Starting phenix.real_space_refine on Mon Aug 25 08:36:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjk_50503/08_2025/9fjk_50503.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjk_50503/08_2025/9fjk_50503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fjk_50503/08_2025/9fjk_50503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjk_50503/08_2025/9fjk_50503.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fjk_50503/08_2025/9fjk_50503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjk_50503/08_2025/9fjk_50503.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 117 5.16 5 C 16967 2.51 5 N 4411 2.21 5 O 5034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26529 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8185 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 58, 'TRANS': 981} Chain breaks: 12 Chain: "B" Number of atoms: 8226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8226 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 59, 'TRANS': 987} Chain breaks: 9 Chain: "C" Number of atoms: 8288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8288 Classifications: {'peptide': 1055} Link IDs: {'PTRANS': 60, 'TRANS': 994} Chain breaks: 7 Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1014 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Time building chain proxies: 6.10, per 1000 atoms: 0.23 Number of scatterers: 26529 At special positions: 0 Unit cell: (132.83, 167.294, 170.884, 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 117 16.00 O 5034 8.00 N 4411 7.00 C 16967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.02 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.04 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.04 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.04 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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: 1.99 Conformation dependent library (CDL) restraints added in 869.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6356 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 52 sheets defined 21.7% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.750A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.601A pdb=" N LEU A 387 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 745 through 753 removed outlier: 4.202A pdb=" N LEU A 751 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 780 Processing helix chain 'A' and resid 813 through 822 removed outlier: 3.631A pdb=" N ASN A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 853 removed outlier: 3.568A pdb=" N LYS A 851 " --> pdb=" O CYS A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 888 removed outlier: 4.073A pdb=" N GLY A 888 " --> pdb=" O PHE A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 909 through 915 removed outlier: 4.309A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.658A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 964 removed outlier: 3.762A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.459A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.835A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.913A pdb=" N ASP B 386 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.861A pdb=" N VAL B 404 " --> pdb=" O GLY B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 620 through 627 removed outlier: 3.801A pdb=" N ASP B 624 " --> pdb=" O ILE B 621 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLN B 625 " --> pdb=" O HIS B 622 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 626 " --> pdb=" O ALA B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 removed outlier: 3.583A pdb=" N TYR B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.567A pdb=" N LEU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 Processing helix chain 'B' and resid 813 through 820 Processing helix chain 'B' and resid 846 through 853 removed outlier: 3.688A pdb=" N ALA B 849 " --> pdb=" O LEU B 846 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 851 " --> pdb=" O CYS B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 909 through 915 removed outlier: 4.217A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 937 Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.896A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 979 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.463A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1142 Processing helix chain 'C' and resid 291 through 300 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.779A pdb=" N PHE C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 386 Processing helix chain 'C' and resid 402 through 407 removed outlier: 5.716A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 406 " --> pdb=" O GLU C 403 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 407 " --> pdb=" O VAL C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 402 through 407' Processing helix chain 'C' and resid 621 through 627 removed outlier: 3.871A pdb=" N GLN C 625 " --> pdb=" O HIS C 622 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 627 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 749 through 753 Processing helix chain 'C' and resid 756 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 850 through 853 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 4.075A pdb=" N GLY C 888 " --> pdb=" O PHE C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.608A pdb=" N ALA C 900 " --> pdb=" O PRO C 896 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 915 removed outlier: 4.114A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 937 Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.642A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.907A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 4.002A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.865A pdb=" N GLU L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.098A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.214A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.189A pdb=" N GLY A 101 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 166 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP H 98 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 133 removed outlier: 6.784A pdb=" N GLN A 132 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 7.098A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 646 " --> pdb=" O TYR A 609 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 355 removed outlier: 3.638A pdb=" N PHE A 397 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 535 through 540 removed outlier: 3.523A pdb=" N GLY A 547 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 545 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 550 " --> pdb=" O ASP A 583 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY A 563 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE A 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.967A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 698 through 701 removed outlier: 6.447A pdb=" N ALA A 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LYS C 787 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN A 700 " --> pdb=" O LYS C 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.522A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.522A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.488A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 784 through 787 Processing sheet with id=AB7, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.752A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.522A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS B 182 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE B 205 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 201 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE B 196 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP B 225 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 198 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 44 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.503A pdb=" N ASP B 53 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 83 removed outlier: 3.539A pdb=" N GLY B 105 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY B 101 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 104 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLU B 130 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS B 161 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLN B 132 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N ASN B 159 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 308 through 315 removed outlier: 5.300A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 392 through 394 removed outlier: 3.608A pdb=" N TYR B 505 " --> pdb=" O ILE B 399 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 392 through 394 Processing sheet with id=AC6, first strand: chain 'B' and resid 449 through 450 Processing sheet with id=AC7, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.586A pdb=" N TYR B 470 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 536 through 540 removed outlier: 3.945A pdb=" N THR B 550 " --> pdb=" O ASP B 583 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY B 563 " --> pdb=" O ASP B 571 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.068A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.538A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.538A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.439A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 784 through 787 removed outlier: 5.748A pdb=" N ILE B 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.391A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.163A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR C 203 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU C 186 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS C 201 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 188 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 190 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 224 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER C 200 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.877A pdb=" N ASP C 53 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 273 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.508A pdb=" N LEU C 82 " --> pdb=" O PHE C 235 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AE1, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.439A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 322 through 325 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.840A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.137A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 450 through 451 Processing sheet with id=AE6, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE7, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.118A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.621A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.621A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.480A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.547A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.011A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.589A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.589A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL L 97 " --> pdb=" O SER L 90 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 19 through 24 1015 hydrogen bonds defined for protein. 2721 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.64 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8361 1.34 - 1.46: 6394 1.46 - 1.58: 12247 1.58 - 1.71: 0 1.71 - 1.83: 146 Bond restraints: 27148 Sorted by residual: bond pdb=" C VAL B 317 " pdb=" N GLN B 318 " ideal model delta sigma weight residual 1.330 1.412 -0.081 1.37e-02 5.33e+03 3.53e+01 bond pdb=" C ALA A 369 " pdb=" N PRO A 370 " ideal model delta sigma weight residual 1.334 1.431 -0.097 2.34e-02 1.83e+03 1.72e+01 bond pdb=" N ASP A 291 " pdb=" CA ASP A 291 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.25e-02 6.40e+03 8.57e+00 bond pdb=" N VAL A 154 " pdb=" CA VAL A 154 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.02e+00 bond pdb=" N ASP A 287 " pdb=" CA ASP A 287 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.27e-02 6.20e+03 7.24e+00 ... (remaining 27143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 35802 2.35 - 4.71: 981 4.71 - 7.06: 109 7.06 - 9.41: 35 9.41 - 11.76: 7 Bond angle restraints: 36934 Sorted by residual: angle pdb=" C LYS B 421 " pdb=" N LEU B 422 " pdb=" CA LEU B 422 " ideal model delta sigma weight residual 120.94 131.31 -10.37 1.90e+00 2.77e-01 2.98e+01 angle pdb=" CA TYR H 100A" pdb=" CB TYR H 100A" pdb=" CG TYR H 100A" ideal model delta sigma weight residual 113.90 123.02 -9.12 1.80e+00 3.09e-01 2.57e+01 angle pdb=" C GLY L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 131.17 -9.63 1.91e+00 2.74e-01 2.54e+01 angle pdb=" C ASP A 287 " pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta sigma weight residual 110.79 103.25 7.54 1.63e+00 3.76e-01 2.14e+01 angle pdb=" C MET A 172 " pdb=" N ASP A 173 " pdb=" CA ASP A 173 " ideal model delta sigma weight residual 121.70 129.83 -8.13 1.80e+00 3.09e-01 2.04e+01 ... (remaining 36929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 15394 17.74 - 35.49: 618 35.49 - 53.23: 127 53.23 - 70.97: 51 70.97 - 88.72: 31 Dihedral angle restraints: 16221 sinusoidal: 6360 harmonic: 9861 Sorted by residual: dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual 93.00 177.74 -84.74 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS C 740 " pdb=" SG CYS C 740 " pdb=" SG CYS C 746 " pdb=" CB CYS C 746 " ideal model delta sinusoidal sigma weight residual -86.00 -20.34 -65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CA TYR H 100J" pdb=" C TYR H 100J" pdb=" N PHE H 100K" pdb=" CA PHE H 100K" ideal model delta harmonic sigma weight residual 180.00 148.13 31.87 0 5.00e+00 4.00e-02 4.06e+01 ... (remaining 16218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 3723 0.096 - 0.192: 443 0.192 - 0.288: 12 0.288 - 0.384: 1 0.384 - 0.480: 1 Chirality restraints: 4180 Sorted by residual: chirality pdb=" CB VAL C 617 " pdb=" CA VAL C 617 " pdb=" CG1 VAL C 617 " pdb=" CG2 VAL C 617 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CB ILE C 205 " pdb=" CA ILE C 205 " pdb=" CG1 ILE C 205 " pdb=" CG2 ILE C 205 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB VAL H 67 " pdb=" CA VAL H 67 " pdb=" CG1 VAL H 67 " pdb=" CG2 VAL H 67 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 4177 not shown) Planarity restraints: 4779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 153 " 0.430 9.50e-02 1.11e+02 1.93e-01 2.28e+01 pdb=" NE ARG A 153 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 153 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 153 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 153 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 226 " 0.047 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO A 227 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 227 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 227 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 203 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO C 204 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 204 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 204 " -0.038 5.00e-02 4.00e+02 ... (remaining 4776 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.82: 21 1.82 - 2.59: 201 2.59 - 3.36: 31124 3.36 - 4.13: 65875 4.13 - 4.90: 116112 Nonbonded interactions: 213333 Sorted by model distance: nonbonded pdb=" CZ PHE A 43 " pdb=" CG GLN B 560 " model vdw 1.056 3.740 nonbonded pdb=" CE2 PHE A 43 " pdb=" CG GLN B 560 " model vdw 1.145 3.740 nonbonded pdb=" CZ PHE A 43 " pdb=" CD GLN B 560 " model vdw 1.222 3.570 nonbonded pdb=" CE2 PHE A 43 " pdb=" CD GLN B 560 " model vdw 1.232 3.570 nonbonded pdb=" NH1 ARG A 44 " pdb=" O ARG B 564 " model vdw 1.280 3.120 ... (remaining 213328 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 17 through 368 or resid 374 through 1144)) selection = (chain 'B' and (resid 17 through 401 or resid 403 through 407 or resid 414 throu \ gh 415 or resid 417 through 419 or resid 421 through 464 or resid 468 through 49 \ 5 or resid 503 through 1144)) selection = (chain 'C' and (resid 17 through 368 or resid 374 through 401 or resid 403 throu \ gh 407 or resid 414 through 415 or resid 417 through 419 or resid 421 through 46 \ 4 or resid 468 through 495 or resid 503 through 1144)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.070 Find NCS groups from input model: 0.550 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: 0.010 Load rotamer database and sin/cos tables:5.830 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 : 0.005 0.097 27179 Z= 0.233 Angle : 0.905 11.763 36996 Z= 0.506 Chirality : 0.057 0.480 4180 Planarity : 0.008 0.193 4779 Dihedral : 11.574 88.718 9772 Min Nonbonded Distance : 1.056 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.30 % Allowed : 0.24 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -1.55 (0.13), residues: 3316 helix: -0.71 (0.18), residues: 619 sheet: -0.00 (0.20), residues: 597 loop : -1.50 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 34 TYR 0.033 0.002 TYR A 262 PHE 0.035 0.003 PHE C 163 TRP 0.046 0.003 TRP B 350 HIS 0.014 0.002 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00479 (27148) covalent geometry : angle 0.90280 (36934) SS BOND : bond 0.00356 ( 31) SS BOND : angle 1.67552 ( 62) hydrogen bonds : bond 0.20878 ( 971) hydrogen bonds : angle 8.88004 ( 2721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 298 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.1791 (OUTLIER) cc_final: 0.0837 (pmt170) REVERT: A 172 MET cc_start: 0.4767 (mmt) cc_final: 0.4360 (mmt) REVERT: A 287 ASP cc_start: 0.5037 (OUTLIER) cc_final: 0.4731 (t0) REVERT: A 290 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7236 (tp) REVERT: A 302 SER cc_start: 0.8508 (t) cc_final: 0.8216 (p) REVERT: A 600 ASN cc_start: 0.7720 (t0) cc_final: 0.7514 (m-40) REVERT: A 648 ILE cc_start: 0.8270 (mt) cc_final: 0.7906 (mm) REVERT: A 651 GLU cc_start: 0.7635 (tt0) cc_final: 0.6993 (tm-30) REVERT: A 773 LYS cc_start: 0.7887 (tptt) cc_final: 0.7300 (ttpp) REVERT: A 822 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7644 (mtpp) REVERT: A 947 ASP cc_start: 0.7907 (m-30) cc_final: 0.7702 (m-30) REVERT: A 954 GLN cc_start: 0.6905 (tt0) cc_final: 0.6612 (tm-30) REVERT: A 1035 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8135 (mptt) REVERT: A 1070 LYS cc_start: 0.7964 (tttt) cc_final: 0.7427 (mttt) REVERT: A 1133 THR cc_start: 0.8817 (m) cc_final: 0.8448 (t) REVERT: B 53 ASP cc_start: 0.6416 (t0) cc_final: 0.6185 (t0) REVERT: B 186 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6533 (mt-10) REVERT: B 263 TYR cc_start: 0.4507 (m-80) cc_final: 0.4004 (m-80) REVERT: B 306 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7522 (mm-30) REVERT: B 314 ASN cc_start: 0.8279 (m-40) cc_final: 0.8033 (m110) REVERT: B 555 LYS cc_start: 0.8029 (mmtt) cc_final: 0.6551 (pttm) REVERT: B 571 ASP cc_start: 0.6541 (t70) cc_final: 0.6229 (t0) REVERT: B 580 GLU cc_start: 0.6769 (pt0) cc_final: 0.5957 (mm-30) REVERT: B 610 GLN cc_start: 0.8874 (mt0) cc_final: 0.8661 (mt0) REVERT: B 773 LYS cc_start: 0.8086 (tttm) cc_final: 0.7518 (tttm) REVERT: B 777 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7676 (pt0) REVERT: B 787 LYS cc_start: 0.8332 (mttt) cc_final: 0.7853 (mmtt) REVERT: B 1042 LYS cc_start: 0.8290 (tppt) cc_final: 0.8019 (tmtt) REVERT: B 1124 ASP cc_start: 0.7706 (m-30) cc_final: 0.7378 (m-30) REVERT: C 172 MET cc_start: 0.2341 (ptm) cc_final: 0.1987 (mtt) REVERT: C 302 SER cc_start: 0.8779 (t) cc_final: 0.8506 (p) REVERT: C 311 GLN cc_start: 0.8457 (tt0) cc_final: 0.7925 (tm-30) REVERT: C 600 ASN cc_start: 0.7820 (t0) cc_final: 0.7600 (m-40) REVERT: C 643 ARG cc_start: 0.7598 (mtp180) cc_final: 0.7068 (ttp80) REVERT: C 872 SER cc_start: 0.8507 (t) cc_final: 0.8270 (m) REVERT: C 918 LYS cc_start: 0.7696 (tttm) cc_final: 0.7226 (ttpt) REVERT: C 954 GLN cc_start: 0.7144 (mt0) cc_final: 0.6475 (tm-30) REVERT: C 1016 ARG cc_start: 0.7654 (tpt170) cc_final: 0.6427 (ttm110) REVERT: C 1124 ASP cc_start: 0.8486 (m-30) cc_final: 0.8239 (m-30) REVERT: C 1135 TYR cc_start: 0.7546 (m-80) cc_final: 0.7326 (m-80) outliers start: 9 outliers final: 1 residues processed: 307 average time/residue: 0.5795 time to fit residues: 207.8415 Evaluate side-chains 197 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 193 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0980 chunk 298 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 123 ASN A 168 GLN A 748 ASN A 904 ASN A 952 ASN A1110 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 GLN B 910 GLN ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 61 ASN C 202 HIS ** C 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 GLN C 759 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.231174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142192 restraints weight = 31610.491| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.96 r_work: 0.3299 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 27179 Z= 0.236 Angle : 0.679 11.230 36996 Z= 0.359 Chirality : 0.049 0.223 4180 Planarity : 0.005 0.073 4779 Dihedral : 5.546 48.353 3637 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.28 % Allowed : 4.20 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -1.04 (0.14), residues: 3316 helix: 0.47 (0.21), residues: 626 sheet: -0.02 (0.20), residues: 622 loop : -1.33 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 234 TYR 0.029 0.002 TYR A1064 PHE 0.038 0.002 PHE A 43 TRP 0.025 0.002 TRP B 883 HIS 0.008 0.002 HIS B1055 Details of bonding type rmsd covalent geometry : bond 0.00562 (27148) covalent geometry : angle 0.67571 (36934) SS BOND : bond 0.00564 ( 31) SS BOND : angle 1.81722 ( 62) hydrogen bonds : bond 0.05410 ( 971) hydrogen bonds : angle 6.41769 ( 2721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 153 ARG cc_start: 0.2484 (OUTLIER) cc_final: 0.1643 (ptp-170) REVERT: A 172 MET cc_start: 0.5084 (mmt) cc_final: 0.4073 (mmt) REVERT: A 236 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7261 (tm-30) REVERT: A 266 TYR cc_start: 0.8067 (m-80) cc_final: 0.7602 (m-10) REVERT: A 287 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6083 (t0) REVERT: A 302 SER cc_start: 0.8783 (t) cc_final: 0.8428 (p) REVERT: A 600 ASN cc_start: 0.7880 (t0) cc_final: 0.7661 (m-40) REVERT: A 651 GLU cc_start: 0.7857 (tt0) cc_final: 0.7365 (tm-30) REVERT: A 748 ASN cc_start: 0.8019 (m110) cc_final: 0.7778 (m-40) REVERT: A 947 ASP cc_start: 0.8227 (m-30) cc_final: 0.8017 (m-30) REVERT: A 1035 LYS cc_start: 0.8883 (mtpp) cc_final: 0.8379 (mptt) REVERT: B 263 TYR cc_start: 0.5232 (m-80) cc_final: 0.4657 (m-80) REVERT: B 306 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7638 (mm-30) REVERT: B 532 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8142 (ttmm) REVERT: B 551 GLU cc_start: 0.7401 (mp0) cc_final: 0.7200 (mm-30) REVERT: B 555 LYS cc_start: 0.8317 (mmtt) cc_final: 0.6909 (pttm) REVERT: B 571 ASP cc_start: 0.7328 (t70) cc_final: 0.6959 (t0) REVERT: B 732 SER cc_start: 0.9023 (t) cc_final: 0.8738 (p) REVERT: B 756 PHE cc_start: 0.6769 (t80) cc_final: 0.6529 (t80) REVERT: B 773 LYS cc_start: 0.8742 (tttm) cc_final: 0.8247 (tttm) REVERT: B 787 LYS cc_start: 0.8562 (mttt) cc_final: 0.8195 (mmtt) REVERT: B 999 GLN cc_start: 0.8352 (tp40) cc_final: 0.8086 (tp40) REVERT: B 1042 LYS cc_start: 0.8576 (tppt) cc_final: 0.8251 (tmtt) REVERT: B 1124 ASP cc_start: 0.7989 (m-30) cc_final: 0.7763 (m-30) REVERT: C 172 MET cc_start: 0.2697 (ptm) cc_final: 0.2063 (ptp) REVERT: C 302 SER cc_start: 0.8981 (t) cc_final: 0.8611 (p) REVERT: C 311 GLN cc_start: 0.8454 (tt0) cc_final: 0.7935 (tm-30) REVERT: C 589 PHE cc_start: 0.7612 (p90) cc_final: 0.7334 (p90) REVERT: C 643 ARG cc_start: 0.7788 (mtp180) cc_final: 0.7191 (tmm-80) REVERT: C 777 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8621 (mt-10) REVERT: C 918 LYS cc_start: 0.8279 (tttm) cc_final: 0.8012 (ttpt) REVERT: C 1016 ARG cc_start: 0.8280 (tpt170) cc_final: 0.7185 (ttm110) REVERT: C 1135 TYR cc_start: 0.7847 (m-80) cc_final: 0.6873 (t80) REVERT: C 1141 GLU cc_start: 0.6654 (mm-30) cc_final: 0.5831 (mt-10) REVERT: H 82 MET cc_start: 0.2929 (mmp) cc_final: 0.2115 (tmm) REVERT: H 103 TRP cc_start: 0.6249 (m100) cc_final: 0.5872 (m-90) outliers start: 38 outliers final: 18 residues processed: 223 average time/residue: 0.5512 time to fit residues: 147.1459 Evaluate side-chains 186 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 761 LYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1130 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 56 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 299 optimal weight: 0.6980 chunk 271 optimal weight: 0.2980 chunk 268 optimal weight: 8.9990 chunk 34 optimal weight: 0.4980 chunk 112 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 105 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 GLN B 641 GLN B 759 GLN B 952 ASN B 954 GLN B1007 GLN C 610 GLN C 672 GLN C 752 GLN C 801 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.233381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141764 restraints weight = 31787.211| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.31 r_work: 0.3398 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27179 Z= 0.112 Angle : 0.550 11.265 36996 Z= 0.287 Chirality : 0.044 0.182 4180 Planarity : 0.004 0.047 4779 Dihedral : 4.951 50.619 3634 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 1.18 % Allowed : 6.39 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.14), residues: 3316 helix: 1.23 (0.21), residues: 625 sheet: -0.03 (0.19), residues: 629 loop : -1.18 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.024 0.001 TYR A 262 PHE 0.023 0.001 PHE C 90 TRP 0.018 0.001 TRP B 350 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00245 (27148) covalent geometry : angle 0.54775 (36934) SS BOND : bond 0.00287 ( 31) SS BOND : angle 1.23846 ( 62) hydrogen bonds : bond 0.04220 ( 971) hydrogen bonds : angle 5.90595 ( 2721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 153 ARG cc_start: 0.2586 (OUTLIER) cc_final: 0.1848 (ptp-170) REVERT: A 172 MET cc_start: 0.5061 (mmt) cc_final: 0.4093 (mmt) REVERT: A 236 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7074 (tm-30) REVERT: A 266 TYR cc_start: 0.7884 (m-80) cc_final: 0.7358 (m-10) REVERT: A 274 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6939 (mp) REVERT: A 275 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.7007 (tppp) REVERT: A 287 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6383 (t0) REVERT: A 302 SER cc_start: 0.8531 (t) cc_final: 0.8239 (p) REVERT: A 316 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.6061 (mmt180) REVERT: A 325 ARG cc_start: 0.5144 (tpt90) cc_final: 0.4941 (ttt90) REVERT: A 616 GLU cc_start: 0.7183 (tp30) cc_final: 0.6980 (mm-30) REVERT: A 651 GLU cc_start: 0.7732 (tt0) cc_final: 0.7193 (tm-30) REVERT: A 947 ASP cc_start: 0.8074 (m-30) cc_final: 0.7827 (m-30) REVERT: A 1035 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8365 (mptt) REVERT: B 186 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6477 (mt-10) REVERT: B 263 TYR cc_start: 0.4982 (m-80) cc_final: 0.4521 (m-80) REVERT: B 306 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7457 (mm-30) REVERT: B 555 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7267 (mppt) REVERT: B 571 ASP cc_start: 0.7117 (t70) cc_final: 0.6794 (t0) REVERT: B 580 GLU cc_start: 0.7102 (pt0) cc_final: 0.6549 (mm-30) REVERT: B 732 SER cc_start: 0.8981 (t) cc_final: 0.8670 (p) REVERT: B 734 ASP cc_start: 0.7613 (t0) cc_final: 0.7321 (t70) REVERT: B 773 LYS cc_start: 0.8538 (tttm) cc_final: 0.8021 (tttm) REVERT: B 787 LYS cc_start: 0.8536 (mttt) cc_final: 0.8167 (mmtt) REVERT: B 999 GLN cc_start: 0.8131 (tp40) cc_final: 0.7786 (tp40) REVERT: B 1042 LYS cc_start: 0.8452 (tppt) cc_final: 0.8125 (tmtt) REVERT: C 302 SER cc_start: 0.8950 (t) cc_final: 0.8653 (p) REVERT: C 311 GLN cc_start: 0.8280 (tt0) cc_final: 0.7740 (tm-30) REVERT: C 589 PHE cc_start: 0.7433 (p90) cc_final: 0.7120 (p90) REVERT: C 610 GLN cc_start: 0.8310 (mt0) cc_final: 0.8109 (mt0) REVERT: C 643 ARG cc_start: 0.7646 (mtp180) cc_final: 0.6974 (mpp80) REVERT: C 777 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8410 (mt-10) REVERT: C 788 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8806 (p) REVERT: C 918 LYS cc_start: 0.8087 (tttm) cc_final: 0.7834 (ttpt) REVERT: C 954 GLN cc_start: 0.7505 (mt0) cc_final: 0.6981 (tm-30) REVERT: C 1016 ARG cc_start: 0.8093 (tpt170) cc_final: 0.7105 (ttm110) REVERT: C 1135 TYR cc_start: 0.7660 (m-80) cc_final: 0.6761 (t80) REVERT: C 1141 GLU cc_start: 0.6679 (mm-30) cc_final: 0.5864 (mt-10) REVERT: H 82 MET cc_start: 0.3207 (mmp) cc_final: 0.2446 (tmm) REVERT: H 102 TYR cc_start: 0.4628 (t80) cc_final: 0.4336 (t80) REVERT: H 103 TRP cc_start: 0.5950 (m100) cc_final: 0.5723 (m-90) outliers start: 35 outliers final: 12 residues processed: 218 average time/residue: 0.5119 time to fit residues: 133.1810 Evaluate side-chains 190 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 117 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 229 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 260 optimal weight: 0.7980 chunk 312 optimal weight: 0.0470 chunk 124 optimal weight: 10.0000 chunk 313 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 672 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.232776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142053 restraints weight = 31505.640| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.81 r_work: 0.3372 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27179 Z= 0.116 Angle : 0.531 10.380 36996 Z= 0.276 Chirality : 0.044 0.217 4180 Planarity : 0.004 0.047 4779 Dihedral : 4.717 53.499 3634 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 1.18 % Allowed : 7.50 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.14), residues: 3316 helix: 1.53 (0.21), residues: 619 sheet: 0.04 (0.19), residues: 631 loop : -1.03 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.021 0.001 TYR A1064 PHE 0.026 0.001 PHE C 90 TRP 0.015 0.001 TRP B 350 HIS 0.004 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00263 (27148) covalent geometry : angle 0.52895 (36934) SS BOND : bond 0.00262 ( 31) SS BOND : angle 1.14540 ( 62) hydrogen bonds : bond 0.03987 ( 971) hydrogen bonds : angle 5.63850 ( 2721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 153 ARG cc_start: 0.2754 (OUTLIER) cc_final: 0.2024 (ptp-170) REVERT: A 164 GLU cc_start: 0.7934 (tt0) cc_final: 0.7615 (tt0) REVERT: A 172 MET cc_start: 0.5119 (mmt) cc_final: 0.4210 (mmt) REVERT: A 236 GLN cc_start: 0.7774 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 266 TYR cc_start: 0.7990 (m-80) cc_final: 0.7413 (m-10) REVERT: A 287 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6674 (t0) REVERT: A 302 SER cc_start: 0.8582 (t) cc_final: 0.8355 (p) REVERT: A 316 ARG cc_start: 0.6578 (mtt90) cc_final: 0.6107 (mmt180) REVERT: A 651 GLU cc_start: 0.7787 (tt0) cc_final: 0.7283 (tm-30) REVERT: A 947 ASP cc_start: 0.8119 (m-30) cc_final: 0.7864 (m-30) REVERT: B 186 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6608 (mt-10) REVERT: B 263 TYR cc_start: 0.5086 (m-80) cc_final: 0.4680 (m-80) REVERT: B 306 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 544 LYS cc_start: 0.7512 (mtpt) cc_final: 0.6627 (mmmt) REVERT: B 555 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7256 (mppt) REVERT: B 571 ASP cc_start: 0.7168 (t70) cc_final: 0.6841 (t0) REVERT: B 672 GLN cc_start: 0.6584 (mm-40) cc_final: 0.5993 (mt0) REVERT: B 732 SER cc_start: 0.8999 (t) cc_final: 0.8667 (p) REVERT: B 734 ASP cc_start: 0.7654 (t0) cc_final: 0.7240 (t70) REVERT: B 773 LYS cc_start: 0.8552 (tttm) cc_final: 0.8033 (tttm) REVERT: B 787 LYS cc_start: 0.8574 (mttt) cc_final: 0.8184 (mmtt) REVERT: B 999 GLN cc_start: 0.8160 (tp40) cc_final: 0.7767 (tp40) REVERT: B 1042 LYS cc_start: 0.8495 (tppt) cc_final: 0.8147 (tmtt) REVERT: C 302 SER cc_start: 0.8954 (t) cc_final: 0.8661 (p) REVERT: C 311 GLN cc_start: 0.8372 (tt0) cc_final: 0.7808 (tm-30) REVERT: C 589 PHE cc_start: 0.7398 (p90) cc_final: 0.7159 (p90) REVERT: C 643 ARG cc_start: 0.7640 (mtp180) cc_final: 0.6936 (mpp80) REVERT: C 777 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8464 (mt-10) REVERT: C 805 ASP cc_start: 0.7833 (t0) cc_final: 0.7455 (m-30) REVERT: C 918 LYS cc_start: 0.8131 (tttm) cc_final: 0.7882 (ttpt) REVERT: C 954 GLN cc_start: 0.7538 (mt0) cc_final: 0.7009 (tm-30) REVERT: C 1016 ARG cc_start: 0.8162 (tpt170) cc_final: 0.7151 (ttm110) REVERT: C 1089 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7621 (mp0) REVERT: C 1135 TYR cc_start: 0.7736 (m-80) cc_final: 0.6770 (t80) REVERT: C 1141 GLU cc_start: 0.6643 (mm-30) cc_final: 0.5839 (mt-10) REVERT: H 82 MET cc_start: 0.3448 (mmp) cc_final: 0.2787 (tmm) REVERT: H 100 TYR cc_start: 0.6855 (m-10) cc_final: 0.5489 (m-10) REVERT: H 103 TRP cc_start: 0.5950 (m100) cc_final: 0.5743 (m-90) outliers start: 35 outliers final: 17 residues processed: 215 average time/residue: 0.5863 time to fit residues: 148.9654 Evaluate side-chains 187 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 56 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 245 optimal weight: 20.0000 chunk 288 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN A 904 ASN B 529 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 132 GLN C 672 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.227984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137771 restraints weight = 31274.272| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.89 r_work: 0.3258 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 27179 Z= 0.251 Angle : 0.646 12.097 36996 Z= 0.335 Chirality : 0.049 0.182 4180 Planarity : 0.004 0.047 4779 Dihedral : 5.157 59.768 3634 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 2.02 % Allowed : 7.67 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.14), residues: 3316 helix: 1.22 (0.21), residues: 618 sheet: 0.09 (0.19), residues: 654 loop : -1.25 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 564 TYR 0.033 0.002 TYR A 262 PHE 0.029 0.002 PHE C 90 TRP 0.015 0.002 TRP B 883 HIS 0.008 0.002 HIS B1055 Details of bonding type rmsd covalent geometry : bond 0.00601 (27148) covalent geometry : angle 0.64134 (36934) SS BOND : bond 0.00481 ( 31) SS BOND : angle 2.00277 ( 62) hydrogen bonds : bond 0.05087 ( 971) hydrogen bonds : angle 5.96486 ( 2721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 181 time to evaluate : 0.685 Fit side-chains REVERT: A 153 ARG cc_start: 0.3281 (OUTLIER) cc_final: 0.2586 (ptp-170) REVERT: A 167 SER cc_start: 0.7475 (t) cc_final: 0.7128 (p) REVERT: A 172 MET cc_start: 0.5338 (mmt) cc_final: 0.4332 (mmt) REVERT: A 221 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: A 236 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7395 (tm-30) REVERT: A 266 TYR cc_start: 0.8394 (m-80) cc_final: 0.7682 (m-10) REVERT: A 274 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7329 (mp) REVERT: A 276 TYR cc_start: 0.7337 (m-80) cc_final: 0.6876 (m-80) REVERT: A 287 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.6630 (t0) REVERT: A 302 SER cc_start: 0.8799 (t) cc_final: 0.8437 (p) REVERT: A 651 GLU cc_start: 0.7822 (tt0) cc_final: 0.7215 (tm-30) REVERT: A 947 ASP cc_start: 0.8253 (m-30) cc_final: 0.8047 (m-30) REVERT: B 186 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6706 (mt-10) REVERT: B 263 TYR cc_start: 0.5215 (m-80) cc_final: 0.4697 (m-80) REVERT: B 306 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7599 (mm-30) REVERT: B 532 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8252 (ttmm) REVERT: B 555 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7455 (mppt) REVERT: B 571 ASP cc_start: 0.7258 (t70) cc_final: 0.6945 (t0) REVERT: B 658 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7252 (mm-30) REVERT: B 672 GLN cc_start: 0.6673 (mm-40) cc_final: 0.6120 (mt0) REVERT: B 734 ASP cc_start: 0.7716 (t0) cc_final: 0.7140 (m-30) REVERT: B 756 PHE cc_start: 0.7015 (t80) cc_final: 0.6467 (t80) REVERT: B 773 LYS cc_start: 0.8720 (tttm) cc_final: 0.8273 (tttm) REVERT: B 787 LYS cc_start: 0.8578 (mttt) cc_final: 0.8150 (mmtt) REVERT: B 999 GLN cc_start: 0.8397 (tp40) cc_final: 0.8093 (tp40) REVERT: B 1042 LYS cc_start: 0.8666 (tppt) cc_final: 0.8378 (tmtt) REVERT: C 163 PHE cc_start: 0.0709 (OUTLIER) cc_final: -0.0401 (m-80) REVERT: C 302 SER cc_start: 0.8936 (t) cc_final: 0.8730 (t) REVERT: C 311 GLN cc_start: 0.8331 (tt0) cc_final: 0.7791 (tm-30) REVERT: C 643 ARG cc_start: 0.7759 (mtp180) cc_final: 0.6930 (mpp80) REVERT: C 777 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8596 (mt-10) REVERT: C 915 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: C 918 LYS cc_start: 0.8299 (tttm) cc_final: 0.7954 (ttpt) REVERT: C 954 GLN cc_start: 0.7759 (mt0) cc_final: 0.7145 (tm-30) REVERT: C 1016 ARG cc_start: 0.8289 (tpt170) cc_final: 0.7244 (ttm110) REVERT: C 1135 TYR cc_start: 0.7916 (m-80) cc_final: 0.6857 (t80) REVERT: C 1141 GLU cc_start: 0.6654 (mm-30) cc_final: 0.5821 (mt-10) REVERT: H 82 MET cc_start: 0.3620 (mmp) cc_final: 0.3025 (tmm) REVERT: H 98 ASP cc_start: 0.6896 (t70) cc_final: 0.6411 (t0) outliers start: 60 outliers final: 27 residues processed: 230 average time/residue: 0.5451 time to fit residues: 148.6879 Evaluate side-chains 202 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1130 VAL Chi-restraints excluded: chain L residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 148 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 271 optimal weight: 0.0980 chunk 90 optimal weight: 0.5980 chunk 322 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 chunk 185 optimal weight: 0.5980 chunk 110 optimal weight: 9.9990 chunk 303 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 ASN B 674 GLN B 759 GLN B 904 ASN B 954 GLN C 672 GLN C 752 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.232198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.144495 restraints weight = 31304.536| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.71 r_work: 0.3351 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27179 Z= 0.107 Angle : 0.525 9.971 36996 Z= 0.273 Chirality : 0.044 0.197 4180 Planarity : 0.004 0.055 4779 Dihedral : 4.690 57.145 3634 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 1.61 % Allowed : 8.68 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.14), residues: 3316 helix: 1.78 (0.21), residues: 613 sheet: 0.01 (0.19), residues: 642 loop : -1.07 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 564 TYR 0.019 0.001 TYR C1064 PHE 0.031 0.001 PHE C 90 TRP 0.015 0.001 TRP B 350 HIS 0.003 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00236 (27148) covalent geometry : angle 0.52229 (36934) SS BOND : bond 0.00263 ( 31) SS BOND : angle 1.29200 ( 62) hydrogen bonds : bond 0.03863 ( 971) hydrogen bonds : angle 5.53123 ( 2721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.883 Fit side-chains REVERT: A 153 ARG cc_start: 0.3426 (OUTLIER) cc_final: 0.2650 (ptp-170) REVERT: A 167 SER cc_start: 0.7247 (t) cc_final: 0.6960 (p) REVERT: A 172 MET cc_start: 0.5433 (mmt) cc_final: 0.4545 (mmt) REVERT: A 236 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7385 (tm-30) REVERT: A 266 TYR cc_start: 0.8258 (m-80) cc_final: 0.7553 (m-10) REVERT: A 287 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6788 (t0) REVERT: A 302 SER cc_start: 0.8644 (t) cc_final: 0.8388 (p) REVERT: A 316 ARG cc_start: 0.6631 (mmt90) cc_final: 0.5993 (mmt180) REVERT: A 651 GLU cc_start: 0.7773 (tt0) cc_final: 0.7226 (tm-30) REVERT: A 947 ASP cc_start: 0.8126 (m-30) cc_final: 0.7859 (m-30) REVERT: B 90 PHE cc_start: 0.5680 (t80) cc_final: 0.4435 (m-80) REVERT: B 186 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6738 (mt-10) REVERT: B 263 TYR cc_start: 0.5142 (m-80) cc_final: 0.4699 (m-80) REVERT: B 306 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7392 (mm-30) REVERT: B 555 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7354 (mppt) REVERT: B 571 ASP cc_start: 0.7165 (t70) cc_final: 0.6876 (t0) REVERT: B 580 GLU cc_start: 0.7291 (pt0) cc_final: 0.6629 (mm-30) REVERT: B 672 GLN cc_start: 0.6613 (mm-40) cc_final: 0.6045 (mt0) REVERT: B 734 ASP cc_start: 0.7555 (t0) cc_final: 0.7220 (t70) REVERT: B 757 CYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6533 (m) REVERT: B 773 LYS cc_start: 0.8614 (tttm) cc_final: 0.8056 (tttm) REVERT: B 787 LYS cc_start: 0.8573 (mttt) cc_final: 0.8157 (mmtt) REVERT: B 970 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7036 (pt) REVERT: B 999 GLN cc_start: 0.8191 (tp40) cc_final: 0.7853 (tp40) REVERT: B 1042 LYS cc_start: 0.8617 (tppt) cc_final: 0.8246 (tmtt) REVERT: C 163 PHE cc_start: 0.0378 (OUTLIER) cc_final: -0.0647 (m-10) REVERT: C 302 SER cc_start: 0.8922 (t) cc_final: 0.8511 (p) REVERT: C 311 GLN cc_start: 0.8259 (tt0) cc_final: 0.7670 (tm-30) REVERT: C 643 ARG cc_start: 0.7685 (mtp180) cc_final: 0.6923 (mpp80) REVERT: C 918 LYS cc_start: 0.8192 (tttm) cc_final: 0.7934 (ttpt) REVERT: C 954 GLN cc_start: 0.7603 (mt0) cc_final: 0.7061 (tm-30) REVERT: C 1016 ARG cc_start: 0.8210 (tpt170) cc_final: 0.7219 (ttm110) REVERT: C 1135 TYR cc_start: 0.7758 (m-80) cc_final: 0.6755 (t80) REVERT: C 1141 GLU cc_start: 0.6694 (mm-30) cc_final: 0.5883 (mt-10) REVERT: H 82 MET cc_start: 0.3910 (mmp) cc_final: 0.3241 (tmm) REVERT: H 98 ASP cc_start: 0.6458 (t70) cc_final: 0.5913 (t0) REVERT: H 103 TRP cc_start: 0.4783 (m-90) cc_final: 0.4407 (m-90) outliers start: 48 outliers final: 20 residues processed: 223 average time/residue: 0.5359 time to fit residues: 143.5234 Evaluate side-chains 197 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain C residue 1124 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 264 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 214 optimal weight: 4.9990 chunk 257 optimal weight: 10.0000 chunk 325 optimal weight: 0.3980 chunk 111 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN B 529 ASN B 932 GLN C 672 GLN C 752 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.229945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138850 restraints weight = 31220.203| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.69 r_work: 0.3336 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27179 Z= 0.135 Angle : 0.540 10.317 36996 Z= 0.281 Chirality : 0.045 0.187 4180 Planarity : 0.004 0.055 4779 Dihedral : 4.606 52.449 3634 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 1.48 % Allowed : 9.28 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.14), residues: 3316 helix: 1.82 (0.21), residues: 614 sheet: 0.10 (0.19), residues: 651 loop : -1.06 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 564 TYR 0.048 0.001 TYR H 100A PHE 0.031 0.001 PHE A 589 TRP 0.013 0.001 TRP B 350 HIS 0.004 0.001 HIS B1055 Details of bonding type rmsd covalent geometry : bond 0.00317 (27148) covalent geometry : angle 0.53749 (36934) SS BOND : bond 0.00289 ( 31) SS BOND : angle 1.26805 ( 62) hydrogen bonds : bond 0.04081 ( 971) hydrogen bonds : angle 5.48171 ( 2721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 1.098 Fit side-chains REVERT: A 86 ASP cc_start: 0.7400 (t0) cc_final: 0.6912 (p0) REVERT: A 153 ARG cc_start: 0.3705 (OUTLIER) cc_final: 0.2776 (ptp-170) REVERT: A 164 GLU cc_start: 0.7977 (tt0) cc_final: 0.7652 (tt0) REVERT: A 167 SER cc_start: 0.7204 (t) cc_final: 0.6900 (p) REVERT: A 172 MET cc_start: 0.5493 (mmt) cc_final: 0.4637 (mmt) REVERT: A 236 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 266 TYR cc_start: 0.8242 (m-80) cc_final: 0.7557 (m-10) REVERT: A 287 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6800 (t0) REVERT: A 302 SER cc_start: 0.8615 (t) cc_final: 0.8337 (p) REVERT: A 316 ARG cc_start: 0.6665 (mmt90) cc_final: 0.6008 (mmt180) REVERT: A 651 GLU cc_start: 0.7771 (tt0) cc_final: 0.7204 (tm-30) REVERT: A 913 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8307 (tt) REVERT: B 186 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6576 (mt-10) REVERT: B 263 TYR cc_start: 0.5086 (m-80) cc_final: 0.4552 (m-80) REVERT: B 306 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7438 (mm-30) REVERT: B 555 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7321 (mppt) REVERT: B 571 ASP cc_start: 0.7158 (t70) cc_final: 0.6859 (t0) REVERT: B 579 LEU cc_start: 0.7372 (mt) cc_final: 0.7108 (mm) REVERT: B 580 GLU cc_start: 0.7217 (pt0) cc_final: 0.6503 (mm-30) REVERT: B 672 GLN cc_start: 0.6641 (mm-40) cc_final: 0.6095 (mt0) REVERT: B 773 LYS cc_start: 0.8615 (tttm) cc_final: 0.8100 (tttm) REVERT: B 787 LYS cc_start: 0.8564 (mttt) cc_final: 0.8125 (mmtt) REVERT: B 970 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7069 (pt) REVERT: B 992 ARG cc_start: 0.7734 (ttm-80) cc_final: 0.7368 (ttm-80) REVERT: B 999 GLN cc_start: 0.8225 (tp40) cc_final: 0.7904 (tp40) REVERT: B 1042 LYS cc_start: 0.8598 (tppt) cc_final: 0.8311 (tmtt) REVERT: C 163 PHE cc_start: 0.0474 (OUTLIER) cc_final: -0.0598 (m-80) REVERT: C 268 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6899 (mt0) REVERT: C 302 SER cc_start: 0.8923 (t) cc_final: 0.8495 (p) REVERT: C 311 GLN cc_start: 0.8283 (tt0) cc_final: 0.7693 (tm-30) REVERT: C 643 ARG cc_start: 0.7717 (mtp180) cc_final: 0.6915 (mpp80) REVERT: C 915 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: C 918 LYS cc_start: 0.8195 (tttm) cc_final: 0.7923 (ttpt) REVERT: C 954 GLN cc_start: 0.7588 (mt0) cc_final: 0.7058 (tm-30) REVERT: C 1016 ARG cc_start: 0.8235 (tpt170) cc_final: 0.7187 (ttm110) REVERT: C 1135 TYR cc_start: 0.7785 (m-80) cc_final: 0.6775 (t80) REVERT: C 1141 GLU cc_start: 0.6718 (mm-30) cc_final: 0.5890 (mt-10) REVERT: H 82 MET cc_start: 0.3884 (mmp) cc_final: 0.3106 (tmm) REVERT: H 98 ASP cc_start: 0.6550 (t70) cc_final: 0.6056 (t0) REVERT: H 103 TRP cc_start: 0.4942 (m-90) cc_final: 0.4380 (m-90) outliers start: 44 outliers final: 19 residues processed: 214 average time/residue: 0.5873 time to fit residues: 150.7412 Evaluate side-chains 196 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 1097 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 183 optimal weight: 0.4980 chunk 210 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 216 optimal weight: 20.0000 chunk 307 optimal weight: 2.9990 chunk 313 optimal weight: 0.1980 chunk 186 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 236 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 chunk 70 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 954 GLN B 962 GLN C 672 GLN C 752 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.231855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.146810 restraints weight = 31324.068| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.00 r_work: 0.3333 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27179 Z= 0.098 Angle : 0.509 11.967 36996 Z= 0.263 Chirality : 0.043 0.181 4180 Planarity : 0.004 0.054 4779 Dihedral : 4.388 48.967 3634 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.41 % Rotamer: Outliers : 1.24 % Allowed : 9.82 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.14), residues: 3316 helix: 2.11 (0.21), residues: 607 sheet: 0.08 (0.19), residues: 662 loop : -1.01 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 564 TYR 0.050 0.001 TYR H 100A PHE 0.033 0.001 PHE C 90 TRP 0.015 0.001 TRP B 350 HIS 0.003 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00218 (27148) covalent geometry : angle 0.50735 (36934) SS BOND : bond 0.00277 ( 31) SS BOND : angle 1.06143 ( 62) hydrogen bonds : bond 0.03612 ( 971) hydrogen bonds : angle 5.25955 ( 2721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 1.230 Fit side-chains REVERT: A 53 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7206 (t70) REVERT: A 86 ASP cc_start: 0.7398 (t0) cc_final: 0.6974 (p0) REVERT: A 153 ARG cc_start: 0.3884 (OUTLIER) cc_final: 0.2815 (ptp-170) REVERT: A 164 GLU cc_start: 0.8093 (tt0) cc_final: 0.7794 (tt0) REVERT: A 167 SER cc_start: 0.7383 (t) cc_final: 0.7108 (p) REVERT: A 172 MET cc_start: 0.5492 (mmt) cc_final: 0.4719 (mmt) REVERT: A 236 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7470 (tm-30) REVERT: A 266 TYR cc_start: 0.8259 (m-80) cc_final: 0.7611 (m-10) REVERT: A 302 SER cc_start: 0.8692 (t) cc_final: 0.8480 (p) REVERT: A 651 GLU cc_start: 0.7849 (tt0) cc_final: 0.7294 (tm-30) REVERT: A 913 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8324 (tp) REVERT: B 90 PHE cc_start: 0.5740 (t80) cc_final: 0.4444 (m-80) REVERT: B 189 PHE cc_start: 0.6068 (m-10) cc_final: 0.5865 (m-10) REVERT: B 263 TYR cc_start: 0.5244 (m-80) cc_final: 0.4704 (m-80) REVERT: B 306 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7461 (mm-30) REVERT: B 555 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7379 (mppt) REVERT: B 571 ASP cc_start: 0.7197 (t70) cc_final: 0.6900 (t0) REVERT: B 579 LEU cc_start: 0.7463 (mt) cc_final: 0.7162 (mm) REVERT: B 580 GLU cc_start: 0.7281 (pt0) cc_final: 0.6578 (mm-30) REVERT: B 672 GLN cc_start: 0.6764 (mm-40) cc_final: 0.6239 (mt0) REVERT: B 773 LYS cc_start: 0.8624 (tttm) cc_final: 0.8140 (tttm) REVERT: B 787 LYS cc_start: 0.8632 (mttt) cc_final: 0.8232 (mmtt) REVERT: B 970 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6762 (pt) REVERT: B 999 GLN cc_start: 0.8265 (tp40) cc_final: 0.7947 (tp40) REVERT: B 1042 LYS cc_start: 0.8614 (tppt) cc_final: 0.8262 (tmtt) REVERT: C 163 PHE cc_start: 0.0328 (OUTLIER) cc_final: -0.0718 (m-10) REVERT: C 268 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7024 (mt0) REVERT: C 275 LYS cc_start: 0.6749 (tttm) cc_final: 0.6335 (ttmt) REVERT: C 302 SER cc_start: 0.8951 (t) cc_final: 0.8592 (p) REVERT: C 311 GLN cc_start: 0.8362 (tt0) cc_final: 0.7791 (tm-30) REVERT: C 643 ARG cc_start: 0.7808 (mtp180) cc_final: 0.7031 (mpp80) REVERT: C 918 LYS cc_start: 0.8212 (tttm) cc_final: 0.7954 (ttpt) REVERT: C 954 GLN cc_start: 0.7689 (mt0) cc_final: 0.7169 (tm-30) REVERT: C 1016 ARG cc_start: 0.8315 (tpt170) cc_final: 0.7324 (ttm110) REVERT: C 1135 TYR cc_start: 0.7759 (m-80) cc_final: 0.6778 (t80) REVERT: H 98 ASP cc_start: 0.6546 (t70) cc_final: 0.6048 (t0) REVERT: H 103 TRP cc_start: 0.5044 (m-90) cc_final: 0.4659 (m-90) outliers start: 37 outliers final: 17 residues processed: 216 average time/residue: 0.5436 time to fit residues: 142.2710 Evaluate side-chains 194 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 752 GLN Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 1097 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 71 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 213 optimal weight: 7.9990 chunk 330 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 270 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 904 ASN C 672 GLN C 752 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.229738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136781 restraints weight = 31150.910| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.09 r_work: 0.3370 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27179 Z= 0.147 Angle : 0.540 10.617 36996 Z= 0.280 Chirality : 0.045 0.177 4180 Planarity : 0.004 0.055 4779 Dihedral : 4.488 45.718 3632 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.78 % Rotamer: Outliers : 1.45 % Allowed : 9.82 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.14), residues: 3316 helix: 1.92 (0.21), residues: 619 sheet: 0.16 (0.19), residues: 661 loop : -1.02 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 564 TYR 0.053 0.001 TYR H 100A PHE 0.035 0.001 PHE C 90 TRP 0.014 0.001 TRP B 350 HIS 0.004 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00347 (27148) covalent geometry : angle 0.53808 (36934) SS BOND : bond 0.00294 ( 31) SS BOND : angle 1.22870 ( 62) hydrogen bonds : bond 0.04057 ( 971) hydrogen bonds : angle 5.37815 ( 2721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7007 (t70) REVERT: A 86 ASP cc_start: 0.7308 (t0) cc_final: 0.6906 (p0) REVERT: A 153 ARG cc_start: 0.4071 (OUTLIER) cc_final: 0.2961 (ptp-170) REVERT: A 167 SER cc_start: 0.7022 (t) cc_final: 0.6696 (p) REVERT: A 172 MET cc_start: 0.5455 (mmt) cc_final: 0.4687 (mmt) REVERT: A 221 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: A 236 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 266 TYR cc_start: 0.8169 (m-80) cc_final: 0.7493 (m-10) REVERT: A 302 SER cc_start: 0.8595 (t) cc_final: 0.8333 (p) REVERT: A 316 ARG cc_start: 0.6377 (mmt90) cc_final: 0.5853 (mmt180) REVERT: A 651 GLU cc_start: 0.7758 (tt0) cc_final: 0.7232 (tm-30) REVERT: A 913 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8277 (tt) REVERT: B 263 TYR cc_start: 0.5026 (m-80) cc_final: 0.4427 (m-80) REVERT: B 306 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7374 (mm-30) REVERT: B 525 LYS cc_start: 0.7238 (mmmt) cc_final: 0.6812 (mmtt) REVERT: B 555 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7347 (mppt) REVERT: B 571 ASP cc_start: 0.7104 (t70) cc_final: 0.6813 (t0) REVERT: B 579 LEU cc_start: 0.7374 (mt) cc_final: 0.7108 (mm) REVERT: B 580 GLU cc_start: 0.7159 (pt0) cc_final: 0.6476 (mm-30) REVERT: B 672 GLN cc_start: 0.6674 (mm-40) cc_final: 0.6153 (mt0) REVERT: B 773 LYS cc_start: 0.8553 (tttm) cc_final: 0.8049 (tttm) REVERT: B 787 LYS cc_start: 0.8542 (mttt) cc_final: 0.8122 (mmtt) REVERT: B 970 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.6885 (pt) REVERT: B 999 GLN cc_start: 0.8196 (tp40) cc_final: 0.7873 (tp40) REVERT: B 1042 LYS cc_start: 0.8578 (tppt) cc_final: 0.8300 (tmtt) REVERT: C 163 PHE cc_start: 0.0430 (OUTLIER) cc_final: -0.0632 (m-80) REVERT: C 268 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6944 (mt0) REVERT: C 275 LYS cc_start: 0.6591 (tttm) cc_final: 0.6186 (ttmt) REVERT: C 302 SER cc_start: 0.8917 (t) cc_final: 0.8494 (p) REVERT: C 311 GLN cc_start: 0.8249 (tt0) cc_final: 0.7630 (tm-30) REVERT: C 643 ARG cc_start: 0.7719 (mtp180) cc_final: 0.6949 (mpp80) REVERT: C 918 LYS cc_start: 0.8145 (tttm) cc_final: 0.7894 (ttpt) REVERT: C 954 GLN cc_start: 0.7527 (mt0) cc_final: 0.7016 (tm-30) REVERT: C 1016 ARG cc_start: 0.8152 (tpt170) cc_final: 0.7148 (ttm110) REVERT: C 1135 TYR cc_start: 0.7740 (m-80) cc_final: 0.6759 (t80) REVERT: C 1138 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5587 (tm) REVERT: H 98 ASP cc_start: 0.6458 (t70) cc_final: 0.6001 (t0) REVERT: H 103 TRP cc_start: 0.5051 (m-90) cc_final: 0.4454 (m-90) outliers start: 43 outliers final: 23 residues processed: 206 average time/residue: 0.4680 time to fit residues: 116.6665 Evaluate side-chains 200 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 658 GLU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 752 GLN Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain C residue 1138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 137 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 283 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 904 ASN B 954 GLN C 672 GLN C 752 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.229740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.143873 restraints weight = 31203.185| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.29 r_work: 0.3310 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27179 Z= 0.139 Angle : 0.537 10.676 36996 Z= 0.279 Chirality : 0.045 0.176 4180 Planarity : 0.004 0.054 4779 Dihedral : 4.471 42.638 3632 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.93 % Rotamer: Outliers : 1.28 % Allowed : 9.99 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.14), residues: 3316 helix: 1.99 (0.21), residues: 608 sheet: 0.14 (0.19), residues: 652 loop : -1.03 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 564 TYR 0.052 0.001 TYR H 100A PHE 0.041 0.001 PHE C 90 TRP 0.016 0.001 TRP B 350 HIS 0.004 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00327 (27148) covalent geometry : angle 0.53483 (36934) SS BOND : bond 0.00275 ( 31) SS BOND : angle 1.19160 ( 62) hydrogen bonds : bond 0.04008 ( 971) hydrogen bonds : angle 5.35636 ( 2721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7252 (t70) REVERT: A 86 ASP cc_start: 0.7445 (t0) cc_final: 0.7098 (p0) REVERT: A 153 ARG cc_start: 0.4297 (OUTLIER) cc_final: 0.3098 (ptp-170) REVERT: A 167 SER cc_start: 0.7445 (t) cc_final: 0.7194 (p) REVERT: A 172 MET cc_start: 0.5537 (mmt) cc_final: 0.4790 (mmt) REVERT: A 221 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: A 236 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7576 (tm-30) REVERT: A 266 TYR cc_start: 0.8292 (m-80) cc_final: 0.7694 (m-10) REVERT: A 302 SER cc_start: 0.8712 (t) cc_final: 0.8498 (p) REVERT: A 316 ARG cc_start: 0.6582 (mmt90) cc_final: 0.6083 (mmt180) REVERT: A 651 GLU cc_start: 0.7896 (tt0) cc_final: 0.7440 (tm-30) REVERT: A 913 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8414 (tt) REVERT: B 263 TYR cc_start: 0.5282 (m-80) cc_final: 0.4767 (m-80) REVERT: B 306 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7549 (mm-30) REVERT: B 555 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7447 (mppt) REVERT: B 571 ASP cc_start: 0.7259 (t70) cc_final: 0.6965 (t0) REVERT: B 672 GLN cc_start: 0.6873 (mm-40) cc_final: 0.6358 (mt0) REVERT: B 773 LYS cc_start: 0.8785 (tttm) cc_final: 0.8336 (tttm) REVERT: B 787 LYS cc_start: 0.8647 (mttt) cc_final: 0.8269 (mmtt) REVERT: B 970 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.6911 (pt) REVERT: B 999 GLN cc_start: 0.8348 (tp40) cc_final: 0.8055 (tp40) REVERT: B 1042 LYS cc_start: 0.8678 (tppt) cc_final: 0.8435 (tmtt) REVERT: C 163 PHE cc_start: 0.0407 (OUTLIER) cc_final: -0.0685 (m-80) REVERT: C 268 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7140 (mt0) REVERT: C 275 LYS cc_start: 0.6905 (tttm) cc_final: 0.6479 (ttmt) REVERT: C 302 SER cc_start: 0.8984 (t) cc_final: 0.8583 (p) REVERT: C 311 GLN cc_start: 0.8374 (tt0) cc_final: 0.7842 (tm-30) REVERT: C 643 ARG cc_start: 0.7913 (mtp180) cc_final: 0.7147 (mpp80) REVERT: C 918 LYS cc_start: 0.8354 (tttm) cc_final: 0.8131 (ttpt) REVERT: C 954 GLN cc_start: 0.7846 (mt0) cc_final: 0.7371 (tm-30) REVERT: C 1016 ARG cc_start: 0.8419 (tpt170) cc_final: 0.7492 (ttm110) REVERT: C 1135 TYR cc_start: 0.7883 (m-80) cc_final: 0.6948 (t80) REVERT: C 1141 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6007 (mt-10) REVERT: H 98 ASP cc_start: 0.6890 (t70) cc_final: 0.6446 (t0) outliers start: 38 outliers final: 26 residues processed: 200 average time/residue: 0.5819 time to fit residues: 139.7864 Evaluate side-chains 201 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 658 GLU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 752 GLN Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 1097 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 194 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 301 optimal weight: 0.7980 chunk 234 optimal weight: 0.7980 chunk 293 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 275 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 144 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 672 GLN C 752 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.232254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144090 restraints weight = 31037.725| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.07 r_work: 0.3340 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27179 Z= 0.105 Angle : 0.520 10.624 36996 Z= 0.269 Chirality : 0.044 0.173 4180 Planarity : 0.004 0.062 4779 Dihedral : 4.363 40.480 3632 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 1.28 % Allowed : 9.99 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.14), residues: 3316 helix: 2.06 (0.21), residues: 614 sheet: 0.16 (0.19), residues: 658 loop : -1.00 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 564 TYR 0.054 0.001 TYR H 100A PHE 0.041 0.001 PHE C 90 TRP 0.016 0.001 TRP H 103 HIS 0.003 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00237 (27148) covalent geometry : angle 0.51861 (36934) SS BOND : bond 0.00248 ( 31) SS BOND : angle 1.05082 ( 62) hydrogen bonds : bond 0.03727 ( 971) hydrogen bonds : angle 5.24645 ( 2721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12719.78 seconds wall clock time: 216 minutes 51.14 seconds (13011.14 seconds total)