ASN C 901 GLN C 925 ASN C 935 GLN C 954 GLN C 965 GLN C 969 ASN C1005 GLN C1036 GLN C1054 GLN C1058 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.083770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.053415 restraints weight = 99923.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.055503 restraints weight = 47735.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.056891 restraints weight = 30017.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.057835 restraints weight = 22175.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058466 restraints weight = 18161.259| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24750 Z= 0.166 Angle : 0.671 11.024 33696 Z= 0.352 Chirality : 0.046 0.223 3831 Planarity : 0.005 0.066 4365 Dihedral : 5.828 42.368 3306 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 1.52 % Allowed : 11.99 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.14), residues: 3045 helix: 0.35 (0.20), residues: 654 sheet: -2.88 (0.19), residues: 595 loop : -3.27 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 102 TYR 0.018 0.001 TYR C 266 PHE 0.028 0.002 PHE B 329 TRP 0.011 0.002 TRP C 353 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00357 (24713) covalent geometry : angle 0.66843 (33622) SS BOND : bond 0.00409 ( 37) SS BOND : angle 1.40527 ( 74) hydrogen bonds : bond 0.05457 ( 778) hydrogen bonds : angle 6.65278 ( 2088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.6776 (pm20) cc_final: 0.6054 (pm20) REVERT: A 223 LEU cc_start: 0.8769 (mt) cc_final: 0.8552 (mt) REVERT: A 426 PRO cc_start: 0.8468 (Cg_exo) cc_final: 0.8197 (Cg_endo) REVERT: A 456 PHE cc_start: 0.8792 (m-80) cc_final: 0.8378 (m-80) REVERT: A 731 MET cc_start: 0.9305 (ptm) cc_final: 0.8932 (ptp) REVERT: A 773 GLU cc_start: 0.8687 (tp30) cc_final: 0.8314 (tp30) REVERT: A 869 MET cc_start: 0.9175 (mtt) cc_final: 0.8846 (mtt) REVERT: A 1050 MET cc_start: 0.9027 (ptp) cc_final: 0.8600 (ptm) REVERT: A 1138 TYR cc_start: 0.8446 (t80) cc_final: 0.7589 (t80) REVERT: B 118 LEU cc_start: 0.9430 (tt) cc_final: 0.8969 (mt) REVERT: B 377 PHE cc_start: 0.6876 (t80) cc_final: 0.6462 (t80) REVERT: B 858 LEU cc_start: 0.9722 (mp) cc_final: 0.9475 (mp) REVERT: B 900 MET cc_start: 0.8605 (mtp) cc_final: 0.8346 (mtt) REVERT: B 954 GLN cc_start: 0.9296 (mt0) cc_final: 0.8851 (mt0) REVERT: B 995 ARG cc_start: 0.9228 (mtt180) cc_final: 0.8930 (mmm-85) REVERT: B 1029 MET cc_start: 0.9728 (tpp) cc_final: 0.9429 (tpp) REVERT: C 166 CYS cc_start: 0.4562 (OUTLIER) cc_final: 0.4349 (t) REVERT: C 378 LYS cc_start: 0.9438 (mmtt) cc_final: 0.9110 (pttp) REVERT: C 671 CYS cc_start: 0.4846 (OUTLIER) cc_final: 0.4118 (p) REVERT: C 740 MET cc_start: 0.9446 (tpp) cc_final: 0.9241 (tpp) REVERT: C 759 PHE cc_start: 0.8735 (m-80) cc_final: 0.8143 (m-80) REVERT: C 762 GLN cc_start: 0.9427 (tp40) cc_final: 0.9200 (tp40) REVERT: C 780 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8044 (mt-10) REVERT: C 1002 GLN cc_start: 0.9336 (tp40) cc_final: 0.8755 (tm-30) REVERT: C 1005 GLN cc_start: 0.9556 (tp40) cc_final: 0.9235 (tp40) REVERT: C 1017 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8659 (tp30) REVERT: C 1029 MET cc_start: 0.9465 (tpp) cc_final: 0.9155 (tpp) outliers start: 41 outliers final: 16 residues processed: 153 average time/residue: 0.1503 time to fit residues: 38.1572 Evaluate side-chains 114 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1008 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 9 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 102 optimal weight: 0.0060 chunk 227 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 580 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B1036 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 965 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.084821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.054350 restraints weight = 99070.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.056497 restraints weight = 46591.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.057928 restraints weight = 29119.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.058905 restraints weight = 21378.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.059521 restraints weight = 17449.311| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24750 Z= 0.121 Angle : 0.602 11.772 33696 Z= 0.312 Chirality : 0.044 0.225 3831 Planarity : 0.004 0.066 4365 Dihedral : 5.309 40.215 3304 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.81 % Allowed : 13.43 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.15), residues: 3045 helix: 1.02 (0.21), residues: 672 sheet: -2.38 (0.19), residues: 607 loop : -2.94 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 983 TYR 0.020 0.001 TYR A 369 PHE 0.024 0.001 PHE B 329 TRP 0.015 0.002 TRP A 353 HIS 0.009 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00255 (24713) covalent geometry : angle 0.59931 (33622) SS BOND : bond 0.00373 ( 37) SS BOND : angle 1.33398 ( 74) hydrogen bonds : bond 0.04661 ( 778) hydrogen bonds : angle 5.97319 ( 2088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 0.990 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: A 191 GLU cc_start: 0.6615 (pm20) cc_final: 0.5791 (pm20) REVERT: A 456 PHE cc_start: 0.9039 (m-80) cc_final: 0.8749 (m-80) REVERT: A 505 TYR cc_start: 0.9106 (m-80) cc_final: 0.8862 (m-80) REVERT: A 731 MET cc_start: 0.9310 (ptm) cc_final: 0.9003 (ptp) REVERT: A 773 GLU cc_start: 0.8792 (tp30) cc_final: 0.8351 (tp30) REVERT: A 855 PHE cc_start: 0.7706 (m-80) cc_final: 0.7141 (m-80) REVERT: A 869 MET cc_start: 0.9230 (mtt) cc_final: 0.8683 (mtp) REVERT: A 1138 TYR cc_start: 0.8427 (t80) cc_final: 0.7539 (t80) REVERT: B 177 MET cc_start: 0.0644 (ttp) cc_final: 0.0018 (ttp) REVERT: B 740 MET cc_start: 0.9243 (tpp) cc_final: 0.8963 (tpp) REVERT: B 858 LEU cc_start: 0.9716 (mp) cc_final: 0.9456 (mp) REVERT: B 869 MET cc_start: 0.9274 (mtt) cc_final: 0.9033 (mtt) REVERT: B 900 MET cc_start: 0.8551 (mtp) cc_final: 0.8307 (mtt) REVERT: B 954 GLN cc_start: 0.9246 (mt0) cc_final: 0.8813 (mt0) REVERT: B 965 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8597 (tm-30) REVERT: B 995 ARG cc_start: 0.9180 (mtt180) cc_final: 0.8847 (mmm-85) REVERT: B 1029 MET cc_start: 0.9706 (tpp) cc_final: 0.9370 (tpp) REVERT: B 1031 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8075 (mt-10) REVERT: C 717 ASN cc_start: 0.6565 (OUTLIER) cc_final: 0.6323 (t0) REVERT: C 740 MET cc_start: 0.9452 (tpp) cc_final: 0.9220 (tpp) REVERT: C 777 ASN cc_start: 0.9142 (t0) cc_final: 0.8663 (t0) REVERT: C 780 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8202 (mp0) REVERT: C 900 MET cc_start: 0.9036 (mmm) cc_final: 0.8763 (mmt) REVERT: C 1002 GLN cc_start: 0.9397 (tp40) cc_final: 0.8702 (tm-30) REVERT: C 1005 GLN cc_start: 0.9436 (tp40) cc_final: 0.9131 (tp40) REVERT: C 1017 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8585 (tp30) outliers start: 49 outliers final: 28 residues processed: 167 average time/residue: 0.1384 time to fit residues: 38.9605 Evaluate side-chains 125 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 237 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 213 optimal weight: 20.0000 chunk 268 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 519 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.083955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.053462 restraints weight = 99039.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.055550 restraints weight = 47185.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.056966 restraints weight = 29632.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057924 restraints weight = 21795.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.058519 restraints weight = 17825.769| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24750 Z= 0.147 Angle : 0.594 11.409 33696 Z= 0.307 Chirality : 0.044 0.216 3831 Planarity : 0.004 0.065 4365 Dihedral : 5.150 39.555 3304 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.48 % Allowed : 14.73 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.15), residues: 3045 helix: 1.16 (0.21), residues: 675 sheet: -2.20 (0.20), residues: 599 loop : -2.79 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.015 0.001 TYR B 160 PHE 0.030 0.001 PHE A 855 TRP 0.023 0.002 TRP A 353 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00327 (24713) covalent geometry : angle 0.59051 (33622) SS BOND : bond 0.00431 ( 37) SS BOND : angle 1.49225 ( 74) hydrogen bonds : bond 0.04399 ( 778) hydrogen bonds : angle 5.77725 ( 2088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 103 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8167 (mmmt) REVERT: A 223 LEU cc_start: 0.8721 (mt) cc_final: 0.8459 (mt) REVERT: A 456 PHE cc_start: 0.9081 (m-80) cc_final: 0.8741 (m-80) REVERT: A 505 TYR cc_start: 0.9143 (m-80) cc_final: 0.8924 (m-80) REVERT: A 731 MET cc_start: 0.9263 (ptm) cc_final: 0.8974 (ptp) REVERT: A 740 MET cc_start: 0.9061 (tpp) cc_final: 0.8840 (tpp) REVERT: A 773 GLU cc_start: 0.8887 (tp30) cc_final: 0.8623 (tp30) REVERT: A 855 PHE cc_start: 0.7871 (m-80) cc_final: 0.7354 (m-80) REVERT: A 869 MET cc_start: 0.9188 (mtt) cc_final: 0.8674 (mtp) REVERT: A 1138 TYR cc_start: 0.8447 (t80) cc_final: 0.7537 (t80) REVERT: B 81 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7734 (p0) REVERT: B 177 MET cc_start: 0.0429 (ttp) cc_final: -0.0105 (ttp) REVERT: B 740 MET cc_start: 0.9261 (tpp) cc_final: 0.9005 (tpp) REVERT: B 858 LEU cc_start: 0.9735 (mp) cc_final: 0.9479 (mp) REVERT: B 869 MET cc_start: 0.9313 (mtt) cc_final: 0.9014 (mtt) REVERT: B 900 MET cc_start: 0.8538 (mtp) cc_final: 0.8331 (mtt) REVERT: B 954 GLN cc_start: 0.9277 (mt0) cc_final: 0.8835 (mt0) REVERT: B 965 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8637 (tm-30) REVERT: B 995 ARG cc_start: 0.9199 (mtt180) cc_final: 0.8687 (mmm-85) REVERT: B 1031 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8107 (mt-10) REVERT: C 298 GLU cc_start: 0.9513 (mm-30) cc_final: 0.8824 (mp0) REVERT: C 697 MET cc_start: 0.8994 (ptp) cc_final: 0.8730 (ptm) REVERT: C 717 ASN cc_start: 0.6567 (OUTLIER) cc_final: 0.6244 (t0) REVERT: C 729 VAL cc_start: 0.9392 (OUTLIER) cc_final: 0.9067 (p) REVERT: C 731 MET cc_start: 0.9191 (ptm) cc_final: 0.8583 (ptp) REVERT: C 780 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8055 (mt-10) REVERT: C 900 MET cc_start: 0.9084 (mmm) cc_final: 0.8776 (mmt) REVERT: C 1002 GLN cc_start: 0.9390 (tp40) cc_final: 0.8907 (tp-100) REVERT: C 1005 GLN cc_start: 0.9462 (tp40) cc_final: 0.9163 (tp40) REVERT: C 1017 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8706 (tp30) outliers start: 67 outliers final: 45 residues processed: 165 average time/residue: 0.1379 time to fit residues: 38.6879 Evaluate side-chains 137 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 89 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1012 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 8 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 171 optimal weight: 0.0980 chunk 299 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 176 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 40.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS C1088 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.083806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.053249 restraints weight = 99920.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.055309 restraints weight = 47802.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.056714 restraints weight = 30165.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.057635 restraints weight = 22290.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058305 restraints weight = 18215.191| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24750 Z= 0.174 Angle : 0.602 11.289 33696 Z= 0.310 Chirality : 0.044 0.428 3831 Planarity : 0.004 0.065 4365 Dihedral : 5.104 39.270 3304 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.66 % Allowed : 15.66 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.15), residues: 3045 helix: 1.24 (0.21), residues: 670 sheet: -2.02 (0.20), residues: 614 loop : -2.72 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 983 TYR 0.015 0.001 TYR A 365 PHE 0.022 0.001 PHE A 855 TRP 0.010 0.001 TRP B 886 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00386 (24713) covalent geometry : angle 0.59848 (33622) SS BOND : bond 0.00391 ( 37) SS BOND : angle 1.46305 ( 74) hydrogen bonds : bond 0.04366 ( 778) hydrogen bonds : angle 5.73012 ( 2088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 95 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.9094 (m-80) cc_final: 0.8755 (m-80) REVERT: A 505 TYR cc_start: 0.9160 (m-80) cc_final: 0.8727 (m-80) REVERT: A 725 GLU cc_start: 0.8565 (tt0) cc_final: 0.8235 (tt0) REVERT: A 731 MET cc_start: 0.9265 (ptm) cc_final: 0.8873 (ptp) REVERT: A 773 GLU cc_start: 0.8883 (tp30) cc_final: 0.8587 (tp30) REVERT: A 855 PHE cc_start: 0.7833 (m-80) cc_final: 0.7404 (m-80) REVERT: A 869 MET cc_start: 0.9186 (mtt) cc_final: 0.8732 (mtp) REVERT: A 1138 TYR cc_start: 0.8444 (t80) cc_final: 0.7538 (t80) REVERT: B 81 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7706 (p0) REVERT: B 177 MET cc_start: 0.0341 (ttp) cc_final: -0.0101 (ttp) REVERT: B 740 MET cc_start: 0.9248 (tpp) cc_final: 0.9036 (tpp) REVERT: B 858 LEU cc_start: 0.9753 (mp) cc_final: 0.9503 (mp) REVERT: B 869 MET cc_start: 0.9348 (mtt) cc_final: 0.9054 (mtt) REVERT: B 900 MET cc_start: 0.8540 (mtp) cc_final: 0.8318 (mtt) REVERT: B 954 GLN cc_start: 0.9305 (mt0) cc_final: 0.8840 (mt0) REVERT: B 995 ARG cc_start: 0.9248 (mtt180) cc_final: 0.8605 (mmm-85) REVERT: B 1029 MET cc_start: 0.9690 (tpp) cc_final: 0.9460 (tpp) REVERT: B 1031 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8124 (mt-10) REVERT: B 1115 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8978 (mp) REVERT: C 489 TYR cc_start: 0.8481 (m-10) cc_final: 0.8017 (m-80) REVERT: C 697 MET cc_start: 0.9000 (ptp) cc_final: 0.8649 (ptm) REVERT: C 717 ASN cc_start: 0.6632 (OUTLIER) cc_final: 0.6248 (t0) REVERT: C 731 MET cc_start: 0.9305 (ptm) cc_final: 0.8630 (ptp) REVERT: C 900 MET cc_start: 0.9096 (mmm) cc_final: 0.8769 (mmt) REVERT: C 1002 GLN cc_start: 0.9423 (tp40) cc_final: 0.8913 (tp-100) REVERT: C 1005 GLN cc_start: 0.9496 (tp40) cc_final: 0.9202 (tp40) REVERT: C 1017 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8699 (tp30) outliers start: 72 outliers final: 50 residues processed: 163 average time/residue: 0.1387 time to fit residues: 38.9251 Evaluate side-chains 140 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 87 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1012 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 195 optimal weight: 6.9990 chunk 263 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 276 optimal weight: 4.9990 chunk 265 optimal weight: 5.9990 chunk 296 optimal weight: 3.9990 chunk 139 optimal weight: 50.0000 chunk 180 optimal weight: 4.9990 chunk 301 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 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 = 0.3629 r_free = 0.3629 target = 0.081967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.051517 restraints weight = 99217.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.053469 restraints weight = 48218.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.054780 restraints weight = 30641.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.055616 restraints weight = 22758.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.056210 restraints weight = 18762.223| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24750 Z= 0.229 Angle : 0.631 11.145 33696 Z= 0.325 Chirality : 0.044 0.209 3831 Planarity : 0.004 0.064 4365 Dihedral : 5.140 39.190 3304 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.85 % Allowed : 16.17 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.15), residues: 3045 helix: 1.19 (0.21), residues: 670 sheet: -2.01 (0.20), residues: 618 loop : -2.69 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.021 0.001 TYR A 369 PHE 0.020 0.001 PHE B 329 TRP 0.012 0.001 TRP B 886 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00506 (24713) covalent geometry : angle 0.62829 (33622) SS BOND : bond 0.00427 ( 37) SS BOND : angle 1.41410 ( 74) hydrogen bonds : bond 0.04477 ( 778) hydrogen bonds : angle 5.77536 ( 2088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 86 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.9124 (m-80) cc_final: 0.8802 (m-80) REVERT: A 725 GLU cc_start: 0.8470 (tt0) cc_final: 0.8093 (tt0) REVERT: A 731 MET cc_start: 0.9268 (ptm) cc_final: 0.8931 (ptp) REVERT: A 773 GLU cc_start: 0.8905 (tp30) cc_final: 0.8600 (tp30) REVERT: A 855 PHE cc_start: 0.7865 (m-80) cc_final: 0.7457 (m-80) REVERT: A 869 MET cc_start: 0.9182 (mtt) cc_final: 0.8677 (mtp) REVERT: A 1050 MET cc_start: 0.9073 (ptp) cc_final: 0.8783 (ptm) REVERT: A 1138 TYR cc_start: 0.8454 (t80) cc_final: 0.7559 (t80) REVERT: B 740 MET cc_start: 0.9259 (tpp) cc_final: 0.8885 (tpp) REVERT: B 858 LEU cc_start: 0.9772 (mp) cc_final: 0.9531 (mp) REVERT: B 869 MET cc_start: 0.9361 (mtt) cc_final: 0.9055 (mtt) REVERT: B 900 MET cc_start: 0.8570 (mtp) cc_final: 0.8307 (mtt) REVERT: B 995 ARG cc_start: 0.9265 (mtt180) cc_final: 0.8952 (mtp-110) REVERT: B 1029 MET cc_start: 0.9707 (tpp) cc_final: 0.9438 (tpp) REVERT: B 1031 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8198 (mt-10) REVERT: C 489 TYR cc_start: 0.8476 (m-10) cc_final: 0.8023 (m-80) REVERT: C 775 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8626 (t70) REVERT: C 900 MET cc_start: 0.9114 (mmm) cc_final: 0.8734 (mmt) REVERT: C 1002 GLN cc_start: 0.9485 (tp40) cc_final: 0.8968 (tp-100) REVERT: C 1005 GLN cc_start: 0.9549 (tp40) cc_final: 0.9239 (tp40) REVERT: C 1017 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8729 (tp30) outliers start: 77 outliers final: 62 residues processed: 158 average time/residue: 0.1441 time to fit residues: 38.9235 Evaluate side-chains 143 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 80 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1012 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 302 optimal weight: 0.7980 chunk 258 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 210 optimal weight: 8.9990 chunk 220 optimal weight: 9.9990 chunk 173 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 69 optimal weight: 0.0470 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 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 = 0.3656 r_free = 0.3656 target = 0.083125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.052463 restraints weight = 98628.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.054482 restraints weight = 47187.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.055832 restraints weight = 29842.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.056741 restraints weight = 22121.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.057285 restraints weight = 18141.151| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24750 Z= 0.132 Angle : 0.576 11.117 33696 Z= 0.296 Chirality : 0.043 0.212 3831 Planarity : 0.004 0.065 4365 Dihedral : 4.937 39.233 3304 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.74 % Allowed : 16.58 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.15), residues: 3045 helix: 1.42 (0.21), residues: 666 sheet: -1.87 (0.20), residues: 618 loop : -2.55 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.013 0.001 TYR B 160 PHE 0.019 0.001 PHE B 329 TRP 0.028 0.002 TRP A 353 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00293 (24713) covalent geometry : angle 0.57293 (33622) SS BOND : bond 0.00434 ( 37) SS BOND : angle 1.36304 ( 74) hydrogen bonds : bond 0.04203 ( 778) hydrogen bonds : angle 5.47198 ( 2088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 91 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.6038 (pm20) cc_final: 0.5778 (pm20) REVERT: A 202 LYS cc_start: 0.8464 (mmmt) cc_final: 0.8256 (mmmt) REVERT: A 456 PHE cc_start: 0.9131 (m-80) cc_final: 0.8812 (m-80) REVERT: A 725 GLU cc_start: 0.8459 (tt0) cc_final: 0.8066 (tt0) REVERT: A 731 MET cc_start: 0.9251 (ptm) cc_final: 0.8905 (ptp) REVERT: A 773 GLU cc_start: 0.8800 (tp30) cc_final: 0.8467 (tp30) REVERT: A 855 PHE cc_start: 0.7922 (m-80) cc_final: 0.7617 (m-80) REVERT: A 869 MET cc_start: 0.9182 (mtt) cc_final: 0.8724 (mtp) REVERT: A 1050 MET cc_start: 0.8940 (ptp) cc_final: 0.8657 (ptm) REVERT: A 1138 TYR cc_start: 0.8457 (t80) cc_final: 0.7544 (t80) REVERT: B 224 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: B 858 LEU cc_start: 0.9740 (mp) cc_final: 0.9488 (mp) REVERT: B 869 MET cc_start: 0.9370 (mtt) cc_final: 0.9017 (mtt) REVERT: B 900 MET cc_start: 0.8611 (mtp) cc_final: 0.8388 (mtt) REVERT: B 995 ARG cc_start: 0.9275 (mtt180) cc_final: 0.8905 (mtp-110) REVERT: B 1029 MET cc_start: 0.9713 (tpp) cc_final: 0.9375 (tpp) REVERT: B 1031 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8142 (mt-10) REVERT: C 378 LYS cc_start: 0.9324 (mmtt) cc_final: 0.9124 (mmtt) REVERT: C 489 TYR cc_start: 0.8463 (m-10) cc_final: 0.8003 (m-80) REVERT: C 697 MET cc_start: 0.8942 (ptp) cc_final: 0.8674 (ptm) REVERT: C 900 MET cc_start: 0.9101 (mmm) cc_final: 0.8747 (mmt) REVERT: C 1002 GLN cc_start: 0.9446 (tp40) cc_final: 0.8903 (tp-100) REVERT: C 1005 GLN cc_start: 0.9481 (tp40) cc_final: 0.9178 (tp40) REVERT: C 1017 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8687 (tp30) REVERT: C 1029 MET cc_start: 0.9428 (tpp) cc_final: 0.8871 (tpp) outliers start: 74 outliers final: 60 residues processed: 160 average time/residue: 0.1440 time to fit residues: 39.3821 Evaluate side-chains 147 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 86 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 61 optimal weight: 0.0670 chunk 239 optimal weight: 20.0000 chunk 272 optimal weight: 2.9990 chunk 253 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 274 optimal weight: 3.9990 chunk 219 optimal weight: 0.5980 chunk 154 optimal weight: 9.9990 chunk 247 optimal weight: 30.0000 chunk 83 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 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 = 0.3674 r_free = 0.3674 target = 0.083892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.053412 restraints weight = 97866.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.055459 restraints weight = 46682.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.056856 restraints weight = 29393.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.057792 restraints weight = 21693.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058357 restraints weight = 17764.548| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24750 Z= 0.108 Angle : 0.561 11.064 33696 Z= 0.288 Chirality : 0.043 0.214 3831 Planarity : 0.004 0.066 4365 Dihedral : 4.725 38.087 3304 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.52 % Allowed : 16.91 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.15), residues: 3045 helix: 1.57 (0.21), residues: 662 sheet: -1.75 (0.20), residues: 618 loop : -2.43 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.011 0.001 TYR B 160 PHE 0.017 0.001 PHE B 329 TRP 0.016 0.001 TRP A 353 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00237 (24713) covalent geometry : angle 0.55824 (33622) SS BOND : bond 0.00334 ( 37) SS BOND : angle 1.24767 ( 74) hydrogen bonds : bond 0.03993 ( 778) hydrogen bonds : angle 5.28839 ( 2088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 102 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.6125 (pm20) cc_final: 0.5820 (pm20) REVERT: A 369 TYR cc_start: 0.7332 (m-10) cc_final: 0.7122 (m-10) REVERT: A 725 GLU cc_start: 0.8457 (tt0) cc_final: 0.8060 (tt0) REVERT: A 731 MET cc_start: 0.9245 (ptm) cc_final: 0.8905 (ptp) REVERT: A 742 ILE cc_start: 0.9466 (mt) cc_final: 0.9234 (tt) REVERT: A 773 GLU cc_start: 0.8819 (tp30) cc_final: 0.8086 (tp30) REVERT: A 777 ASN cc_start: 0.8887 (m-40) cc_final: 0.8353 (m110) REVERT: A 855 PHE cc_start: 0.7872 (m-80) cc_final: 0.7602 (m-80) REVERT: A 869 MET cc_start: 0.9051 (mtt) cc_final: 0.8563 (mtp) REVERT: A 1050 MET cc_start: 0.8960 (ptp) cc_final: 0.8680 (ptm) REVERT: A 1138 TYR cc_start: 0.8459 (t80) cc_final: 0.7524 (t80) REVERT: B 177 MET cc_start: 0.2264 (ttp) cc_final: 0.1838 (mtp) REVERT: B 298 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8797 (mp0) REVERT: B 740 MET cc_start: 0.9215 (tpp) cc_final: 0.8823 (ttm) REVERT: B 858 LEU cc_start: 0.9724 (mp) cc_final: 0.9475 (mp) REVERT: B 869 MET cc_start: 0.9406 (mtt) cc_final: 0.9024 (mtt) REVERT: B 900 MET cc_start: 0.8562 (mtp) cc_final: 0.8355 (mtt) REVERT: B 954 GLN cc_start: 0.9301 (mt0) cc_final: 0.9014 (mt0) REVERT: B 995 ARG cc_start: 0.9273 (mtt180) cc_final: 0.8906 (mtp-110) REVERT: B 1029 MET cc_start: 0.9700 (tpp) cc_final: 0.9371 (tpp) REVERT: B 1031 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8040 (mt-10) REVERT: B 1041 ASP cc_start: 0.8275 (t70) cc_final: 0.7875 (t70) REVERT: C 378 LYS cc_start: 0.9367 (mmtt) cc_final: 0.9151 (mmtt) REVERT: C 400 PHE cc_start: 0.9224 (p90) cc_final: 0.8796 (p90) REVERT: C 489 TYR cc_start: 0.8445 (m-10) cc_final: 0.7981 (m-80) REVERT: C 697 MET cc_start: 0.9012 (ptp) cc_final: 0.8644 (ptm) REVERT: C 900 MET cc_start: 0.9126 (mmm) cc_final: 0.8837 (mmt) REVERT: C 1002 GLN cc_start: 0.9404 (tp40) cc_final: 0.8864 (tp-100) REVERT: C 1005 GLN cc_start: 0.9428 (tp40) cc_final: 0.9150 (mm-40) REVERT: C 1017 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8691 (tp30) REVERT: C 1029 MET cc_start: 0.9339 (tpp) cc_final: 0.8720 (tpp) outliers start: 68 outliers final: 58 residues processed: 168 average time/residue: 0.1588 time to fit residues: 45.2559 Evaluate side-chains 150 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 92 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 6 optimal weight: 7.9990 chunk 292 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 209 optimal weight: 0.0270 chunk 184 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 169 optimal weight: 0.3980 chunk 40 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.4980 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 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 = 0.3673 r_free = 0.3673 target = 0.083796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.053279 restraints weight = 98154.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.055316 restraints weight = 46954.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.056708 restraints weight = 29587.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.057610 restraints weight = 21863.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058249 restraints weight = 17930.965| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24750 Z= 0.116 Angle : 0.567 11.246 33696 Z= 0.291 Chirality : 0.043 0.218 3831 Planarity : 0.004 0.067 4365 Dihedral : 4.667 37.719 3304 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.26 % Allowed : 17.28 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.15), residues: 3045 helix: 1.72 (0.21), residues: 660 sheet: -1.65 (0.20), residues: 617 loop : -2.35 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 983 TYR 0.010 0.001 TYR B 160 PHE 0.015 0.001 PHE B 329 TRP 0.015 0.001 TRP A 353 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00260 (24713) covalent geometry : angle 0.55984 (33622) SS BOND : bond 0.00404 ( 37) SS BOND : angle 1.97404 ( 74) hydrogen bonds : bond 0.03916 ( 778) hydrogen bonds : angle 5.23602 ( 2088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 94 time to evaluate : 0.901 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: A 191 GLU cc_start: 0.6143 (pm20) cc_final: 0.5156 (pm20) REVERT: A 369 TYR cc_start: 0.7195 (m-10) cc_final: 0.6992 (m-10) REVERT: A 725 GLU cc_start: 0.8475 (tt0) cc_final: 0.8076 (tt0) REVERT: A 731 MET cc_start: 0.9267 (ptm) cc_final: 0.8929 (ptp) REVERT: A 740 MET cc_start: 0.9131 (tpp) cc_final: 0.8515 (tpt) REVERT: A 742 ILE cc_start: 0.9443 (mt) cc_final: 0.9140 (tt) REVERT: A 773 GLU cc_start: 0.8845 (tp30) cc_final: 0.8271 (tp30) REVERT: A 777 ASN cc_start: 0.8853 (m-40) cc_final: 0.8400 (m110) REVERT: A 869 MET cc_start: 0.9055 (mtt) cc_final: 0.8547 (mtp) REVERT: A 1050 MET cc_start: 0.8942 (ptp) cc_final: 0.8642 (ptm) REVERT: A 1138 TYR cc_start: 0.8463 (t80) cc_final: 0.7527 (t80) REVERT: B 94 SER cc_start: 0.7753 (OUTLIER) cc_final: 0.7485 (p) REVERT: B 177 MET cc_start: 0.2468 (ttp) cc_final: 0.2167 (mtp) REVERT: B 224 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: B 740 MET cc_start: 0.9224 (tpp) cc_final: 0.8297 (mtp) REVERT: B 762 GLN cc_start: 0.9350 (tt0) cc_final: 0.8789 (mt0) REVERT: B 858 LEU cc_start: 0.9715 (mp) cc_final: 0.9468 (mp) REVERT: B 869 MET cc_start: 0.9410 (mtt) cc_final: 0.9027 (mtt) REVERT: B 900 MET cc_start: 0.8584 (mtp) cc_final: 0.8380 (mtt) REVERT: B 1029 MET cc_start: 0.9702 (tpp) cc_final: 0.9363 (tpp) REVERT: B 1041 ASP cc_start: 0.8306 (t70) cc_final: 0.7917 (t70) REVERT: C 378 LYS cc_start: 0.9358 (mmtt) cc_final: 0.9145 (mmtt) REVERT: C 400 PHE cc_start: 0.9221 (p90) cc_final: 0.8872 (p90) REVERT: C 489 TYR cc_start: 0.8445 (m-10) cc_final: 0.7982 (m-80) REVERT: C 900 MET cc_start: 0.9153 (mmm) cc_final: 0.8813 (mmt) REVERT: C 1002 GLN cc_start: 0.9377 (tp40) cc_final: 0.8843 (tp-100) REVERT: C 1005 GLN cc_start: 0.9442 (tp40) cc_final: 0.9155 (mm-40) REVERT: C 1017 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8716 (tp30) REVERT: C 1029 MET cc_start: 0.9344 (tpp) cc_final: 0.8670 (tpp) outliers start: 61 outliers final: 56 residues processed: 153 average time/residue: 0.1382 time to fit residues: 36.7282 Evaluate side-chains 147 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 89 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 269 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 159 optimal weight: 0.0770 chunk 66 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 295 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.084394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.053902 restraints weight = 97879.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.055900 restraints weight = 46980.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.057361 restraints weight = 29798.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.058248 restraints weight = 21947.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.058876 restraints weight = 17989.532| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24750 Z= 0.106 Angle : 0.561 11.144 33696 Z= 0.287 Chirality : 0.043 0.229 3831 Planarity : 0.004 0.070 4365 Dihedral : 4.547 37.386 3304 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.18 % Allowed : 17.43 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.15), residues: 3045 helix: 1.78 (0.21), residues: 661 sheet: -1.49 (0.20), residues: 631 loop : -2.30 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 983 TYR 0.009 0.001 TYR B 160 PHE 0.015 0.001 PHE A 456 TRP 0.014 0.001 TRP A 353 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00236 (24713) covalent geometry : angle 0.55638 (33622) SS BOND : bond 0.00319 ( 37) SS BOND : angle 1.67254 ( 74) hydrogen bonds : bond 0.03792 ( 778) hydrogen bonds : angle 5.13296 ( 2088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 94 time to evaluate : 0.949 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: A 223 LEU cc_start: 0.8425 (mt) cc_final: 0.8034 (mt) REVERT: A 226 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8531 (mm) REVERT: A 369 TYR cc_start: 0.7196 (m-10) cc_final: 0.6991 (m-10) REVERT: A 725 GLU cc_start: 0.8447 (tt0) cc_final: 0.8059 (tt0) REVERT: A 731 MET cc_start: 0.9256 (ptm) cc_final: 0.8918 (ptp) REVERT: A 740 MET cc_start: 0.9124 (tpp) cc_final: 0.8513 (tpt) REVERT: A 773 GLU cc_start: 0.8846 (tp30) cc_final: 0.8248 (tp30) REVERT: A 777 ASN cc_start: 0.8775 (m-40) cc_final: 0.8388 (m110) REVERT: A 855 PHE cc_start: 0.7880 (m-80) cc_final: 0.7678 (m-80) REVERT: A 988 GLU cc_start: 0.9375 (mp0) cc_final: 0.9171 (mp0) REVERT: A 1050 MET cc_start: 0.8927 (ptp) cc_final: 0.8639 (ptm) REVERT: A 1138 TYR cc_start: 0.8462 (t80) cc_final: 0.7515 (t80) REVERT: B 94 SER cc_start: 0.7718 (OUTLIER) cc_final: 0.7430 (p) REVERT: B 177 MET cc_start: 0.2076 (ttp) cc_final: 0.1852 (mtp) REVERT: B 740 MET cc_start: 0.9182 (tpp) cc_final: 0.8337 (mtp) REVERT: B 858 LEU cc_start: 0.9721 (mp) cc_final: 0.9484 (mp) REVERT: B 869 MET cc_start: 0.9403 (mtt) cc_final: 0.9040 (mtt) REVERT: B 1029 MET cc_start: 0.9705 (tpp) cc_final: 0.9415 (tpp) REVERT: B 1041 ASP cc_start: 0.8291 (t70) cc_final: 0.7897 (t70) REVERT: C 378 LYS cc_start: 0.9368 (mmtt) cc_final: 0.9152 (mmtt) REVERT: C 400 PHE cc_start: 0.9206 (p90) cc_final: 0.8940 (p90) REVERT: C 489 TYR cc_start: 0.8459 (m-10) cc_final: 0.7981 (m-80) REVERT: C 900 MET cc_start: 0.9117 (mmm) cc_final: 0.8791 (mmt) REVERT: C 1002 GLN cc_start: 0.9342 (tp40) cc_final: 0.8815 (tp-100) REVERT: C 1005 GLN cc_start: 0.9415 (tp40) cc_final: 0.9130 (mm-40) REVERT: C 1017 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8709 (tp30) REVERT: C 1029 MET cc_start: 0.9342 (tpp) cc_final: 0.8715 (tpp) outliers start: 59 outliers final: 49 residues processed: 151 average time/residue: 0.1415 time to fit residues: 37.1128 Evaluate side-chains 141 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 90 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 73 optimal weight: 5.9990 chunk 181 optimal weight: 0.0370 chunk 254 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.081800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.051240 restraints weight = 100012.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.053146 restraints weight = 48906.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.054437 restraints weight = 31290.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.055260 restraints weight = 23267.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.055854 restraints weight = 19194.331| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 24750 Z= 0.281 Angle : 0.673 10.907 33696 Z= 0.347 Chirality : 0.045 0.215 3831 Planarity : 0.004 0.065 4365 Dihedral : 4.942 37.403 3304 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 2.18 % Allowed : 17.54 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.15), residues: 3045 helix: 1.38 (0.21), residues: 666 sheet: -1.66 (0.20), residues: 632 loop : -2.39 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 983 TYR 0.016 0.001 TYR A 170 PHE 0.016 0.002 PHE A 888 TRP 0.016 0.002 TRP B 886 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00618 (24713) covalent geometry : angle 0.66843 (33622) SS BOND : bond 0.00450 ( 37) SS BOND : angle 1.88117 ( 74) hydrogen bonds : bond 0.04494 ( 778) hydrogen bonds : angle 5.58153 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4259.09 seconds wall clock time: 74 minutes 32.07 seconds (4472.07 seconds total)