Starting phenix.real_space_refine on Sun May 25 08:39:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjk_50503/05_2025/9fjk_50503.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjk_50503/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fjk_50503/05_2025/9fjk_50503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjk_50503/05_2025/9fjk_50503.map" model { file = "/net/cci-nas-00/data/ceres_data/9fjk_50503/05_2025/9fjk_50503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjk_50503/05_2025/9fjk_50503.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.36, per 1000 atoms: 0.65 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: 7.23 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 4.83 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: 12.48 Time building geometry restraints manager: 8.44 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: 21.060 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 64.630 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.560 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (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 TRP 0.046 0.003 TRP B 350 HIS 0.014 0.002 HIS A1045 PHE 0.035 0.003 PHE C 163 TYR 0.033 0.002 TYR A 262 ARG 0.016 0.001 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.20878 ( 971) hydrogen bonds : angle 8.88004 ( 2721) SS BOND : bond 0.00356 ( 31) SS BOND : angle 1.67552 ( 62) covalent geometry : bond 0.00479 (27148) covalent geometry : angle 0.90280 (36934) *********************** 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 : 2.736 Fit side-chains 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: 0.7645 (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: 0.6186 (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: 0.6230 (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: 0.7677 (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: 0.7379 (m-30) REVERT: C 172 MET cc_start: 0.2341 (ptm) cc_final: 0.1986 (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: 0.7924 (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: 0.6428 (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: 1.3114 time to fit residues: 471.9882 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 : 2.824 ------------------------------------------------------------------------------- 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 283 optimal weight: 4.9990 chunk 254 optimal weight: 0.3980 chunk 141 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 263 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 801 GLN A 904 ASN A 932 GLN A 952 ASN A1110 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN B 954 GLN C 61 ASN C 202 HIS ** C 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN C 672 GLN C 759 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.232846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141441 restraints weight = 31681.418| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.64 r_work: 0.3378 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27179 Z= 0.188 Angle : 0.635 10.240 36996 Z= 0.335 Chirality : 0.047 0.210 4180 Planarity : 0.005 0.064 4779 Dihedral : 5.409 56.054 3637 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.04 % Allowed : 4.27 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3316 helix: 0.57 (0.21), residues: 629 sheet: -0.02 (0.20), residues: 615 loop : -1.28 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 883 HIS 0.006 0.001 HIS B1055 PHE 0.024 0.002 PHE A 43 TYR 0.026 0.002 TYR A1064 ARG 0.009 0.001 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.04932 ( 971) hydrogen bonds : angle 6.33659 ( 2721) SS BOND : bond 0.00402 ( 31) SS BOND : angle 1.59160 ( 62) covalent geometry : bond 0.00441 (27148) covalent geometry : angle 0.63246 (36934) *********************** 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 236 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 2.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.2336 (OUTLIER) cc_final: 0.1494 (ptp-170) REVERT: A 172 MET cc_start: 0.4982 (mmt) cc_final: 0.4001 (mmt) REVERT: A 236 GLN cc_start: 0.7449 (tm-30) cc_final: 0.6952 (tm-30) REVERT: A 266 TYR cc_start: 0.7729 (m-80) cc_final: 0.7487 (m-10) REVERT: A 287 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.5927 (t0) REVERT: A 302 SER cc_start: 0.8632 (t) cc_final: 0.8303 (p) REVERT: A 588 SER cc_start: 0.7971 (m) cc_final: 0.7644 (p) REVERT: A 616 GLU cc_start: 0.7196 (tp30) cc_final: 0.6901 (mm-30) REVERT: A 651 GLU cc_start: 0.7707 (tt0) cc_final: 0.7229 (tm-30) REVERT: A 773 LYS cc_start: 0.8301 (tptt) cc_final: 0.7758 (ttpt) REVERT: A 947 ASP cc_start: 0.8072 (m-30) cc_final: 0.7843 (m-30) REVERT: A 1035 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8372 (mptt) REVERT: A 1115 ASP cc_start: 0.8157 (p0) cc_final: 0.7793 (m-30) REVERT: B 263 TYR cc_start: 0.5136 (m-80) cc_final: 0.4609 (m-80) REVERT: B 306 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7562 (mm-30) REVERT: B 532 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8055 (ttmm) REVERT: B 555 LYS cc_start: 0.8273 (mmtt) cc_final: 0.6872 (pttm) REVERT: B 571 ASP cc_start: 0.7172 (t70) cc_final: 0.6826 (t0) REVERT: B 579 LEU cc_start: 0.7029 (mp) cc_final: 0.6812 (mm) REVERT: B 580 GLU cc_start: 0.7144 (pt0) cc_final: 0.6625 (mm-30) REVERT: B 773 LYS cc_start: 0.8599 (tttm) cc_final: 0.8026 (tttm) REVERT: B 787 LYS cc_start: 0.8507 (mttt) cc_final: 0.8163 (mmtt) REVERT: B 999 GLN cc_start: 0.8224 (tp40) cc_final: 0.7922 (tp40) REVERT: B 1042 LYS cc_start: 0.8438 (tppt) cc_final: 0.8139 (tmtt) REVERT: B 1124 ASP cc_start: 0.7898 (m-30) cc_final: 0.7686 (m-30) REVERT: C 302 SER cc_start: 0.8914 (t) cc_final: 0.8588 (p) REVERT: C 311 GLN cc_start: 0.8378 (tt0) cc_final: 0.7874 (tm-30) REVERT: C 589 PHE cc_start: 0.7490 (p90) cc_final: 0.7199 (p90) REVERT: C 600 ASN cc_start: 0.7989 (t0) cc_final: 0.7762 (m-40) REVERT: C 610 GLN cc_start: 0.8408 (mt0) cc_final: 0.8166 (mt0) REVERT: C 643 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7150 (tmm-80) REVERT: C 777 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8461 (mt-10) REVERT: C 788 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8782 (p) REVERT: C 872 SER cc_start: 0.8819 (t) cc_final: 0.8548 (m) REVERT: C 918 LYS cc_start: 0.8094 (tttm) cc_final: 0.7783 (ttpt) REVERT: C 1016 ARG cc_start: 0.8067 (tpt170) cc_final: 0.7070 (ttm110) REVERT: C 1081 ASP cc_start: 0.8250 (p0) cc_final: 0.8050 (p0) REVERT: C 1135 TYR cc_start: 0.7686 (m-80) cc_final: 0.6748 (t80) REVERT: C 1141 GLU cc_start: 0.6633 (mm-30) cc_final: 0.5829 (mt-10) REVERT: H 82 MET cc_start: 0.3051 (mmp) cc_final: 0.2224 (tmm) REVERT: H 103 TRP cc_start: 0.5118 (m-90) cc_final: 0.4671 (m-90) outliers start: 31 outliers final: 13 residues processed: 226 average time/residue: 1.1268 time to fit residues: 307.1344 Evaluate side-chains 187 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 2.676 ------------------------------------------------------------------------------- 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 720 THR 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 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 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 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 69 optimal weight: 0.0770 chunk 147 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 chunk 267 optimal weight: 0.1980 chunk 323 optimal weight: 8.9990 chunk 310 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 127 optimal weight: 3.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN A 898 GLN B 641 GLN B 898 GLN B 954 GLN B1007 GLN C 672 GLN C 687 GLN C 752 GLN C 801 GLN C 833 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.235037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145829 restraints weight = 31722.537| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.73 r_work: 0.3414 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1976 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= 0.104 Angle : 0.539 11.655 36996 Z= 0.281 Chirality : 0.044 0.181 4180 Planarity : 0.004 0.049 4779 Dihedral : 4.836 51.316 3634 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 0.91 % Allowed : 6.19 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3316 helix: 1.33 (0.21), residues: 625 sheet: -0.01 (0.19), residues: 630 loop : -1.12 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 350 HIS 0.004 0.001 HIS B 66 PHE 0.024 0.001 PHE C 90 TYR 0.022 0.001 TYR A1135 ARG 0.004 0.000 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 971) hydrogen bonds : angle 5.83242 ( 2721) SS BOND : bond 0.00405 ( 31) SS BOND : angle 1.11365 ( 62) covalent geometry : bond 0.00222 (27148) covalent geometry : angle 0.53739 (36934) *********************** 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 225 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 2.913 Fit side-chains revert: symmetry clash REVERT: A 153 ARG cc_start: 0.2581 (OUTLIER) cc_final: 0.1841 (ptp-170) REVERT: A 172 MET cc_start: 0.5165 (mmt) cc_final: 0.4192 (mmt) REVERT: A 236 GLN cc_start: 0.7723 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 266 TYR cc_start: 0.7760 (m-80) cc_final: 0.7540 (m-10) REVERT: A 287 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6535 (t0) REVERT: A 302 SER cc_start: 0.8537 (t) cc_final: 0.8289 (p) REVERT: A 316 ARG cc_start: 0.6592 (mtt90) cc_final: 0.6203 (mmt180) REVERT: A 616 GLU cc_start: 0.7056 (tp30) cc_final: 0.6851 (mm-30) REVERT: A 651 GLU cc_start: 0.7727 (tt0) cc_final: 0.7237 (tm-30) REVERT: A 773 LYS cc_start: 0.8312 (tptt) cc_final: 0.7786 (ttpt) REVERT: A 947 ASP cc_start: 0.8080 (m-30) cc_final: 0.7825 (m-30) REVERT: A 1035 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8411 (mptt) REVERT: A 1115 ASP cc_start: 0.8121 (p0) cc_final: 0.7849 (m-30) REVERT: B 186 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6632 (mt-10) REVERT: B 263 TYR cc_start: 0.5049 (m-80) cc_final: 0.4596 (m-80) REVERT: B 306 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7469 (mm-30) REVERT: B 555 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7330 (mppt) REVERT: B 571 ASP cc_start: 0.7149 (t70) cc_final: 0.6838 (t0) REVERT: B 580 GLU cc_start: 0.7087 (pt0) cc_final: 0.6575 (mm-30) REVERT: B 732 SER cc_start: 0.8977 (t) cc_final: 0.8720 (p) REVERT: B 773 LYS cc_start: 0.8566 (tttm) cc_final: 0.8111 (tttm) REVERT: B 787 LYS cc_start: 0.8540 (mttt) cc_final: 0.8195 (mmtt) REVERT: B 999 GLN cc_start: 0.8146 (tp40) cc_final: 0.7815 (tp40) REVERT: B 1042 LYS cc_start: 0.8454 (tppt) cc_final: 0.8136 (tmtt) REVERT: C 302 SER cc_start: 0.8919 (t) cc_final: 0.8679 (p) REVERT: C 311 GLN cc_start: 0.8359 (tt0) cc_final: 0.7881 (tm-30) REVERT: C 589 PHE cc_start: 0.7377 (p90) cc_final: 0.7135 (p90) REVERT: C 600 ASN cc_start: 0.8017 (t0) cc_final: 0.7788 (m-40) REVERT: C 610 GLN cc_start: 0.8349 (mt0) cc_final: 0.8116 (mt0) REVERT: C 643 ARG cc_start: 0.7665 (mtp180) cc_final: 0.7045 (mpp80) REVERT: C 753 TYR cc_start: 0.7866 (m-80) cc_final: 0.7621 (m-80) REVERT: C 788 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8782 (p) REVERT: C 918 LYS cc_start: 0.8046 (tttm) cc_final: 0.7806 (ttpt) REVERT: C 954 GLN cc_start: 0.7598 (mt0) cc_final: 0.7089 (tm-30) REVERT: C 1016 ARG cc_start: 0.8132 (tpt170) cc_final: 0.7181 (ttm110) REVERT: C 1081 ASP cc_start: 0.8085 (p0) cc_final: 0.7789 (p0) REVERT: C 1135 TYR cc_start: 0.7647 (m-80) cc_final: 0.6735 (t80) REVERT: C 1141 GLU cc_start: 0.6656 (mm-30) cc_final: 0.5845 (mt-10) REVERT: H 34 TYR cc_start: 0.6978 (m-10) cc_final: 0.6718 (m-10) REVERT: H 82 MET cc_start: 0.3237 (mmp) cc_final: 0.2436 (tmm) REVERT: H 103 TRP cc_start: 0.5166 (m-90) cc_final: 0.4667 (m-90) outliers start: 27 outliers final: 9 residues processed: 211 average time/residue: 1.1907 time to fit residues: 299.3470 Evaluate side-chains 183 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 2.950 ------------------------------------------------------------------------------- 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 612 VAL Chi-restraints excluded: chain A residue 791 ILE 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 603 ASN Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 788 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 147 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 321 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 331 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 ASN A 932 GLN B 529 ASN ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN C 672 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.227050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136602 restraints weight = 31552.435| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.89 r_work: 0.3278 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 27179 Z= 0.297 Angle : 0.695 10.701 36996 Z= 0.362 Chirality : 0.051 0.225 4180 Planarity : 0.005 0.047 4779 Dihedral : 5.367 56.605 3634 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 1.92 % Allowed : 6.89 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 3316 helix: 1.04 (0.21), residues: 610 sheet: 0.02 (0.19), residues: 648 loop : -1.29 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 883 HIS 0.010 0.002 HIS B1055 PHE 0.025 0.002 PHE C 90 TYR 0.040 0.002 TYR A 262 ARG 0.008 0.001 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.05475 ( 971) hydrogen bonds : angle 6.15962 ( 2721) SS BOND : bond 0.00625 ( 31) SS BOND : angle 1.87061 ( 62) covalent geometry : bond 0.00716 (27148) covalent geometry : angle 0.69175 (36934) *********************** 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 240 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 183 time to evaluate : 2.982 Fit side-chains revert: symmetry clash REVERT: A 153 ARG cc_start: 0.3097 (OUTLIER) cc_final: 0.2416 (ptp-170) REVERT: A 172 MET cc_start: 0.5303 (mmt) cc_final: 0.4236 (mmt) REVERT: A 236 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7365 (tm-30) REVERT: A 266 TYR cc_start: 0.8375 (m-80) cc_final: 0.7671 (m-10) REVERT: A 276 TYR cc_start: 0.7298 (m-80) cc_final: 0.6740 (m-80) REVERT: A 287 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.6639 (t0) REVERT: A 302 SER cc_start: 0.8754 (t) cc_final: 0.8337 (p) REVERT: A 616 GLU cc_start: 0.7488 (tp30) cc_final: 0.7281 (mm-30) REVERT: A 651 GLU cc_start: 0.7792 (tt0) cc_final: 0.7167 (tm-30) REVERT: B 186 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6597 (mt-10) REVERT: B 263 TYR cc_start: 0.5193 (m-80) cc_final: 0.4758 (m-80) REVERT: B 306 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7611 (mm-30) REVERT: B 555 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7458 (mppt) REVERT: B 571 ASP cc_start: 0.7257 (t70) cc_final: 0.6913 (t0) REVERT: B 756 PHE cc_start: 0.7079 (t80) cc_final: 0.6643 (t80) REVERT: B 773 LYS cc_start: 0.8726 (tttm) cc_final: 0.8253 (tttm) REVERT: B 787 LYS cc_start: 0.8547 (mttt) cc_final: 0.8095 (mmtt) REVERT: B 999 GLN cc_start: 0.8417 (tp40) cc_final: 0.8119 (tp40) REVERT: B 1042 LYS cc_start: 0.8631 (tppt) cc_final: 0.8355 (tmtt) REVERT: C 172 MET cc_start: 0.2756 (ptp) cc_final: 0.2124 (ptp) REVERT: C 302 SER cc_start: 0.8946 (t) cc_final: 0.8734 (t) REVERT: C 311 GLN cc_start: 0.8370 (tt0) cc_final: 0.7839 (tm-30) REVERT: C 643 ARG cc_start: 0.7735 (mtp180) cc_final: 0.6947 (mpp80) REVERT: C 918 LYS cc_start: 0.8309 (tttm) cc_final: 0.7979 (ttpt) REVERT: C 1016 ARG cc_start: 0.8296 (tpt170) cc_final: 0.7236 (ttp-110) REVERT: C 1081 ASP cc_start: 0.8349 (p0) cc_final: 0.8096 (p0) REVERT: C 1135 TYR cc_start: 0.7894 (m-80) cc_final: 0.6885 (t80) REVERT: C 1141 GLU cc_start: 0.6667 (mm-30) cc_final: 0.5820 (mt-10) REVERT: H 82 MET cc_start: 0.3514 (mmp) cc_final: 0.2808 (tmm) REVERT: H 98 ASP cc_start: 0.6860 (t70) cc_final: 0.6416 (t0) REVERT: H 103 TRP cc_start: 0.5381 (m-90) cc_final: 0.4972 (m-90) outliers start: 57 outliers final: 25 residues processed: 225 average time/residue: 1.1918 time to fit residues: 321.6123 Evaluate side-chains 195 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 2.938 ------------------------------------------------------------------------------- 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 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 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 548 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 1124 ASP 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 788 THR Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 872 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 241 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN B 529 ASN B 759 GLN B 904 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4527 r_free = 0.4527 target = 0.230360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143016 restraints weight = 31347.014| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.98 r_work: 0.3275 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 27179 Z= 0.158 Angle : 0.562 10.103 36996 Z= 0.294 Chirality : 0.046 0.183 4180 Planarity : 0.004 0.048 4779 Dihedral : 4.954 58.975 3634 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 1.92 % Allowed : 8.00 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3316 helix: 1.41 (0.21), residues: 614 sheet: -0.02 (0.19), residues: 656 loop : -1.23 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 350 HIS 0.004 0.001 HIS C1055 PHE 0.026 0.001 PHE C 90 TYR 0.024 0.001 TYR A 262 ARG 0.007 0.000 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 971) hydrogen bonds : angle 5.76659 ( 2721) SS BOND : bond 0.00356 ( 31) SS BOND : angle 2.13922 ( 62) covalent geometry : bond 0.00373 (27148) covalent geometry : angle 0.55560 (36934) *********************** 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 239 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 182 time to evaluate : 2.791 Fit side-chains REVERT: A 153 ARG cc_start: 0.3393 (OUTLIER) cc_final: 0.2714 (ptp-170) REVERT: A 167 SER cc_start: 0.7603 (t) cc_final: 0.7387 (p) REVERT: A 172 MET cc_start: 0.5444 (mmt) cc_final: 0.4593 (mmt) REVERT: A 236 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 266 TYR cc_start: 0.8380 (m-80) cc_final: 0.7760 (m-10) REVERT: A 287 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.6908 (t0) REVERT: A 302 SER cc_start: 0.8773 (t) cc_final: 0.8496 (p) REVERT: A 316 ARG cc_start: 0.6860 (mmt90) cc_final: 0.6241 (mmt180) REVERT: A 651 GLU cc_start: 0.7901 (tt0) cc_final: 0.7418 (tm-30) REVERT: A 947 ASP cc_start: 0.8376 (m-30) cc_final: 0.7836 (m-30) REVERT: B 186 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6809 (mt-10) REVERT: B 263 TYR cc_start: 0.5291 (m-80) cc_final: 0.4768 (m-80) REVERT: B 306 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7632 (mm-30) REVERT: B 532 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8255 (ttmm) REVERT: B 555 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7438 (mppt) REVERT: B 571 ASP cc_start: 0.7293 (t70) cc_final: 0.6994 (t0) REVERT: B 773 LYS cc_start: 0.8783 (tttm) cc_final: 0.8317 (tttm) REVERT: B 787 LYS cc_start: 0.8643 (mttt) cc_final: 0.8248 (mmtt) REVERT: B 970 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6884 (pt) REVERT: B 999 GLN cc_start: 0.8405 (tp40) cc_final: 0.8120 (tp40) REVERT: B 1042 LYS cc_start: 0.8702 (tppt) cc_final: 0.8406 (tmtt) REVERT: C 163 PHE cc_start: 0.0555 (OUTLIER) cc_final: -0.0559 (m-80) REVERT: C 299 THR cc_start: 0.8023 (t) cc_final: 0.7810 (p) REVERT: C 311 GLN cc_start: 0.8341 (tt0) cc_final: 0.7857 (tm-30) REVERT: C 571 ASP cc_start: 0.6686 (t70) cc_final: 0.6441 (t0) REVERT: C 643 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7057 (mpp80) REVERT: C 918 LYS cc_start: 0.8406 (tttm) cc_final: 0.8124 (ttpt) REVERT: C 1016 ARG cc_start: 0.8422 (tpt170) cc_final: 0.7503 (ttm110) REVERT: C 1081 ASP cc_start: 0.8160 (p0) cc_final: 0.7869 (p0) REVERT: C 1135 TYR cc_start: 0.7921 (m-80) cc_final: 0.6969 (t80) REVERT: C 1141 GLU cc_start: 0.6723 (mm-30) cc_final: 0.5892 (mt-10) REVERT: H 82 MET cc_start: 0.3600 (mmp) cc_final: 0.2997 (tmm) REVERT: H 98 ASP cc_start: 0.6867 (t70) cc_final: 0.6414 (t0) REVERT: H 103 TRP cc_start: 0.5437 (m-90) cc_final: 0.5082 (m-90) outliers start: 57 outliers final: 23 residues processed: 222 average time/residue: 1.2281 time to fit residues: 325.8046 Evaluate side-chains 190 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 2.656 ------------------------------------------------------------------------------- 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 228 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 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 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 970 ILE Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 872 SER 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 H residue 100 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 55 optimal weight: 0.1980 chunk 6 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 335 optimal weight: 0.9980 chunk 242 optimal weight: 5.9990 chunk 171 optimal weight: 0.5980 chunk 293 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 253 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4517 r_free = 0.4517 target = 0.229341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141240 restraints weight = 31221.082| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.08 r_work: 0.3276 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27179 Z= 0.166 Angle : 0.565 11.226 36996 Z= 0.294 Chirality : 0.046 0.206 4180 Planarity : 0.004 0.051 4779 Dihedral : 4.835 53.887 3634 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 1.78 % Allowed : 8.88 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3316 helix: 1.53 (0.21), residues: 616 sheet: 0.05 (0.19), residues: 654 loop : -1.24 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 350 HIS 0.005 0.001 HIS B1055 PHE 0.028 0.001 PHE C 90 TYR 0.023 0.001 TYR A1064 ARG 0.011 0.001 ARG B 564 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 971) hydrogen bonds : angle 5.69629 ( 2721) SS BOND : bond 0.00313 ( 31) SS BOND : angle 1.50161 ( 62) covalent geometry : bond 0.00395 (27148) covalent geometry : angle 0.56183 (36934) *********************** 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 221 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 168 time to evaluate : 2.804 Fit side-chains REVERT: A 153 ARG cc_start: 0.3668 (OUTLIER) cc_final: 0.2699 (ptp-170) REVERT: A 167 SER cc_start: 0.7505 (t) cc_final: 0.7269 (p) REVERT: A 172 MET cc_start: 0.5545 (mmt) cc_final: 0.4631 (mmt) REVERT: A 221 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: A 236 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 266 TYR cc_start: 0.8371 (m-80) cc_final: 0.7726 (m-10) REVERT: A 287 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.6893 (t0) REVERT: A 302 SER cc_start: 0.8771 (t) cc_final: 0.8465 (p) REVERT: A 651 GLU cc_start: 0.7897 (tt0) cc_final: 0.7349 (tm-30) REVERT: A 913 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8444 (tt) REVERT: A 947 ASP cc_start: 0.8339 (m-30) cc_final: 0.7754 (m-30) REVERT: B 186 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6764 (mt-10) REVERT: B 263 TYR cc_start: 0.5211 (m-80) cc_final: 0.4668 (m-80) REVERT: B 306 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 551 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6917 (mm-30) REVERT: B 555 LYS cc_start: 0.8368 (mmtt) cc_final: 0.7450 (mppt) REVERT: B 571 ASP cc_start: 0.7260 (t70) cc_final: 0.6964 (t0) REVERT: B 756 PHE cc_start: 0.6966 (t80) cc_final: 0.6702 (t80) REVERT: B 773 LYS cc_start: 0.8676 (tttm) cc_final: 0.8188 (tttm) REVERT: B 787 LYS cc_start: 0.8623 (mttt) cc_final: 0.8177 (mmtt) REVERT: B 999 GLN cc_start: 0.8349 (tp40) cc_final: 0.8036 (tp40) REVERT: B 1042 LYS cc_start: 0.8701 (tppt) cc_final: 0.8428 (tmtt) REVERT: C 163 PHE cc_start: 0.0567 (OUTLIER) cc_final: -0.0522 (m-80) REVERT: C 311 GLN cc_start: 0.8344 (tt0) cc_final: 0.7784 (tm-30) REVERT: C 643 ARG cc_start: 0.7804 (mtp180) cc_final: 0.7006 (mpp80) REVERT: C 918 LYS cc_start: 0.8321 (tttm) cc_final: 0.8051 (ttpt) REVERT: C 1016 ARG cc_start: 0.8357 (tpt170) cc_final: 0.7323 (ttm110) REVERT: C 1081 ASP cc_start: 0.8229 (p0) cc_final: 0.7922 (p0) REVERT: C 1135 TYR cc_start: 0.7866 (m-80) cc_final: 0.6844 (t80) REVERT: H 82 MET cc_start: 0.3896 (mmp) cc_final: 0.3242 (tmm) REVERT: H 98 ASP cc_start: 0.6896 (t70) cc_final: 0.6513 (t0) REVERT: H 103 TRP cc_start: 0.5431 (m-90) cc_final: 0.5118 (m-90) outliers start: 53 outliers final: 28 residues processed: 210 average time/residue: 1.1316 time to fit residues: 287.3029 Evaluate side-chains 192 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 221 GLU 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 600 ASN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 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 389 PHE Chi-restraints excluded: chain B residue 521 VAL 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 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 735 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain L residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 215 optimal weight: 10.0000 chunk 186 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 278 optimal weight: 0.6980 chunk 282 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 319 optimal weight: 1.9990 chunk 288 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 243 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 135 ASN B 529 ASN B 674 GLN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4534 r_free = 0.4534 target = 0.231512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138870 restraints weight = 31244.408| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.07 r_work: 0.3391 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27179 Z= 0.109 Angle : 0.521 10.422 36996 Z= 0.271 Chirality : 0.044 0.184 4180 Planarity : 0.004 0.071 4779 Dihedral : 4.572 50.298 3634 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 1.28 % Allowed : 9.82 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3316 helix: 1.84 (0.21), residues: 614 sheet: 0.03 (0.19), residues: 654 loop : -1.15 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 350 HIS 0.002 0.001 HIS A 516 PHE 0.033 0.001 PHE C 90 TYR 0.043 0.001 TYR H 100A ARG 0.007 0.000 ARG B 564 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 971) hydrogen bonds : angle 5.46208 ( 2721) SS BOND : bond 0.00276 ( 31) SS BOND : angle 1.19485 ( 62) covalent geometry : bond 0.00246 (27148) covalent geometry : angle 0.51883 (36934) *********************** 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 217 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 2.971 Fit side-chains REVERT: A 53 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7031 (t70) REVERT: A 153 ARG cc_start: 0.3861 (OUTLIER) cc_final: 0.2789 (ptp-170) REVERT: A 167 SER cc_start: 0.7087 (t) cc_final: 0.6826 (p) REVERT: A 172 MET cc_start: 0.5443 (mmt) cc_final: 0.4661 (mmt) REVERT: A 236 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7323 (tm-30) REVERT: A 266 TYR cc_start: 0.8205 (m-80) cc_final: 0.7534 (m-10) REVERT: A 302 SER cc_start: 0.8578 (t) cc_final: 0.8310 (p) REVERT: A 316 ARG cc_start: 0.6615 (mmt90) cc_final: 0.6085 (mmt180) REVERT: A 616 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6911 (mm-30) REVERT: A 651 GLU cc_start: 0.7782 (tt0) cc_final: 0.7239 (tm-30) REVERT: A 947 ASP cc_start: 0.8126 (m-30) cc_final: 0.7538 (m-30) REVERT: B 186 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6650 (mt-10) REVERT: B 263 TYR cc_start: 0.5008 (m-80) cc_final: 0.4482 (m-80) REVERT: B 306 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7336 (mm-30) REVERT: B 555 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7362 (mppt) REVERT: B 571 ASP cc_start: 0.7143 (t70) cc_final: 0.6866 (t0) REVERT: B 773 LYS cc_start: 0.8520 (tttm) cc_final: 0.8019 (tttm) REVERT: B 787 LYS cc_start: 0.8568 (mttt) cc_final: 0.8155 (mmtt) REVERT: B 999 GLN cc_start: 0.8197 (tp40) cc_final: 0.7865 (tp40) REVERT: B 1042 LYS cc_start: 0.8619 (tppt) cc_final: 0.8303 (tmtt) REVERT: C 163 PHE cc_start: 0.0444 (OUTLIER) cc_final: -0.0589 (m-80) REVERT: C 268 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6887 (mt0) REVERT: C 311 GLN cc_start: 0.8211 (tt0) cc_final: 0.7627 (tm-30) REVERT: C 643 ARG cc_start: 0.7715 (mtp180) cc_final: 0.6935 (mpp80) REVERT: C 915 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: C 918 LYS cc_start: 0.8168 (tttm) cc_final: 0.7921 (ttpt) REVERT: C 1016 ARG cc_start: 0.8172 (tpt170) cc_final: 0.7207 (ttm110) REVERT: C 1081 ASP cc_start: 0.7980 (p0) cc_final: 0.7703 (p0) REVERT: C 1089 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: C 1135 TYR cc_start: 0.7729 (m-80) cc_final: 0.6802 (t80) REVERT: C 1141 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6008 (mt-10) REVERT: H 82 MET cc_start: 0.3864 (mmp) cc_final: 0.3103 (tmm) REVERT: H 94 ARG cc_start: 0.4223 (ttp-110) cc_final: 0.3425 (ttp80) REVERT: H 98 ASP cc_start: 0.6464 (t70) cc_final: 0.6042 (t0) REVERT: H 102 TYR cc_start: 0.5172 (t80) cc_final: 0.4263 (t80) REVERT: H 103 TRP cc_start: 0.5378 (m-90) cc_final: 0.4981 (m-90) outliers start: 38 outliers final: 20 residues processed: 210 average time/residue: 1.1278 time to fit residues: 285.6859 Evaluate side-chains 186 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 228 ILE 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 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL 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 782 VAL Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 267 optimal weight: 0.8980 chunk 311 optimal weight: 2.9990 chunk 205 optimal weight: 0.0870 chunk 252 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 331 optimal weight: 2.9990 chunk 327 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 219 optimal weight: 0.1980 chunk 185 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN B 529 ASN B 932 GLN C 672 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.231075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142354 restraints weight = 31323.935| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.12 r_work: 0.3345 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27179 Z= 0.103 Angle : 0.508 10.484 36996 Z= 0.263 Chirality : 0.044 0.181 4180 Planarity : 0.004 0.055 4779 Dihedral : 4.375 46.129 3632 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 1.14 % Allowed : 10.39 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3316 helix: 2.04 (0.21), residues: 615 sheet: 0.11 (0.19), residues: 659 loop : -1.07 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 350 HIS 0.003 0.001 HIS A 516 PHE 0.032 0.001 PHE C 90 TYR 0.050 0.001 TYR H 100A ARG 0.006 0.000 ARG B 564 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 971) hydrogen bonds : angle 5.27311 ( 2721) SS BOND : bond 0.00258 ( 31) SS BOND : angle 1.10399 ( 62) covalent geometry : bond 0.00232 (27148) covalent geometry : angle 0.50594 (36934) *********************** 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 209 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 2.765 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7103 (t70) REVERT: A 153 ARG cc_start: 0.3978 (OUTLIER) cc_final: 0.2881 (ptp-170) REVERT: A 167 SER cc_start: 0.7190 (t) cc_final: 0.6906 (p) REVERT: A 172 MET cc_start: 0.5391 (mmt) cc_final: 0.4728 (mmt) REVERT: A 236 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7389 (tm-30) REVERT: A 266 TYR cc_start: 0.8262 (m-80) cc_final: 0.7535 (m-10) REVERT: A 302 SER cc_start: 0.8619 (t) cc_final: 0.8386 (p) REVERT: A 316 ARG cc_start: 0.6615 (mmt90) cc_final: 0.5996 (mmt180) REVERT: A 651 GLU cc_start: 0.7852 (tt0) cc_final: 0.7279 (tm-30) REVERT: A 913 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8279 (tt) REVERT: A 947 ASP cc_start: 0.8118 (m-30) cc_final: 0.7539 (m-30) REVERT: B 90 PHE cc_start: 0.5730 (t80) cc_final: 0.4479 (m-80) REVERT: B 189 PHE cc_start: 0.5985 (m-10) cc_final: 0.5784 (m-10) REVERT: B 263 TYR cc_start: 0.5065 (m-80) cc_final: 0.4614 (m-80) REVERT: B 306 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7400 (mm-30) REVERT: B 555 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7355 (mppt) REVERT: B 571 ASP cc_start: 0.7136 (t70) cc_final: 0.6827 (t0) REVERT: B 773 LYS cc_start: 0.8477 (tttm) cc_final: 0.8014 (tttm) REVERT: B 787 LYS cc_start: 0.8597 (mttt) cc_final: 0.8163 (mmtt) REVERT: B 992 ARG cc_start: 0.7613 (ttm-80) cc_final: 0.7227 (ttm-80) REVERT: B 999 GLN cc_start: 0.8229 (tp40) cc_final: 0.7866 (tp40) REVERT: B 1042 LYS cc_start: 0.8639 (tppt) cc_final: 0.8262 (tmtt) REVERT: C 163 PHE cc_start: 0.0415 (OUTLIER) cc_final: -0.0633 (m-10) REVERT: C 268 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6974 (mt0) REVERT: C 275 LYS cc_start: 0.6574 (tttm) cc_final: 0.6163 (ttmt) REVERT: C 311 GLN cc_start: 0.8326 (tt0) cc_final: 0.7674 (tm-30) REVERT: C 643 ARG cc_start: 0.7762 (mtp180) cc_final: 0.6973 (mpp80) REVERT: C 805 ASP cc_start: 0.7851 (t0) cc_final: 0.7436 (m-30) REVERT: C 1016 ARG cc_start: 0.8224 (tpt170) cc_final: 0.7155 (ttm110) REVERT: C 1081 ASP cc_start: 0.8090 (p0) cc_final: 0.7718 (p0) REVERT: C 1089 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: C 1135 TYR cc_start: 0.7726 (m-80) cc_final: 0.6698 (t80) REVERT: H 94 ARG cc_start: 0.4096 (ttp-110) cc_final: 0.3684 (ttp80) REVERT: H 98 ASP cc_start: 0.6421 (t70) cc_final: 0.5977 (t0) REVERT: H 103 TRP cc_start: 0.5421 (m-90) cc_final: 0.4986 (m-90) outliers start: 34 outliers final: 20 residues processed: 200 average time/residue: 1.0912 time to fit residues: 266.7235 Evaluate side-chains 190 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 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 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL 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 782 VAL Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 231 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 238 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 232 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 0.3980 chunk 207 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 954 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 = 0.4524 r_free = 0.4524 target = 0.229902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.143694 restraints weight = 31359.104| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.00 r_work: 0.3324 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3435 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= 0.123 Angle : 0.521 11.823 36996 Z= 0.269 Chirality : 0.044 0.177 4180 Planarity : 0.004 0.056 4779 Dihedral : 4.388 42.270 3632 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.93 % Rotamer: Outliers : 1.34 % Allowed : 10.56 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3316 helix: 2.00 (0.21), residues: 616 sheet: 0.16 (0.19), residues: 652 loop : -1.05 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 350 HIS 0.003 0.001 HIS C1055 PHE 0.035 0.001 PHE C 90 TYR 0.052 0.001 TYR H 100A ARG 0.006 0.000 ARG B 564 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 971) hydrogen bonds : angle 5.29192 ( 2721) SS BOND : bond 0.00277 ( 31) SS BOND : angle 1.18944 ( 62) covalent geometry : bond 0.00286 (27148) covalent geometry : angle 0.51873 (36934) *********************** 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 211 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 2.633 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7270 (t70) REVERT: A 86 ASP cc_start: 0.7572 (t0) cc_final: 0.6944 (p0) REVERT: A 153 ARG cc_start: 0.4253 (OUTLIER) cc_final: 0.3086 (ptp-170) REVERT: A 167 SER cc_start: 0.7364 (t) cc_final: 0.7125 (p) REVERT: A 172 MET cc_start: 0.5567 (mmt) cc_final: 0.4790 (mmt) REVERT: A 236 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7580 (tm-30) REVERT: A 266 TYR cc_start: 0.8302 (m-80) cc_final: 0.7646 (m-10) REVERT: A 316 ARG cc_start: 0.6766 (mmt90) cc_final: 0.6187 (mmt180) REVERT: A 651 GLU cc_start: 0.7924 (tt0) cc_final: 0.7471 (tm-30) REVERT: A 913 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8408 (tt) REVERT: A 947 ASP cc_start: 0.8339 (m-30) cc_final: 0.7770 (m-30) REVERT: B 90 PHE cc_start: 0.5779 (t80) cc_final: 0.4510 (m-80) REVERT: B 263 TYR cc_start: 0.5246 (m-80) cc_final: 0.4762 (m-80) REVERT: B 306 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7530 (mm-30) REVERT: B 555 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7449 (mppt) REVERT: B 564 ARG cc_start: 0.7951 (mmm-85) cc_final: 0.7743 (mmm-85) REVERT: B 571 ASP cc_start: 0.7238 (t70) cc_final: 0.6948 (t0) REVERT: B 773 LYS cc_start: 0.8722 (tttm) cc_final: 0.8320 (tttm) REVERT: B 787 LYS cc_start: 0.8671 (mttt) cc_final: 0.8276 (mmtt) REVERT: B 992 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7371 (ttm-80) REVERT: B 999 GLN cc_start: 0.8354 (tp40) cc_final: 0.8022 (tp40) REVERT: B 1042 LYS cc_start: 0.8690 (tppt) cc_final: 0.8393 (tmtt) REVERT: C 163 PHE cc_start: 0.0437 (OUTLIER) cc_final: -0.0643 (m-80) REVERT: C 268 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7116 (mt0) REVERT: C 275 LYS cc_start: 0.6853 (tttm) cc_final: 0.6425 (ttmt) REVERT: C 302 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8610 (p) REVERT: C 311 GLN cc_start: 0.8361 (tt0) cc_final: 0.7812 (tm-30) REVERT: C 643 ARG cc_start: 0.7902 (mtp180) cc_final: 0.7144 (mpp80) REVERT: C 1016 ARG cc_start: 0.8384 (tpt170) cc_final: 0.7476 (ttm110) REVERT: C 1081 ASP cc_start: 0.8047 (p0) cc_final: 0.7774 (p0) REVERT: C 1089 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7718 (pt0) REVERT: C 1135 TYR cc_start: 0.7853 (m-80) cc_final: 0.6955 (t80) REVERT: H 82 MET cc_start: 0.2136 (mpm) cc_final: 0.1567 (mpm) REVERT: H 94 ARG cc_start: 0.4023 (ttp-110) cc_final: 0.3781 (ttp80) REVERT: H 98 ASP cc_start: 0.6818 (t70) cc_final: 0.6407 (t0) REVERT: H 103 TRP cc_start: 0.5438 (m-90) cc_final: 0.5065 (m-90) outliers start: 40 outliers final: 22 residues processed: 202 average time/residue: 1.0742 time to fit residues: 263.5111 Evaluate side-chains 193 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 2.741 ------------------------------------------------------------------------------- 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 153 ARG Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 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 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL 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 302 SER 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 782 VAL Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 310 optimal weight: 0.0060 chunk 290 optimal weight: 0.0670 chunk 102 optimal weight: 0.6980 chunk 273 optimal weight: 2.9990 chunk 334 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 chunk 38 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.4334 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.231432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145889 restraints weight = 31116.286| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.12 r_work: 0.3356 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27179 Z= 0.097 Angle : 0.504 10.598 36996 Z= 0.260 Chirality : 0.043 0.173 4180 Planarity : 0.004 0.055 4779 Dihedral : 4.259 39.564 3632 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 1.21 % Allowed : 10.93 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3316 helix: 2.02 (0.21), residues: 627 sheet: 0.18 (0.19), residues: 656 loop : -1.00 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 350 HIS 0.003 0.001 HIS A 516 PHE 0.042 0.001 PHE C 90 TYR 0.054 0.001 TYR H 100A ARG 0.006 0.000 ARG B 564 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 971) hydrogen bonds : angle 5.16228 ( 2721) SS BOND : bond 0.00243 ( 31) SS BOND : angle 1.05507 ( 62) covalent geometry : bond 0.00216 (27148) covalent geometry : angle 0.50270 (36934) ********************** 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 205 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 2.719 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7189 (t70) REVERT: A 86 ASP cc_start: 0.7511 (t0) cc_final: 0.6868 (p0) REVERT: A 153 ARG cc_start: 0.4411 (OUTLIER) cc_final: 0.3232 (ptp-170) REVERT: A 167 SER cc_start: 0.7216 (t) cc_final: 0.6971 (p) REVERT: A 172 MET cc_start: 0.5515 (mmt) cc_final: 0.4915 (mmt) REVERT: A 236 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 266 TYR cc_start: 0.8235 (m-80) cc_final: 0.7565 (m-10) REVERT: A 286 VAL cc_start: 0.7860 (m) cc_final: 0.7609 (p) REVERT: A 316 ARG cc_start: 0.6635 (mmt90) cc_final: 0.6166 (mmt180) REVERT: A 651 GLU cc_start: 0.7878 (tt0) cc_final: 0.7328 (tm-30) REVERT: A 913 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8331 (tp) REVERT: A 947 ASP cc_start: 0.8197 (m-30) cc_final: 0.7620 (m-30) REVERT: B 90 PHE cc_start: 0.5628 (t80) cc_final: 0.4374 (m-80) REVERT: B 263 TYR cc_start: 0.5184 (m-80) cc_final: 0.4689 (m-80) REVERT: B 306 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7443 (mm-30) REVERT: B 555 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7408 (mppt) REVERT: B 571 ASP cc_start: 0.7162 (t70) cc_final: 0.6872 (t0) REVERT: B 579 LEU cc_start: 0.7839 (mm) cc_final: 0.7507 (mt) REVERT: B 580 GLU cc_start: 0.7408 (pt0) cc_final: 0.6710 (mm-30) REVERT: B 773 LYS cc_start: 0.8562 (tttm) cc_final: 0.8152 (tttm) REVERT: B 787 LYS cc_start: 0.8636 (mttt) cc_final: 0.8228 (mmtt) REVERT: B 992 ARG cc_start: 0.7641 (ttm-80) cc_final: 0.7291 (ttm-80) REVERT: B 999 GLN cc_start: 0.8268 (tp40) cc_final: 0.8000 (tp40) REVERT: B 1042 LYS cc_start: 0.8653 (tppt) cc_final: 0.8369 (tmtt) REVERT: C 163 PHE cc_start: 0.0284 (OUTLIER) cc_final: -0.0735 (m-80) REVERT: C 268 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7059 (mt0) REVERT: C 275 LYS cc_start: 0.6684 (tttm) cc_final: 0.6280 (ttmt) REVERT: C 311 GLN cc_start: 0.8356 (tt0) cc_final: 0.7740 (tm-30) REVERT: C 643 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7048 (mpp80) REVERT: C 1016 ARG cc_start: 0.8272 (tpt170) cc_final: 0.7298 (ttm110) REVERT: C 1081 ASP cc_start: 0.8034 (p0) cc_final: 0.7651 (p0) REVERT: C 1089 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7645 (pt0) REVERT: C 1135 TYR cc_start: 0.7738 (m-80) cc_final: 0.6776 (t80) REVERT: H 82 MET cc_start: 0.2132 (mpm) cc_final: 0.1522 (mpm) REVERT: H 94 ARG cc_start: 0.3928 (ttp-110) cc_final: 0.3691 (ttp80) REVERT: H 98 ASP cc_start: 0.6565 (t70) cc_final: 0.6131 (t0) REVERT: H 102 TYR cc_start: 0.5341 (t80) cc_final: 0.4319 (t80) REVERT: H 103 TRP cc_start: 0.5405 (m-90) cc_final: 0.5045 (m-90) outliers start: 36 outliers final: 21 residues processed: 197 average time/residue: 1.1563 time to fit residues: 280.3137 Evaluate side-chains 191 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 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 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL 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 782 VAL Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 63 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 216 optimal weight: 20.0000 chunk 48 optimal weight: 0.4980 chunk 321 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 604 GLN B 954 GLN C 672 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.229532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136115 restraints weight = 31250.534| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.08 r_work: 0.3352 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27179 Z= 0.169 Angle : 0.554 10.766 36996 Z= 0.287 Chirality : 0.045 0.174 4180 Planarity : 0.004 0.056 4779 Dihedral : 4.496 32.974 3632 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 1.38 % Allowed : 10.73 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3316 helix: 1.74 (0.21), residues: 629 sheet: 0.13 (0.19), residues: 642 loop : -1.10 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 350 HIS 0.004 0.001 HIS C1055 PHE 0.041 0.001 PHE C 90 TYR 0.054 0.002 TYR H 100A ARG 0.008 0.000 ARG B 564 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 971) hydrogen bonds : angle 5.42314 ( 2721) SS BOND : bond 0.00314 ( 31) SS BOND : angle 1.36617 ( 62) covalent geometry : bond 0.00404 (27148) covalent geometry : angle 0.55153 (36934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24901.91 seconds wall clock time: 430 minutes 53.21 seconds (25853.21 seconds total)