Starting phenix.real_space_refine on Mon Jun 23 01:30:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjk_50503/06_2025/9fjk_50503.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjk_50503/06_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_50503/06_2025/9fjk_50503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjk_50503/06_2025/9fjk_50503.map" model { file = "/net/cci-nas-00/data/ceres_data/9fjk_50503/06_2025/9fjk_50503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjk_50503/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 18.58, per 1000 atoms: 0.70 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: 6.18 Conformation dependent library (CDL) restraints added in 3.5 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: 4.60 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: 12.28 Time building geometry restraints manager: 7.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8361 1.34 - 1.46: 6394 1.46 - 1.58: 12247 1.58 - 1.71: 0 1.71 - 1.83: 146 Bond restraints: 27148 Sorted by residual: bond pdb=" C VAL B 317 " pdb=" N GLN B 318 " ideal model delta sigma weight residual 1.330 1.412 -0.081 1.37e-02 5.33e+03 3.53e+01 bond pdb=" C ALA A 369 " pdb=" N PRO A 370 " ideal model delta sigma weight residual 1.334 1.431 -0.097 2.34e-02 1.83e+03 1.72e+01 bond pdb=" N ASP A 291 " pdb=" CA ASP A 291 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.25e-02 6.40e+03 8.57e+00 bond pdb=" N VAL A 154 " pdb=" CA VAL A 154 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.02e+00 bond pdb=" N ASP A 287 " pdb=" CA ASP A 287 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.27e-02 6.20e+03 7.24e+00 ... (remaining 27143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 35802 2.35 - 4.71: 981 4.71 - 7.06: 109 7.06 - 9.41: 35 9.41 - 11.76: 7 Bond angle restraints: 36934 Sorted by residual: angle pdb=" C LYS B 421 " pdb=" N LEU B 422 " pdb=" CA LEU B 422 " ideal model delta sigma weight residual 120.94 131.31 -10.37 1.90e+00 2.77e-01 2.98e+01 angle pdb=" CA TYR H 100A" pdb=" CB TYR H 100A" pdb=" CG TYR H 100A" ideal model delta sigma weight residual 113.90 123.02 -9.12 1.80e+00 3.09e-01 2.57e+01 angle pdb=" C GLY L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 131.17 -9.63 1.91e+00 2.74e-01 2.54e+01 angle pdb=" C ASP A 287 " pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta sigma weight residual 110.79 103.25 7.54 1.63e+00 3.76e-01 2.14e+01 angle pdb=" C MET A 172 " pdb=" N ASP A 173 " pdb=" CA ASP A 173 " ideal model delta sigma weight residual 121.70 129.83 -8.13 1.80e+00 3.09e-01 2.04e+01 ... (remaining 36929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 15394 17.74 - 35.49: 618 35.49 - 53.23: 127 53.23 - 70.97: 51 70.97 - 88.72: 31 Dihedral angle restraints: 16221 sinusoidal: 6360 harmonic: 9861 Sorted by residual: dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual 93.00 177.74 -84.74 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS C 740 " pdb=" SG CYS C 740 " pdb=" SG CYS C 746 " pdb=" CB CYS C 746 " ideal model delta sinusoidal sigma weight residual -86.00 -20.34 -65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CA TYR H 100J" pdb=" C TYR H 100J" pdb=" N PHE H 100K" pdb=" CA PHE H 100K" ideal model delta harmonic sigma weight residual 180.00 148.13 31.87 0 5.00e+00 4.00e-02 4.06e+01 ... (remaining 16218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 3723 0.096 - 0.192: 443 0.192 - 0.288: 12 0.288 - 0.384: 1 0.384 - 0.480: 1 Chirality restraints: 4180 Sorted by residual: chirality pdb=" CB VAL C 617 " pdb=" CA VAL C 617 " pdb=" CG1 VAL C 617 " pdb=" CG2 VAL C 617 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CB ILE C 205 " pdb=" CA ILE C 205 " pdb=" CG1 ILE C 205 " pdb=" CG2 ILE C 205 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB VAL H 67 " pdb=" CA VAL H 67 " pdb=" CG1 VAL H 67 " pdb=" CG2 VAL H 67 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 4177 not shown) Planarity restraints: 4779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 153 " 0.430 9.50e-02 1.11e+02 1.93e-01 2.28e+01 pdb=" NE ARG A 153 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 153 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 153 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 153 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 226 " 0.047 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO A 227 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 227 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 227 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 203 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO C 204 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 204 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 204 " -0.038 5.00e-02 4.00e+02 ... (remaining 4776 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.82: 21 1.82 - 2.59: 201 2.59 - 3.36: 31124 3.36 - 4.13: 65875 4.13 - 4.90: 116112 Nonbonded interactions: 213333 Sorted by model distance: nonbonded pdb=" CZ PHE A 43 " pdb=" CG GLN B 560 " model vdw 1.056 3.740 nonbonded pdb=" CE2 PHE A 43 " pdb=" CG GLN B 560 " model vdw 1.145 3.740 nonbonded pdb=" CZ PHE A 43 " pdb=" CD GLN B 560 " model vdw 1.222 3.570 nonbonded pdb=" CE2 PHE A 43 " pdb=" CD GLN B 560 " model vdw 1.232 3.570 nonbonded pdb=" NH1 ARG A 44 " pdb=" O ARG B 564 " model vdw 1.280 3.120 ... (remaining 213328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 368 or resid 374 through 1144)) selection = (chain 'B' and (resid 17 through 401 or resid 403 through 407 or resid 414 throu \ gh 415 or resid 417 through 419 or resid 421 through 464 or resid 468 through 49 \ 5 or resid 503 through 1144)) selection = (chain 'C' and (resid 17 through 368 or resid 374 through 401 or resid 403 throu \ gh 407 or resid 414 through 415 or resid 417 through 419 or resid 421 through 46 \ 4 or resid 468 through 495 or resid 503 through 1144)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.340 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: 0.040 Extract box with map and model: 1.280 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 65.750 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.230 ------------------------------------------------------------------------------- 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 : 2.689 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: 1.3042 time to fit residues: 470.9352 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 : 3.494 ------------------------------------------------------------------------------- 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 = 0.141447 restraints weight = 31681.418| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.64 r_work: 0.3379 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.2346 (OUTLIER) cc_final: 0.1502 (ptp-170) REVERT: A 172 MET cc_start: 0.4988 (mmt) cc_final: 0.4004 (mmt) REVERT: A 236 GLN cc_start: 0.7451 (tm-30) cc_final: 0.6951 (tm-30) REVERT: A 266 TYR cc_start: 0.7728 (m-80) cc_final: 0.7483 (m-10) REVERT: A 287 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.5930 (t0) REVERT: A 302 SER cc_start: 0.8633 (t) cc_final: 0.8305 (p) REVERT: A 588 SER cc_start: 0.7971 (m) cc_final: 0.7645 (p) REVERT: A 616 GLU cc_start: 0.7202 (tp30) cc_final: 0.6908 (mm-30) REVERT: A 651 GLU cc_start: 0.7707 (tt0) cc_final: 0.7231 (tm-30) REVERT: A 773 LYS cc_start: 0.8306 (tptt) cc_final: 0.7764 (ttpt) REVERT: A 947 ASP cc_start: 0.8076 (m-30) cc_final: 0.7847 (m-30) REVERT: A 1035 LYS cc_start: 0.8766 (mtpp) cc_final: 0.8370 (mptt) REVERT: A 1115 ASP cc_start: 0.8158 (p0) cc_final: 0.7794 (m-30) REVERT: B 263 TYR cc_start: 0.5161 (m-80) cc_final: 0.4634 (m-80) REVERT: B 306 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7557 (mm-30) REVERT: B 532 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8059 (ttmm) REVERT: B 555 LYS cc_start: 0.8281 (mmtt) cc_final: 0.6882 (pttm) REVERT: B 571 ASP cc_start: 0.7176 (t70) cc_final: 0.6831 (t0) REVERT: B 579 LEU cc_start: 0.7052 (mp) cc_final: 0.6834 (mm) REVERT: B 580 GLU cc_start: 0.7164 (pt0) cc_final: 0.6643 (mm-30) REVERT: B 773 LYS cc_start: 0.8603 (tttm) cc_final: 0.8032 (tttm) REVERT: B 787 LYS cc_start: 0.8512 (mttt) cc_final: 0.8166 (mmtt) REVERT: B 999 GLN cc_start: 0.8228 (tp40) cc_final: 0.7926 (tp40) REVERT: B 1042 LYS cc_start: 0.8448 (tppt) cc_final: 0.8145 (tmtt) REVERT: B 1124 ASP cc_start: 0.7898 (m-30) cc_final: 0.7685 (m-30) REVERT: C 302 SER cc_start: 0.8914 (t) cc_final: 0.8588 (p) REVERT: C 311 GLN cc_start: 0.8373 (tt0) cc_final: 0.7874 (tm-30) REVERT: C 589 PHE cc_start: 0.7487 (p90) cc_final: 0.7196 (p90) REVERT: C 600 ASN cc_start: 0.7989 (t0) cc_final: 0.7762 (m-40) REVERT: C 610 GLN cc_start: 0.8410 (mt0) cc_final: 0.8169 (mt0) REVERT: C 643 ARG cc_start: 0.7690 (mtp180) cc_final: 0.7149 (tmm-80) REVERT: C 777 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8462 (mt-10) REVERT: C 788 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8780 (p) REVERT: C 872 SER cc_start: 0.8820 (t) cc_final: 0.8549 (m) REVERT: C 918 LYS cc_start: 0.8099 (tttm) cc_final: 0.7788 (ttpt) REVERT: C 1016 ARG cc_start: 0.8072 (tpt170) cc_final: 0.7074 (ttm110) REVERT: C 1081 ASP cc_start: 0.8249 (p0) cc_final: 0.8049 (p0) REVERT: C 1135 TYR cc_start: 0.7686 (m-80) cc_final: 0.6745 (t80) REVERT: C 1141 GLU cc_start: 0.6613 (mm-30) cc_final: 0.5808 (mt-10) REVERT: H 82 MET cc_start: 0.3034 (mmp) cc_final: 0.2223 (tmm) REVERT: H 103 TRP cc_start: 0.5148 (m-90) cc_final: 0.4702 (m-90) outliers start: 31 outliers final: 13 residues processed: 226 average time/residue: 1.4195 time to fit residues: 387.2130 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 : 4.693 ------------------------------------------------------------------------------- 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: 0.0000 chunk 147 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 chunk 267 optimal weight: 0.1980 chunk 323 optimal weight: 3.9990 chunk 310 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 752 GLN C 801 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.233575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142610 restraints weight = 31640.988| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.47 r_work: 0.3409 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27179 Z= 0.121 Angle : 0.551 11.434 36996 Z= 0.287 Chirality : 0.045 0.191 4180 Planarity : 0.004 0.047 4779 Dihedral : 4.897 51.546 3634 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 1.11 % Allowed : 5.95 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3316 helix: 1.26 (0.21), residues: 625 sheet: -0.02 (0.19), residues: 627 loop : -1.15 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 350 HIS 0.003 0.001 HIS C1055 PHE 0.025 0.001 PHE C 90 TYR 0.026 0.001 TYR A 262 ARG 0.005 0.000 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 971) hydrogen bonds : angle 5.87157 ( 2721) SS BOND : bond 0.00277 ( 31) SS BOND : angle 1.23649 ( 62) covalent geometry : bond 0.00272 (27148) covalent geometry : angle 0.54892 (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 232 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 2.906 Fit side-chains revert: symmetry clash REVERT: A 153 ARG cc_start: 0.2617 (OUTLIER) cc_final: 0.1883 (ptp-170) REVERT: A 172 MET cc_start: 0.5160 (mmt) cc_final: 0.4193 (mmt) REVERT: A 236 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7185 (tm-30) REVERT: A 266 TYR cc_start: 0.7854 (m-80) cc_final: 0.7395 (m-10) REVERT: A 287 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6532 (t0) REVERT: A 302 SER cc_start: 0.8532 (t) cc_final: 0.8244 (p) REVERT: A 316 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.6139 (mmt180) REVERT: A 616 GLU cc_start: 0.7138 (tp30) cc_final: 0.6938 (mm-30) REVERT: A 651 GLU cc_start: 0.7717 (tt0) cc_final: 0.7199 (tm-30) REVERT: A 773 LYS cc_start: 0.8304 (tptt) cc_final: 0.7767 (ttpt) REVERT: A 947 ASP cc_start: 0.8096 (m-30) cc_final: 0.7848 (m-30) REVERT: A 1035 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8390 (mptt) REVERT: A 1115 ASP cc_start: 0.8100 (p0) cc_final: 0.7883 (m-30) REVERT: B 186 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6523 (mt-10) REVERT: B 263 TYR cc_start: 0.5043 (m-80) cc_final: 0.4600 (m-80) REVERT: B 306 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 555 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7284 (mppt) REVERT: B 571 ASP cc_start: 0.7135 (t70) cc_final: 0.6824 (t0) REVERT: B 732 SER cc_start: 0.8977 (t) cc_final: 0.8690 (p) REVERT: B 773 LYS cc_start: 0.8566 (tttm) cc_final: 0.8092 (tttm) REVERT: B 787 LYS cc_start: 0.8541 (mttt) cc_final: 0.8171 (mmtt) REVERT: B 999 GLN cc_start: 0.8160 (tp40) cc_final: 0.7816 (tp40) REVERT: B 1042 LYS cc_start: 0.8475 (tppt) cc_final: 0.8150 (tmtt) REVERT: C 302 SER cc_start: 0.8945 (t) cc_final: 0.8676 (p) REVERT: C 311 GLN cc_start: 0.8328 (tt0) cc_final: 0.7855 (tm-30) REVERT: C 589 PHE cc_start: 0.7410 (p90) cc_final: 0.7121 (p90) REVERT: C 600 ASN cc_start: 0.8024 (t0) cc_final: 0.7786 (m-40) REVERT: C 610 GLN cc_start: 0.8348 (mt0) cc_final: 0.8144 (mt0) REVERT: C 643 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7017 (mpp80) REVERT: C 777 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8434 (mt-10) REVERT: C 788 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8802 (p) REVERT: C 918 LYS cc_start: 0.8034 (tttm) cc_final: 0.7789 (ttpt) REVERT: C 954 GLN cc_start: 0.7559 (mt0) cc_final: 0.7044 (tm-30) REVERT: C 1016 ARG cc_start: 0.8123 (tpt170) cc_final: 0.7163 (ttm110) REVERT: C 1081 ASP cc_start: 0.8125 (p0) cc_final: 0.7869 (p0) REVERT: C 1135 TYR cc_start: 0.7685 (m-80) cc_final: 0.6777 (t80) REVERT: C 1141 GLU cc_start: 0.6670 (mm-30) cc_final: 0.5862 (mt-10) REVERT: H 34 TYR cc_start: 0.7001 (m-10) cc_final: 0.6735 (m-10) REVERT: H 82 MET cc_start: 0.3229 (mmp) cc_final: 0.2464 (tmm) REVERT: H 103 TRP cc_start: 0.5179 (m-90) cc_final: 0.4693 (m-90) outliers start: 33 outliers final: 12 residues processed: 217 average time/residue: 1.2709 time to fit residues: 327.5685 Evaluate side-chains 184 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 3.074 ------------------------------------------------------------------------------- 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 316 ARG Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 971 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 147 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 321 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 331 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 216 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 GLN A 904 ASN A 932 GLN B 529 ASN B 904 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 132 GLN ** C 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.223534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139532 restraints weight = 31587.301| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.71 r_work: 0.3219 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.097 27179 Z= 0.494 Angle : 0.850 11.974 36996 Z= 0.443 Chirality : 0.059 0.289 4180 Planarity : 0.006 0.077 4779 Dihedral : 6.015 59.623 3634 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.36 % Rotamer: Outliers : 2.42 % Allowed : 6.96 % Favored : 90.62 % 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: -1.27 (0.14), residues: 3316 helix: 0.45 (0.20), residues: 626 sheet: -0.19 (0.19), residues: 656 loop : -1.55 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 883 HIS 0.014 0.003 HIS C1080 PHE 0.034 0.003 PHE B 512 TYR 0.057 0.003 TYR A 262 ARG 0.009 0.001 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.06447 ( 971) hydrogen bonds : angle 6.50375 ( 2721) SS BOND : bond 0.00934 ( 31) SS BOND : angle 2.32619 ( 62) covalent geometry : bond 0.01204 (27148) covalent geometry : angle 0.84551 (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 254 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 182 time to evaluate : 2.783 Fit side-chains REVERT: A 32 PHE cc_start: 0.7916 (m-80) cc_final: 0.7173 (m-80) REVERT: A 153 ARG cc_start: 0.3562 (OUTLIER) cc_final: 0.2752 (ptp-170) REVERT: A 167 SER cc_start: 0.7572 (t) cc_final: 0.7232 (p) REVERT: A 172 MET cc_start: 0.5440 (mmt) cc_final: 0.4348 (mmt) REVERT: A 236 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 266 TYR cc_start: 0.8333 (m-80) cc_final: 0.8105 (m-80) REVERT: A 276 TYR cc_start: 0.7402 (m-80) cc_final: 0.6870 (m-80) REVERT: A 287 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.6133 (t0) REVERT: A 302 SER cc_start: 0.8751 (t) cc_final: 0.8447 (t) REVERT: A 651 GLU cc_start: 0.7817 (tt0) cc_final: 0.7203 (tm-30) REVERT: A 699 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: B 40 ASP cc_start: 0.6572 (t0) cc_final: 0.5781 (m-30) REVERT: B 53 ASP cc_start: 0.6413 (t70) cc_final: 0.6138 (t70) REVERT: B 186 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6673 (mt-10) REVERT: B 201 LYS cc_start: 0.6273 (tptt) cc_final: 0.5769 (tptt) REVERT: B 263 TYR cc_start: 0.5290 (m-80) cc_final: 0.4895 (m-80) REVERT: B 306 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7614 (mm-30) REVERT: B 555 LYS cc_start: 0.8345 (mmtt) cc_final: 0.7426 (mppt) REVERT: B 571 ASP cc_start: 0.7287 (t70) cc_final: 0.6913 (t0) REVERT: B 756 PHE cc_start: 0.7252 (t80) cc_final: 0.6830 (t80) REVERT: B 773 LYS cc_start: 0.8664 (tttm) cc_final: 0.8229 (tttm) REVERT: B 787 LYS cc_start: 0.8510 (mttt) cc_final: 0.7974 (mmtt) REVERT: B 999 GLN cc_start: 0.8505 (tp40) cc_final: 0.8279 (tp40) REVERT: B 1042 LYS cc_start: 0.8720 (tppt) cc_final: 0.8401 (tmtt) REVERT: C 172 MET cc_start: 0.2965 (ptp) cc_final: 0.2300 (ptp) REVERT: C 302 SER cc_start: 0.8851 (t) cc_final: 0.8574 (t) REVERT: C 311 GLN cc_start: 0.8347 (tt0) cc_final: 0.7733 (tm-30) REVERT: C 589 PHE cc_start: 0.7883 (p90) cc_final: 0.7673 (p90) REVERT: C 643 ARG cc_start: 0.7811 (mtp180) cc_final: 0.6954 (mpp80) REVERT: C 777 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8577 (mt-10) REVERT: C 915 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: C 918 LYS cc_start: 0.8397 (tttm) cc_final: 0.8174 (ttpt) REVERT: C 1016 ARG cc_start: 0.8404 (tpt170) cc_final: 0.7347 (ttm110) REVERT: C 1135 TYR cc_start: 0.7935 (m-80) cc_final: 0.6864 (t80) REVERT: C 1141 GLU cc_start: 0.6768 (mm-30) cc_final: 0.5904 (mt-10) REVERT: H 82 MET cc_start: 0.3674 (mmp) cc_final: 0.2952 (tmm) REVERT: H 98 ASP cc_start: 0.7148 (t70) cc_final: 0.6880 (t0) REVERT: H 103 TRP cc_start: 0.5562 (m-90) cc_final: 0.5158 (m-90) outliers start: 72 outliers final: 26 residues processed: 234 average time/residue: 1.2453 time to fit residues: 347.2445 Evaluate side-chains 197 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 2.507 ------------------------------------------------------------------------------- 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 587 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 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 205 ILE Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 1089 GLU 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: 0.9980 chunk 70 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 34 optimal weight: 0.0870 chunk 41 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 318 GLN A 898 GLN B 529 ASN B 759 GLN ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 672 GLN C 687 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.228579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141269 restraints weight = 31370.812| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.81 r_work: 0.3307 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27179 Z= 0.132 Angle : 0.570 9.963 36996 Z= 0.299 Chirality : 0.045 0.182 4180 Planarity : 0.004 0.051 4779 Dihedral : 5.200 56.476 3634 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 1.88 % Allowed : 8.41 % Favored : 89.71 % 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: -0.82 (0.14), residues: 3316 helix: 1.27 (0.21), residues: 619 sheet: -0.08 (0.19), residues: 652 loop : -1.34 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 350 HIS 0.003 0.001 HIS A 516 PHE 0.027 0.001 PHE C 90 TYR 0.024 0.001 TYR A 262 ARG 0.008 0.000 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 971) hydrogen bonds : angle 5.90894 ( 2721) SS BOND : bond 0.00305 ( 31) SS BOND : angle 2.06881 ( 62) covalent geometry : bond 0.00304 (27148) covalent geometry : angle 0.56365 (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 237 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 3.704 Fit side-chains REVERT: A 153 ARG cc_start: 0.3805 (OUTLIER) cc_final: 0.2881 (ptp-170) REVERT: A 172 MET cc_start: 0.5483 (mmt) cc_final: 0.4633 (mmt) REVERT: A 221 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: A 236 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7627 (tm-30) REVERT: A 266 TYR cc_start: 0.8339 (m-80) cc_final: 0.7736 (m-10) REVERT: A 276 TYR cc_start: 0.7405 (m-80) cc_final: 0.7016 (m-80) REVERT: A 286 VAL cc_start: 0.7772 (m) cc_final: 0.7476 (p) REVERT: A 302 SER cc_start: 0.8803 (t) cc_final: 0.8478 (p) REVERT: A 316 ARG cc_start: 0.6788 (mtt90) cc_final: 0.6334 (mmt180) REVERT: A 651 GLU cc_start: 0.7791 (tt0) cc_final: 0.7280 (tm-30) REVERT: A 777 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8191 (mm-30) REVERT: A 947 ASP cc_start: 0.8435 (m-30) cc_final: 0.7840 (m-30) REVERT: B 40 ASP cc_start: 0.6587 (t0) cc_final: 0.5808 (m-30) REVERT: B 53 ASP cc_start: 0.6413 (t70) cc_final: 0.6175 (t70) REVERT: B 186 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6776 (mt-10) REVERT: B 263 TYR cc_start: 0.5233 (m-80) cc_final: 0.4772 (m-80) REVERT: B 306 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 532 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8287 (ttmm) REVERT: B 551 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7218 (mm-30) REVERT: B 555 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7439 (mppt) REVERT: B 571 ASP cc_start: 0.7292 (t70) cc_final: 0.7002 (t0) REVERT: B 773 LYS cc_start: 0.8752 (tttm) cc_final: 0.8269 (tttm) REVERT: B 787 LYS cc_start: 0.8542 (mttt) cc_final: 0.8216 (mmtt) REVERT: B 992 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7552 (ttm-80) REVERT: B 999 GLN cc_start: 0.8453 (tp40) cc_final: 0.8188 (tp40) REVERT: B 1042 LYS cc_start: 0.8731 (tppt) cc_final: 0.8453 (tmtt) REVERT: C 163 PHE cc_start: 0.0612 (OUTLIER) cc_final: -0.0551 (m-10) REVERT: C 172 MET cc_start: 0.3009 (ptp) cc_final: 0.2383 (ptp) REVERT: C 311 GLN cc_start: 0.8307 (tt0) cc_final: 0.7779 (tm-30) REVERT: C 643 ARG cc_start: 0.7794 (mtp180) cc_final: 0.7034 (mpp80) REVERT: C 915 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: C 918 LYS cc_start: 0.8367 (tttm) cc_final: 0.8105 (ttpt) REVERT: C 947 ASP cc_start: 0.8440 (m-30) cc_final: 0.7992 (m-30) REVERT: C 954 GLN cc_start: 0.8019 (mt0) cc_final: 0.7375 (tm-30) REVERT: C 1016 ARG cc_start: 0.8375 (tpt170) cc_final: 0.7519 (ttm110) REVERT: C 1081 ASP cc_start: 0.8157 (p0) cc_final: 0.7831 (p0) REVERT: C 1135 TYR cc_start: 0.7933 (m-80) cc_final: 0.6975 (t80) REVERT: C 1141 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6005 (mt-10) REVERT: H 82 MET cc_start: 0.3545 (mmp) cc_final: 0.2993 (tmm) REVERT: H 98 ASP cc_start: 0.6869 (t70) cc_final: 0.6475 (t0) REVERT: H 103 TRP cc_start: 0.5523 (m-90) cc_final: 0.5145 (m-90) outliers start: 56 outliers final: 25 residues processed: 219 average time/residue: 1.3532 time to fit residues: 350.1687 Evaluate side-chains 194 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 118 VAL 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 600 ASN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1124 ASP 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 735 CYS Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 752 GLN Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1124 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 268 optimal weight: 8.9990 chunk 335 optimal weight: 0.8980 chunk 242 optimal weight: 0.5980 chunk 171 optimal weight: 0.9990 chunk 293 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 253 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN B 604 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.226676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133576 restraints weight = 31280.586| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.08 r_work: 0.3322 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27179 Z= 0.213 Angle : 0.608 9.648 36996 Z= 0.317 Chirality : 0.047 0.201 4180 Planarity : 0.004 0.057 4779 Dihedral : 5.113 51.230 3632 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.90 % Rotamer: Outliers : 1.71 % Allowed : 9.18 % Favored : 89.11 % 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: -0.85 (0.14), residues: 3316 helix: 1.27 (0.21), residues: 621 sheet: -0.04 (0.19), residues: 651 loop : -1.39 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 350 HIS 0.006 0.001 HIS B1055 PHE 0.028 0.002 PHE C 90 TYR 0.029 0.002 TYR A 262 ARG 0.010 0.001 ARG B 564 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 971) hydrogen bonds : angle 5.88028 ( 2721) SS BOND : bond 0.00426 ( 31) SS BOND : angle 1.82004 ( 62) covalent geometry : bond 0.00513 (27148) covalent geometry : angle 0.60348 (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 216 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 3.174 Fit side-chains REVERT: A 86 ASP cc_start: 0.7499 (t0) cc_final: 0.6874 (p0) REVERT: A 153 ARG cc_start: 0.3924 (OUTLIER) cc_final: 0.2778 (ptp-170) REVERT: A 172 MET cc_start: 0.5660 (mmt) cc_final: 0.4777 (mmt) REVERT: A 236 GLN cc_start: 0.7662 (tm-30) cc_final: 0.7383 (tm-30) REVERT: A 266 TYR cc_start: 0.8257 (m-80) cc_final: 0.7549 (m-10) REVERT: A 276 TYR cc_start: 0.7329 (m-80) cc_final: 0.6890 (m-80) REVERT: A 302 SER cc_start: 0.8729 (t) cc_final: 0.8324 (p) REVERT: A 651 GLU cc_start: 0.7724 (tt0) cc_final: 0.7173 (tm-30) REVERT: A 947 ASP cc_start: 0.8309 (m-30) cc_final: 0.7626 (m-30) REVERT: B 40 ASP cc_start: 0.6412 (t0) cc_final: 0.5633 (m-30) REVERT: B 53 ASP cc_start: 0.6342 (t70) cc_final: 0.6084 (t70) REVERT: B 186 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6627 (mt-10) REVERT: B 263 TYR cc_start: 0.4976 (m-80) cc_final: 0.4478 (m-80) REVERT: B 306 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7414 (mm-30) REVERT: B 555 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7344 (mppt) REVERT: B 571 ASP cc_start: 0.7110 (t70) cc_final: 0.6832 (t0) REVERT: B 756 PHE cc_start: 0.6875 (t80) cc_final: 0.6271 (t80) REVERT: B 773 LYS cc_start: 0.8540 (tttm) cc_final: 0.8056 (tttm) REVERT: B 787 LYS cc_start: 0.8521 (mttt) cc_final: 0.8100 (mmtt) REVERT: B 992 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.7340 (ttm-80) REVERT: B 999 GLN cc_start: 0.8317 (tp40) cc_final: 0.8026 (tp40) REVERT: C 163 PHE cc_start: 0.0649 (OUTLIER) cc_final: -0.0539 (m-10) REVERT: C 172 MET cc_start: 0.2786 (ptp) cc_final: 0.2194 (ptp) REVERT: C 311 GLN cc_start: 0.8191 (tt0) cc_final: 0.7569 (tm-30) REVERT: C 643 ARG cc_start: 0.7689 (mtp180) cc_final: 0.6889 (mpp80) REVERT: C 915 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: C 918 LYS cc_start: 0.8217 (tttm) cc_final: 0.7902 (ttpt) REVERT: C 1016 ARG cc_start: 0.8210 (tpt170) cc_final: 0.7214 (ttm110) REVERT: C 1081 ASP cc_start: 0.8188 (p0) cc_final: 0.7921 (p0) REVERT: C 1135 TYR cc_start: 0.7805 (m-80) cc_final: 0.6815 (t80) REVERT: H 82 MET cc_start: 0.3539 (mmp) cc_final: 0.3067 (tmm) REVERT: H 98 ASP cc_start: 0.6774 (t70) cc_final: 0.6437 (t0) REVERT: H 103 TRP cc_start: 0.5487 (m-90) cc_final: 0.5147 (m-90) outliers start: 51 outliers final: 29 residues processed: 206 average time/residue: 1.2365 time to fit residues: 306.1595 Evaluate side-chains 190 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 600 ASN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 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 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 735 CYS Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 1089 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 215 optimal weight: 10.0000 chunk 186 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 278 optimal weight: 0.0670 chunk 282 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 319 optimal weight: 8.9990 chunk 288 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 0.0970 chunk 243 optimal weight: 5.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 160 ASN A 610 GLN B 529 ASN ** B 904 ASN ** 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 = 0.4530 r_free = 0.4530 target = 0.230955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139720 restraints weight = 31271.463| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.08 r_work: 0.3370 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27179 Z= 0.109 Angle : 0.526 9.798 36996 Z= 0.275 Chirality : 0.044 0.187 4180 Planarity : 0.004 0.073 4779 Dihedral : 4.679 47.524 3632 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.90 % Rotamer: Outliers : 1.51 % Allowed : 9.72 % Favored : 88.77 % 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: -0.55 (0.14), residues: 3316 helix: 1.83 (0.21), residues: 608 sheet: -0.00 (0.19), residues: 633 loop : -1.22 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 36 HIS 0.003 0.001 HIS L 34 PHE 0.033 0.001 PHE C 90 TYR 0.021 0.001 TYR A1135 ARG 0.007 0.000 ARG B 564 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 971) hydrogen bonds : angle 5.52294 ( 2721) SS BOND : bond 0.00332 ( 31) SS BOND : angle 1.29284 ( 62) covalent geometry : bond 0.00245 (27148) covalent geometry : angle 0.52410 (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 225 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 2.961 Fit side-chains revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7506 (t0) cc_final: 0.6878 (p0) REVERT: A 153 ARG cc_start: 0.4149 (OUTLIER) cc_final: 0.2994 (ptp-170) REVERT: A 172 MET cc_start: 0.5950 (mmt) cc_final: 0.5156 (mmt) REVERT: A 266 TYR cc_start: 0.8258 (m-80) cc_final: 0.7582 (m-10) REVERT: A 286 VAL cc_start: 0.7372 (m) cc_final: 0.7169 (p) REVERT: A 302 SER cc_start: 0.8611 (t) cc_final: 0.8329 (p) REVERT: A 316 ARG cc_start: 0.6577 (mmt90) cc_final: 0.6162 (mmt180) REVERT: A 651 GLU cc_start: 0.7749 (tt0) cc_final: 0.7157 (tm-30) REVERT: A 978 PHE cc_start: 0.8013 (m-10) cc_final: 0.7752 (m-10) REVERT: B 90 PHE cc_start: 0.5715 (t80) cc_final: 0.4528 (m-80) REVERT: B 186 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6745 (mt-10) REVERT: B 263 TYR cc_start: 0.5008 (m-80) cc_final: 0.4551 (m-80) REVERT: B 306 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7341 (mm-30) REVERT: B 555 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7284 (mppt) REVERT: B 571 ASP cc_start: 0.7061 (t70) cc_final: 0.6804 (t0) REVERT: B 580 GLU cc_start: 0.7345 (pt0) cc_final: 0.6636 (mm-30) REVERT: B 773 LYS cc_start: 0.8484 (tttm) cc_final: 0.8018 (tttm) REVERT: B 787 LYS cc_start: 0.8515 (mttt) cc_final: 0.8157 (mmtt) REVERT: B 992 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7218 (ttm-80) REVERT: B 999 GLN cc_start: 0.8170 (tp40) cc_final: 0.7816 (tp40) REVERT: B 1042 LYS cc_start: 0.8620 (tppt) cc_final: 0.8335 (tmtt) REVERT: C 163 PHE cc_start: 0.0507 (OUTLIER) cc_final: -0.0604 (m-80) REVERT: C 172 MET cc_start: 0.2773 (ptp) cc_final: 0.2199 (ptp) REVERT: C 268 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6943 (mt0) REVERT: C 311 GLN cc_start: 0.8220 (tt0) cc_final: 0.7557 (tm-30) REVERT: C 643 ARG cc_start: 0.7688 (mtp180) cc_final: 0.6916 (mpp80) REVERT: C 915 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: C 918 LYS cc_start: 0.8127 (tttm) cc_final: 0.7887 (ttpt) REVERT: C 1016 ARG cc_start: 0.8189 (tpt170) cc_final: 0.7222 (ttm110) REVERT: C 1081 ASP cc_start: 0.7953 (p0) cc_final: 0.7646 (p0) REVERT: C 1135 TYR cc_start: 0.7704 (m-80) cc_final: 0.6727 (t80) REVERT: H 82 MET cc_start: 0.3819 (mmp) cc_final: 0.3151 (tmm) REVERT: H 94 ARG cc_start: 0.4213 (ttp-110) cc_final: 0.3428 (ttp80) REVERT: H 98 ASP cc_start: 0.6432 (t70) cc_final: 0.6045 (t0) REVERT: H 102 TYR cc_start: 0.5272 (t80) cc_final: 0.4338 (t80) REVERT: H 103 TRP cc_start: 0.5519 (m-90) cc_final: 0.5094 (m-90) outliers start: 45 outliers final: 21 residues processed: 216 average time/residue: 1.1736 time to fit residues: 304.6868 Evaluate side-chains 191 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1124 ASP 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 735 CYS 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 915 GLU Chi-restraints excluded: chain C residue 1124 ASP 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: 1.9990 chunk 311 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 252 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 113 GLN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4496 r_free = 0.4496 target = 0.226775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.137309 restraints weight = 31219.792| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.10 r_work: 0.3255 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27179 Z= 0.197 Angle : 0.591 11.880 36996 Z= 0.307 Chirality : 0.047 0.183 4180 Planarity : 0.004 0.064 4779 Dihedral : 4.829 42.420 3632 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 1.51 % Allowed : 10.52 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3316 helix: 1.49 (0.21), residues: 623 sheet: 0.01 (0.19), residues: 650 loop : -1.26 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 36 HIS 0.005 0.001 HIS B1055 PHE 0.038 0.002 PHE C 90 TYR 0.032 0.002 TYR A 262 ARG 0.007 0.000 ARG B 564 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 971) hydrogen bonds : angle 5.66681 ( 2721) SS BOND : bond 0.00407 ( 31) SS BOND : angle 1.58816 ( 62) covalent geometry : bond 0.00473 (27148) covalent geometry : angle 0.58837 (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 212 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 2.696 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7224 (t70) REVERT: A 86 ASP cc_start: 0.7592 (t0) cc_final: 0.6927 (p0) REVERT: A 153 ARG cc_start: 0.4426 (OUTLIER) cc_final: 0.3209 (ptp-170) REVERT: A 172 MET cc_start: 0.5829 (mmt) cc_final: 0.5037 (mmt) REVERT: A 236 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7463 (tm-30) REVERT: A 266 TYR cc_start: 0.8364 (m-80) cc_final: 0.7651 (m-10) REVERT: A 286 VAL cc_start: 0.7617 (m) cc_final: 0.7290 (p) REVERT: A 302 SER cc_start: 0.8768 (t) cc_final: 0.8435 (p) REVERT: A 651 GLU cc_start: 0.7876 (tt0) cc_final: 0.7290 (tm-30) REVERT: A 947 ASP cc_start: 0.8374 (m-30) cc_final: 0.7723 (m-30) REVERT: A 978 PHE cc_start: 0.8042 (m-10) cc_final: 0.7777 (m-10) REVERT: B 40 ASP cc_start: 0.6398 (t0) cc_final: 0.5620 (m-30) REVERT: B 263 TYR cc_start: 0.5090 (m-80) cc_final: 0.4558 (m-80) REVERT: B 306 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7505 (mm-30) REVERT: B 555 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7320 (mppt) REVERT: B 571 ASP cc_start: 0.7163 (t70) cc_final: 0.6872 (t0) REVERT: B 580 GLU cc_start: 0.7396 (pt0) cc_final: 0.6711 (mm-30) REVERT: B 756 PHE cc_start: 0.6813 (t80) cc_final: 0.6229 (t80) REVERT: B 773 LYS cc_start: 0.8645 (tttm) cc_final: 0.8210 (tttm) REVERT: B 787 LYS cc_start: 0.8598 (mttt) cc_final: 0.8177 (mmtt) REVERT: B 992 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7252 (ttm-80) REVERT: B 999 GLN cc_start: 0.8376 (tp40) cc_final: 0.8078 (tp40) REVERT: C 163 PHE cc_start: 0.0652 (OUTLIER) cc_final: -0.0539 (m-10) REVERT: C 172 MET cc_start: 0.2796 (ptp) cc_final: 0.2213 (ptp) REVERT: C 268 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7001 (mt0) REVERT: C 302 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8530 (p) REVERT: C 311 GLN cc_start: 0.8374 (tt0) cc_final: 0.7704 (tm-30) REVERT: C 643 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7057 (mpp80) REVERT: C 915 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: C 918 LYS cc_start: 0.8282 (tttm) cc_final: 0.8006 (ttpt) REVERT: C 1016 ARG cc_start: 0.8343 (tpt170) cc_final: 0.7295 (ttm110) REVERT: C 1081 ASP cc_start: 0.8198 (p0) cc_final: 0.7904 (p0) REVERT: C 1089 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: C 1135 TYR cc_start: 0.7855 (m-80) cc_final: 0.6831 (t80) REVERT: H 98 ASP cc_start: 0.6930 (t70) cc_final: 0.6615 (t0) REVERT: H 100 TYR cc_start: 0.6475 (t80) cc_final: 0.6229 (t80) REVERT: H 103 TRP cc_start: 0.5539 (m-90) cc_final: 0.5142 (m-90) outliers start: 45 outliers final: 25 residues processed: 202 average time/residue: 1.2023 time to fit residues: 295.1930 Evaluate side-chains 188 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 2.759 ------------------------------------------------------------------------------- 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 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1115 ASP Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 856 THR 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 735 CYS Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 752 GLN Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 56 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 231 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 238 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 175 optimal weight: 0.4980 chunk 207 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 GLN B 954 GLN C 672 GLN C 752 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.230263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144084 restraints weight = 31254.169| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.87 r_work: 0.3313 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27179 Z= 0.104 Angle : 0.532 10.539 36996 Z= 0.275 Chirality : 0.044 0.176 4180 Planarity : 0.004 0.057 4779 Dihedral : 4.554 39.852 3632 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.90 % Rotamer: Outliers : 1.31 % Allowed : 11.00 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3316 helix: 1.86 (0.21), residues: 615 sheet: 0.03 (0.19), residues: 635 loop : -1.16 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 36 HIS 0.003 0.001 HIS A 516 PHE 0.040 0.001 PHE C 90 TYR 0.025 0.001 TYR A1135 ARG 0.007 0.000 ARG B 564 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 971) hydrogen bonds : angle 5.42210 ( 2721) SS BOND : bond 0.00296 ( 31) SS BOND : angle 1.24438 ( 62) covalent geometry : bond 0.00232 (27148) covalent geometry : angle 0.52990 (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 210 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 3.109 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7399 (t70) REVERT: A 86 ASP cc_start: 0.7631 (t0) cc_final: 0.7025 (p0) REVERT: A 153 ARG cc_start: 0.4462 (OUTLIER) cc_final: 0.3251 (ptp-170) REVERT: A 172 MET cc_start: 0.6067 (mmt) cc_final: 0.5305 (mmt) REVERT: A 236 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 266 TYR cc_start: 0.8351 (m-80) cc_final: 0.7782 (m-10) REVERT: A 286 VAL cc_start: 0.7636 (m) cc_final: 0.7379 (p) REVERT: A 302 SER cc_start: 0.8705 (t) cc_final: 0.8490 (p) REVERT: A 316 ARG cc_start: 0.6658 (mmt90) cc_final: 0.6195 (mmt180) REVERT: A 651 GLU cc_start: 0.7869 (tt0) cc_final: 0.7424 (tm-30) REVERT: A 978 PHE cc_start: 0.8123 (m-10) cc_final: 0.7881 (m-10) REVERT: B 90 PHE cc_start: 0.5981 (t80) cc_final: 0.4782 (m-80) REVERT: B 189 PHE cc_start: 0.6298 (m-10) cc_final: 0.6065 (m-10) REVERT: B 263 TYR cc_start: 0.5302 (m-80) cc_final: 0.4840 (m-80) REVERT: B 306 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7535 (mm-30) REVERT: B 555 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7518 (mppt) REVERT: B 562 PHE cc_start: 0.7160 (p90) cc_final: 0.6811 (p90) REVERT: B 564 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7781 (mmm-85) REVERT: B 571 ASP cc_start: 0.7224 (t70) cc_final: 0.6963 (t0) REVERT: B 580 GLU cc_start: 0.7535 (pt0) cc_final: 0.6872 (mm-30) REVERT: B 773 LYS cc_start: 0.8738 (tttm) cc_final: 0.8344 (tttm) REVERT: B 787 LYS cc_start: 0.8636 (mttt) cc_final: 0.8329 (mmtt) REVERT: B 856 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8592 (p) REVERT: B 992 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7369 (ttm-80) REVERT: B 999 GLN cc_start: 0.8377 (tp40) cc_final: 0.8091 (tp40) REVERT: B 1042 LYS cc_start: 0.8713 (tppt) cc_final: 0.8510 (tmtt) REVERT: C 163 PHE cc_start: 0.0444 (OUTLIER) cc_final: -0.0681 (m-80) REVERT: C 172 MET cc_start: 0.2887 (ptp) cc_final: 0.2279 (ptp) REVERT: C 268 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7159 (mt0) REVERT: C 311 GLN cc_start: 0.8374 (tt0) cc_final: 0.7819 (tm-30) REVERT: C 643 ARG cc_start: 0.7898 (mtp180) cc_final: 0.7186 (mpp80) REVERT: C 1016 ARG cc_start: 0.8438 (tpt170) cc_final: 0.7568 (ttm110) REVERT: C 1081 ASP cc_start: 0.8038 (p0) cc_final: 0.7718 (p0) REVERT: C 1089 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: C 1135 TYR cc_start: 0.7904 (m-80) cc_final: 0.6999 (t80) REVERT: C 1138 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5677 (tm) REVERT: H 82 MET cc_start: 0.2100 (mpm) cc_final: 0.1620 (mpm) REVERT: H 98 ASP cc_start: 0.6888 (t70) cc_final: 0.6552 (t0) REVERT: H 103 TRP cc_start: 0.5563 (m-90) cc_final: 0.5120 (m-90) outliers start: 39 outliers final: 23 residues processed: 198 average time/residue: 1.1939 time to fit residues: 283.8551 Evaluate side-chains 189 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 3.024 ------------------------------------------------------------------------------- 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 791 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 954 GLN 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 856 THR Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 992 ARG 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 735 CYS Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 752 GLN Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1138 LEU 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: 0.7980 chunk 290 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 334 optimal weight: 6.9990 chunk 177 optimal weight: 0.0980 chunk 294 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 93 optimal weight: 0.0570 chunk 159 optimal weight: 8.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- 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 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.228923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136882 restraints weight = 31085.557| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.07 r_work: 0.3377 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3646 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= 0.121 Angle : 0.534 10.209 36996 Z= 0.277 Chirality : 0.044 0.175 4180 Planarity : 0.004 0.056 4779 Dihedral : 4.518 38.057 3632 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 1.11 % Allowed : 11.26 % Favored : 87.63 % 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: -0.43 (0.14), residues: 3316 helix: 1.89 (0.21), residues: 621 sheet: 0.02 (0.19), residues: 635 loop : -1.12 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 36 HIS 0.003 0.001 HIS A 516 PHE 0.040 0.001 PHE C 90 TYR 0.047 0.001 TYR H 100A ARG 0.007 0.000 ARG B 564 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 971) hydrogen bonds : angle 5.38990 ( 2721) SS BOND : bond 0.00300 ( 31) SS BOND : angle 1.26770 ( 62) covalent geometry : bond 0.00281 (27148) covalent geometry : angle 0.53198 (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 196 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 2.932 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7128 (t70) REVERT: A 86 ASP cc_start: 0.7478 (t0) cc_final: 0.6856 (p0) REVERT: A 172 MET cc_start: 0.5971 (mmt) cc_final: 0.5218 (mmt) REVERT: A 236 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 266 TYR cc_start: 0.8236 (m-80) cc_final: 0.7584 (m-10) REVERT: A 286 VAL cc_start: 0.7392 (m) cc_final: 0.7175 (p) REVERT: A 302 SER cc_start: 0.8614 (t) cc_final: 0.8341 (p) REVERT: A 316 ARG cc_start: 0.6401 (mmt90) cc_final: 0.5885 (mmt180) REVERT: A 651 GLU cc_start: 0.7730 (tt0) cc_final: 0.7203 (tm-30) REVERT: A 913 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8291 (tp) REVERT: A 978 PHE cc_start: 0.8017 (m-10) cc_final: 0.7765 (m-10) REVERT: B 40 ASP cc_start: 0.6383 (t0) cc_final: 0.5541 (m-30) REVERT: B 263 TYR cc_start: 0.5030 (m-80) cc_final: 0.4484 (m-80) REVERT: B 306 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7371 (mm-30) REVERT: B 555 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7407 (mppt) REVERT: B 562 PHE cc_start: 0.6961 (p90) cc_final: 0.6615 (p90) REVERT: B 564 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7571 (mmm-85) REVERT: B 571 ASP cc_start: 0.7069 (t70) cc_final: 0.6807 (t0) REVERT: B 580 GLU cc_start: 0.7327 (pt0) cc_final: 0.6682 (mm-30) REVERT: B 773 LYS cc_start: 0.8497 (tttm) cc_final: 0.8051 (tttm) REVERT: B 787 LYS cc_start: 0.8546 (mttt) cc_final: 0.8198 (mmtt) REVERT: B 856 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8408 (p) REVERT: B 992 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7202 (ttm-80) REVERT: B 999 GLN cc_start: 0.8196 (tp40) cc_final: 0.7872 (tp40) REVERT: B 1042 LYS cc_start: 0.8608 (tppt) cc_final: 0.8367 (tmtt) REVERT: C 163 PHE cc_start: 0.0435 (OUTLIER) cc_final: -0.0668 (m-80) REVERT: C 268 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6984 (mt0) REVERT: C 275 LYS cc_start: 0.6697 (tttm) cc_final: 0.6258 (ttmt) REVERT: C 311 GLN cc_start: 0.8245 (tt0) cc_final: 0.7594 (tm-30) REVERT: C 643 ARG cc_start: 0.7712 (mtp180) cc_final: 0.6953 (mpp80) REVERT: C 915 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: C 1016 ARG cc_start: 0.8193 (tpt170) cc_final: 0.7205 (ttm110) REVERT: C 1081 ASP cc_start: 0.7977 (p0) cc_final: 0.7700 (p0) REVERT: C 1089 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7577 (pt0) REVERT: C 1135 TYR cc_start: 0.7754 (m-80) cc_final: 0.6789 (t80) REVERT: H 82 MET cc_start: 0.2207 (mpm) cc_final: 0.1877 (mmm) REVERT: H 98 ASP cc_start: 0.6523 (t70) cc_final: 0.6191 (t0) REVERT: H 103 TRP cc_start: 0.5472 (m-90) cc_final: 0.5049 (m-90) outliers start: 33 outliers final: 20 residues processed: 188 average time/residue: 1.3181 time to fit residues: 306.4519 Evaluate side-chains 188 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP 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 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 856 THR Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 992 ARG 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 735 CYS 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 915 GLU Chi-restraints excluded: chain C residue 1089 GLU 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: 3.9990 chunk 163 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 321 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN B 604 GLN B 904 ASN B 954 GLN C 672 GLN C 752 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.226007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132253 restraints weight = 31259.697| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.06 r_work: 0.3304 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 27179 Z= 0.264 Angle : 0.642 10.403 36996 Z= 0.334 Chirality : 0.049 0.189 4180 Planarity : 0.004 0.057 4779 Dihedral : 4.936 27.198 3628 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.37 % Favored : 94.60 % Rotamer: Outliers : 1.55 % Allowed : 11.00 % Favored : 87.46 % 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: -0.77 (0.14), residues: 3316 helix: 1.39 (0.21), residues: 622 sheet: 0.03 (0.20), residues: 638 loop : -1.36 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 36 HIS 0.008 0.002 HIS C1045 PHE 0.044 0.002 PHE C 90 TYR 0.059 0.002 TYR H 100A ARG 0.008 0.001 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.04999 ( 971) hydrogen bonds : angle 5.80396 ( 2721) SS BOND : bond 0.00475 ( 31) SS BOND : angle 1.83465 ( 62) covalent geometry : bond 0.00639 (27148) covalent geometry : angle 0.63849 (36934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27675.90 seconds wall clock time: 483 minutes 1.34 seconds (28981.34 seconds total)