Starting phenix.real_space_refine on Mon Aug 25 08:36:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fmw_50574/08_2025/9fmw_50574.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fmw_50574/08_2025/9fmw_50574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fmw_50574/08_2025/9fmw_50574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fmw_50574/08_2025/9fmw_50574.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fmw_50574/08_2025/9fmw_50574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fmw_50574/08_2025/9fmw_50574.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16967 2.51 5 N 4411 2.21 5 O 5034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26529 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8185 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 58, 'TRANS': 981} Chain breaks: 12 Chain: "B" Number of atoms: 8226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8226 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 59, 'TRANS': 987} Chain breaks: 9 Chain: "C" Number of atoms: 8288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8288 Classifications: {'peptide': 1055} Link IDs: {'PTRANS': 60, 'TRANS': 994} Chain breaks: 7 Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1014 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Time building chain proxies: 6.80, per 1000 atoms: 0.26 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: 2.63 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.7 microseconds 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6356 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 52 sheets defined 21.7% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 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: 6.92 Time building geometry restraints manager: 3.40 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 28.650 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 27179 Z= 0.233 Angle : 0.905 11.763 36996 Z= 0.506 Chirality : 0.057 0.480 4180 Planarity : 0.008 0.193 4779 Dihedral : 11.574 88.718 9772 Min Nonbonded Distance : 1.056 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.30 % Allowed : 0.24 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.13), residues: 3316 helix: -0.71 (0.18), residues: 619 sheet: -0.00 (0.20), residues: 597 loop : -1.50 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 34 TYR 0.033 0.002 TYR A 262 PHE 0.035 0.003 PHE C 163 TRP 0.046 0.003 TRP B 350 HIS 0.014 0.002 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00479 (27148) covalent geometry : angle 0.90280 (36934) SS BOND : bond 0.00356 ( 31) SS BOND : angle 1.67552 ( 62) hydrogen bonds : bond 0.20878 ( 971) hydrogen bonds : angle 8.88004 ( 2721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 305 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.5546 (mmt) cc_final: 0.5217 (mmm) REVERT: A 281 THR cc_start: 0.8367 (m) cc_final: 0.8083 (p) REVERT: A 301 LYS cc_start: 0.7402 (mmtm) cc_final: 0.7153 (ttpt) REVERT: A 612 VAL cc_start: 0.8208 (m) cc_final: 0.7982 (p) REVERT: A 651 GLU cc_start: 0.7771 (tt0) cc_final: 0.7088 (tm-30) REVERT: A 773 LYS cc_start: 0.7785 (tptt) cc_final: 0.7432 (ttpp) REVERT: A 954 GLN cc_start: 0.7170 (tt0) cc_final: 0.6609 (tp40) REVERT: A 980 ARG cc_start: 0.7009 (mtt-85) cc_final: 0.6699 (mtm-85) REVERT: A 1035 LYS cc_start: 0.7974 (mtpp) cc_final: 0.7566 (mptt) REVERT: A 1070 LYS cc_start: 0.8139 (tttt) cc_final: 0.7783 (mttt) REVERT: A 1133 THR cc_start: 0.8287 (m) cc_final: 0.8039 (t) REVERT: B 263 TYR cc_start: 0.4734 (m-80) cc_final: 0.4002 (m-80) REVERT: B 306 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7359 (mm-30) REVERT: B 555 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8046 (mppt) REVERT: B 571 ASP cc_start: 0.6935 (t70) cc_final: 0.6686 (t0) REVERT: B 610 GLN cc_start: 0.8232 (mt0) cc_final: 0.8023 (mt0) REVERT: B 751 LEU cc_start: 0.8413 (mt) cc_final: 0.8198 (mp) REVERT: B 787 LYS cc_start: 0.7955 (mttt) cc_final: 0.7630 (mmtt) REVERT: B 791 ILE cc_start: 0.7756 (pt) cc_final: 0.7554 (mm) REVERT: B 822 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7552 (mtpt) REVERT: B 952 ASN cc_start: 0.7267 (t0) cc_final: 0.7029 (m-40) REVERT: B 977 ILE cc_start: 0.7060 (mm) cc_final: 0.6856 (mt) REVERT: B 1124 ASP cc_start: 0.7612 (m-30) cc_final: 0.7301 (m-30) REVERT: C 172 MET cc_start: 0.2542 (ptm) cc_final: 0.2214 (mtt) REVERT: C 268 GLN cc_start: 0.7602 (tp-100) cc_final: 0.7276 (tt0) REVERT: C 302 SER cc_start: 0.8433 (t) cc_final: 0.7964 (p) REVERT: C 316 ARG cc_start: 0.6367 (ttm110) cc_final: 0.6129 (ttm110) REVERT: C 643 ARG cc_start: 0.7438 (mtp180) cc_final: 0.7175 (ttp80) REVERT: C 751 LEU cc_start: 0.6415 (mm) cc_final: 0.6065 (mt) REVERT: C 752 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7808 (mm-40) REVERT: C 918 LYS cc_start: 0.8010 (tttm) cc_final: 0.7776 (ttpp) REVERT: C 954 GLN cc_start: 0.7059 (mt0) cc_final: 0.6679 (tm-30) REVERT: C 1016 ARG cc_start: 0.6982 (tpt170) cc_final: 0.6507 (ttp80) REVERT: C 1081 ASP cc_start: 0.7927 (p0) cc_final: 0.7602 (p0) REVERT: C 1124 ASP cc_start: 0.8382 (m-30) cc_final: 0.8031 (m-30) REVERT: H 43 LYS cc_start: 0.8354 (mmtm) cc_final: 0.7880 (ttmt) REVERT: H 67 VAL cc_start: 0.1250 (p) cc_final: 0.1019 (t) REVERT: L 33 VAL cc_start: 0.7422 (t) cc_final: 0.6942 (p) outliers start: 9 outliers final: 2 residues processed: 313 average time/residue: 0.2060 time to fit residues: 99.4816 Evaluate side-chains 225 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 295 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.0040 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.8980 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 748 ASN A 801 GLN A 904 ASN A 932 GLN A 952 ASN B 66 HIS B 604 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 GLN C 771 GLN C 999 GLN H 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.148359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.124901 restraints weight = 53956.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.123031 restraints weight = 84121.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.120749 restraints weight = 78874.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.119800 restraints weight = 93127.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.118437 restraints weight = 77128.829| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27179 Z= 0.146 Angle : 0.595 9.263 36996 Z= 0.316 Chirality : 0.046 0.206 4180 Planarity : 0.005 0.050 4779 Dihedral : 5.210 48.670 3632 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.20 % Rotamer: Outliers : 0.57 % Allowed : 3.53 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.14), residues: 3316 helix: 0.63 (0.21), residues: 625 sheet: 0.08 (0.20), residues: 619 loop : -1.26 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 564 TYR 0.024 0.002 TYR A 262 PHE 0.027 0.002 PHE C 90 TRP 0.022 0.002 TRP B 350 HIS 0.004 0.001 HIS A1055 Details of bonding type rmsd covalent geometry : bond 0.00332 (27148) covalent geometry : angle 0.59225 (36934) SS BOND : bond 0.00431 ( 31) SS BOND : angle 1.49380 ( 62) hydrogen bonds : bond 0.04696 ( 971) hydrogen bonds : angle 6.41619 ( 2721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7648 (tp) REVERT: A 658 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6614 (tt0) REVERT: A 760 LEU cc_start: 0.7952 (mp) cc_final: 0.7607 (tt) REVERT: A 899 MET cc_start: 0.7946 (tpt) cc_final: 0.7696 (mmt) REVERT: B 263 TYR cc_start: 0.5555 (m-80) cc_final: 0.5341 (m-80) REVERT: B 818 LEU cc_start: 0.8252 (tt) cc_final: 0.8030 (tp) REVERT: B 977 ILE cc_start: 0.8446 (mm) cc_final: 0.8140 (mt) REVERT: C 172 MET cc_start: 0.3766 (ptm) cc_final: 0.3294 (mtp) REVERT: C 302 SER cc_start: 0.8653 (t) cc_final: 0.8348 (p) REVERT: C 1081 ASP cc_start: 0.7252 (p0) cc_final: 0.7005 (p0) REVERT: H 43 LYS cc_start: 0.8061 (mmtm) cc_final: 0.7722 (ttmt) REVERT: L 33 VAL cc_start: 0.7481 (t) cc_final: 0.7249 (p) outliers start: 17 outliers final: 12 residues processed: 254 average time/residue: 0.1980 time to fit residues: 79.1885 Evaluate side-chains 224 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 271 optimal weight: 0.5980 chunk 268 optimal weight: 0.0570 chunk 34 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 105 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 898 GLN A 922 ASN A 954 GLN ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN B 604 GLN B 641 GLN B 898 GLN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS ** C 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN C 672 GLN C 759 GLN C 801 GLN H 76 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.150954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.126539 restraints weight = 52352.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125063 restraints weight = 101905.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.123196 restraints weight = 92966.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.121785 restraints weight = 96619.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.120866 restraints weight = 100981.936| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27179 Z= 0.176 Angle : 0.594 10.795 36996 Z= 0.311 Chirality : 0.046 0.187 4180 Planarity : 0.004 0.049 4779 Dihedral : 5.026 56.736 3632 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 1.14 % Allowed : 5.14 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.14), residues: 3316 helix: 1.19 (0.21), residues: 621 sheet: 0.02 (0.20), residues: 599 loop : -1.11 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 94 TYR 0.025 0.002 TYR A1064 PHE 0.025 0.002 PHE C 90 TRP 0.020 0.002 TRP B 350 HIS 0.007 0.001 HIS B1055 Details of bonding type rmsd covalent geometry : bond 0.00414 (27148) covalent geometry : angle 0.59168 (36934) SS BOND : bond 0.00321 ( 31) SS BOND : angle 1.47031 ( 62) hydrogen bonds : bond 0.04634 ( 971) hydrogen bonds : angle 5.93320 ( 2721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7678 (tp) REVERT: A 760 LEU cc_start: 0.8067 (mp) cc_final: 0.7791 (tt) REVERT: B 579 LEU cc_start: 0.7414 (mt) cc_final: 0.7202 (mt) REVERT: B 732 SER cc_start: 0.8686 (t) cc_final: 0.8415 (p) REVERT: B 773 LYS cc_start: 0.7931 (tttm) cc_final: 0.7697 (tttm) REVERT: B 818 LEU cc_start: 0.8360 (tt) cc_final: 0.8135 (tp) REVERT: C 172 MET cc_start: 0.4099 (ptm) cc_final: 0.3488 (mtp) REVERT: C 302 SER cc_start: 0.8665 (t) cc_final: 0.8352 (p) REVERT: C 1081 ASP cc_start: 0.7489 (p0) cc_final: 0.7207 (p0) REVERT: H 43 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7700 (ttmm) REVERT: L 62 PHE cc_start: 0.6758 (t80) cc_final: 0.6548 (t80) outliers start: 34 outliers final: 18 residues processed: 256 average time/residue: 0.1871 time to fit residues: 76.8052 Evaluate side-chains 234 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 117 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 229 optimal weight: 5.9990 chunk 267 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 260 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 313 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 ASN ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C1002 GLN H 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.147096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.122511 restraints weight = 53385.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.120091 restraints weight = 99428.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.118588 restraints weight = 99356.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.118051 restraints weight = 101209.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.117216 restraints weight = 97329.921| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27179 Z= 0.165 Angle : 0.566 9.692 36996 Z= 0.296 Chirality : 0.045 0.206 4180 Planarity : 0.004 0.043 4779 Dihedral : 4.773 44.842 3629 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 1.28 % Allowed : 6.05 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.14), residues: 3316 helix: 1.44 (0.21), residues: 614 sheet: 0.01 (0.20), residues: 617 loop : -1.07 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 997 TYR 0.024 0.001 TYR A 262 PHE 0.022 0.002 PHE B 756 TRP 0.015 0.001 TRP B 350 HIS 0.005 0.001 HIS B1055 Details of bonding type rmsd covalent geometry : bond 0.00394 (27148) covalent geometry : angle 0.56187 (36934) SS BOND : bond 0.00339 ( 31) SS BOND : angle 1.72617 ( 62) hydrogen bonds : bond 0.04269 ( 971) hydrogen bonds : angle 5.78436 ( 2721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7736 (tp) REVERT: A 760 LEU cc_start: 0.8041 (mp) cc_final: 0.7801 (tt) REVERT: B 579 LEU cc_start: 0.7568 (mt) cc_final: 0.7277 (mt) REVERT: B 732 SER cc_start: 0.8730 (t) cc_final: 0.8452 (p) REVERT: B 818 LEU cc_start: 0.8347 (tt) cc_final: 0.8128 (tp) REVERT: C 172 MET cc_start: 0.4102 (ptm) cc_final: 0.3425 (mtp) REVERT: C 302 SER cc_start: 0.8724 (t) cc_final: 0.8393 (p) REVERT: C 728 MET cc_start: 0.8465 (ptt) cc_final: 0.8228 (ptt) REVERT: C 1081 ASP cc_start: 0.7374 (p0) cc_final: 0.6996 (p0) REVERT: C 1141 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6584 (mt-10) REVERT: H 43 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7740 (ttmm) outliers start: 38 outliers final: 27 residues processed: 243 average time/residue: 0.1759 time to fit residues: 70.1916 Evaluate side-chains 236 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 245 optimal weight: 8.9990 chunk 288 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 289 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 318 GLN A 898 GLN A 922 ASN A 932 GLN ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN B 904 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN C 311 GLN C 655 ASN C 672 GLN H 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.156375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132906 restraints weight = 53542.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129907 restraints weight = 91426.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127178 restraints weight = 87140.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126367 restraints weight = 96196.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125604 restraints weight = 79177.553| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 27179 Z= 0.333 Angle : 0.706 10.480 36996 Z= 0.367 Chirality : 0.051 0.201 4180 Planarity : 0.005 0.052 4779 Dihedral : 5.241 27.532 3628 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 1.88 % Allowed : 6.59 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.14), residues: 3316 helix: 0.97 (0.21), residues: 623 sheet: -0.00 (0.20), residues: 627 loop : -1.30 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1036 TYR 0.043 0.002 TYR A 262 PHE 0.026 0.002 PHE L 62 TRP 0.021 0.002 TRP A 64 HIS 0.011 0.002 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00813 (27148) covalent geometry : angle 0.70138 (36934) SS BOND : bond 0.00521 ( 31) SS BOND : angle 2.09133 ( 62) hydrogen bonds : bond 0.05369 ( 971) hydrogen bonds : angle 6.11941 ( 2721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7820 (tp) REVERT: B 579 LEU cc_start: 0.7840 (mt) cc_final: 0.7590 (mt) REVERT: B 696 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8150 (mp) REVERT: B 818 LEU cc_start: 0.8488 (tt) cc_final: 0.8263 (tp) REVERT: C 163 PHE cc_start: -0.0373 (OUTLIER) cc_final: -0.1495 (m-10) REVERT: C 172 MET cc_start: 0.4214 (ptm) cc_final: 0.3593 (ptp) REVERT: C 302 SER cc_start: 0.8805 (t) cc_final: 0.8379 (m) REVERT: C 915 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: C 1081 ASP cc_start: 0.7464 (p0) cc_final: 0.6967 (p0) REVERT: H 43 LYS cc_start: 0.8122 (mmtm) cc_final: 0.7757 (ttmm) REVERT: H 100 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6450 (p90) outliers start: 56 outliers final: 36 residues processed: 259 average time/residue: 0.1886 time to fit residues: 78.1892 Evaluate side-chains 244 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 357 ASN 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 569 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 672 GLN Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 148 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 271 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 322 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 303 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN A 898 GLN ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 610 GLN C 672 GLN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.146413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.121480 restraints weight = 53189.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.118793 restraints weight = 96634.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.116958 restraints weight = 92999.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.115736 restraints weight = 98145.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.114984 restraints weight = 93371.033| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27179 Z= 0.139 Angle : 0.563 9.747 36996 Z= 0.294 Chirality : 0.045 0.177 4180 Planarity : 0.004 0.046 4779 Dihedral : 4.789 29.951 3628 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 1.68 % Allowed : 7.40 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.14), residues: 3316 helix: 1.50 (0.21), residues: 617 sheet: -0.12 (0.20), residues: 608 loop : -1.17 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 564 TYR 0.026 0.001 TYR A 262 PHE 0.029 0.001 PHE C 90 TRP 0.016 0.001 TRP B 350 HIS 0.003 0.001 HIS C1055 Details of bonding type rmsd covalent geometry : bond 0.00321 (27148) covalent geometry : angle 0.55928 (36934) SS BOND : bond 0.00275 ( 31) SS BOND : angle 1.57311 ( 62) hydrogen bonds : bond 0.04170 ( 971) hydrogen bonds : angle 5.76707 ( 2721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7726 (tp) REVERT: B 579 LEU cc_start: 0.7796 (mt) cc_final: 0.7544 (mt) REVERT: B 696 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8198 (mp) REVERT: C 163 PHE cc_start: -0.0481 (OUTLIER) cc_final: -0.1636 (m-10) REVERT: C 172 MET cc_start: 0.4094 (ptm) cc_final: 0.3488 (ptp) REVERT: C 302 SER cc_start: 0.8798 (t) cc_final: 0.8361 (p) REVERT: C 915 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: C 1081 ASP cc_start: 0.7295 (p0) cc_final: 0.6807 (p0) REVERT: H 4 LEU cc_start: 0.8342 (mm) cc_final: 0.8111 (mp) REVERT: H 43 LYS cc_start: 0.8123 (mmtm) cc_final: 0.7750 (ttmm) outliers start: 50 outliers final: 31 residues processed: 251 average time/residue: 0.1746 time to fit residues: 71.5410 Evaluate side-chains 244 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain B residue 78 ASP 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 569 THR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 672 GLN Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 264 optimal weight: 0.0980 chunk 75 optimal weight: 0.0980 chunk 160 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 325 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 5 optimal weight: 0.0970 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 ASN ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN C 311 GLN C 672 GLN H 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.147286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.121233 restraints weight = 53232.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.118983 restraints weight = 102491.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.118177 restraints weight = 119123.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.117312 restraints weight = 103533.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.117500 restraints weight = 86285.656| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27179 Z= 0.108 Angle : 0.531 8.678 36996 Z= 0.276 Chirality : 0.044 0.191 4180 Planarity : 0.004 0.052 4779 Dihedral : 4.504 26.520 3628 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 1.28 % Allowed : 8.10 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.14), residues: 3316 helix: 1.80 (0.22), residues: 618 sheet: 0.01 (0.20), residues: 598 loop : -1.04 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 564 TYR 0.020 0.001 TYR B1064 PHE 0.031 0.001 PHE C 90 TRP 0.014 0.001 TRP B 350 HIS 0.002 0.001 HIS A1055 Details of bonding type rmsd covalent geometry : bond 0.00243 (27148) covalent geometry : angle 0.52799 (36934) SS BOND : bond 0.00261 ( 31) SS BOND : angle 1.49059 ( 62) hydrogen bonds : bond 0.03762 ( 971) hydrogen bonds : angle 5.48796 ( 2721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 122 THR cc_start: 0.8360 (p) cc_final: 0.8024 (t) REVERT: A 184 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7678 (tp) REVERT: A 658 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6493 (tt0) REVERT: B 579 LEU cc_start: 0.7698 (mt) cc_final: 0.7418 (mt) REVERT: B 696 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8250 (mp) REVERT: C 163 PHE cc_start: -0.0522 (OUTLIER) cc_final: -0.1727 (m-80) REVERT: C 302 SER cc_start: 0.8760 (t) cc_final: 0.8395 (p) REVERT: C 672 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.5632 (pt0) REVERT: C 915 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: C 1081 ASP cc_start: 0.7318 (p0) cc_final: 0.6851 (p0) REVERT: C 1141 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6674 (mt-10) REVERT: H 4 LEU cc_start: 0.8274 (mm) cc_final: 0.7917 (mp) REVERT: H 43 LYS cc_start: 0.8086 (mmtm) cc_final: 0.7797 (ttmt) REVERT: H 100 TYR cc_start: 0.6496 (OUTLIER) cc_final: 0.6049 (p90) outliers start: 38 outliers final: 23 residues processed: 246 average time/residue: 0.1801 time to fit residues: 72.0978 Evaluate side-chains 238 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 1122 ASN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 672 GLN Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 183 optimal weight: 0.9980 chunk 210 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 216 optimal weight: 20.0000 chunk 307 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 186 optimal weight: 0.6980 chunk 254 optimal weight: 8.9990 chunk 236 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 672 GLN C 962 GLN H 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.153215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.129411 restraints weight = 50443.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.126709 restraints weight = 92752.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.125371 restraints weight = 83642.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.123981 restraints weight = 82718.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.122818 restraints weight = 90760.849| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27179 Z= 0.163 Angle : 0.562 9.455 36996 Z= 0.289 Chirality : 0.045 0.182 4180 Planarity : 0.004 0.054 4779 Dihedral : 4.527 25.406 3628 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 1.34 % Allowed : 8.14 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.14), residues: 3316 helix: 1.74 (0.21), residues: 623 sheet: -0.01 (0.20), residues: 624 loop : -1.09 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 564 TYR 0.024 0.001 TYR A1064 PHE 0.027 0.001 PHE C 90 TRP 0.014 0.001 TRP B 350 HIS 0.004 0.001 HIS B1055 Details of bonding type rmsd covalent geometry : bond 0.00390 (27148) covalent geometry : angle 0.55922 (36934) SS BOND : bond 0.00291 ( 31) SS BOND : angle 1.46156 ( 62) hydrogen bonds : bond 0.04064 ( 971) hydrogen bonds : angle 5.52022 ( 2721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 122 THR cc_start: 0.8424 (p) cc_final: 0.8091 (t) REVERT: A 184 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7730 (tp) REVERT: B 579 LEU cc_start: 0.7688 (mt) cc_final: 0.7433 (mt) REVERT: B 696 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8240 (mp) REVERT: C 163 PHE cc_start: -0.0619 (OUTLIER) cc_final: -0.1897 (m-80) REVERT: C 302 SER cc_start: 0.8767 (t) cc_final: 0.8356 (p) REVERT: C 915 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: C 1081 ASP cc_start: 0.7319 (p0) cc_final: 0.6802 (p0) REVERT: H 43 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7738 (ttmm) REVERT: H 100 TYR cc_start: 0.6796 (OUTLIER) cc_final: 0.6262 (p90) outliers start: 40 outliers final: 29 residues processed: 238 average time/residue: 0.1693 time to fit residues: 65.1138 Evaluate side-chains 243 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1122 ASN Chi-restraints excluded: chain B residue 78 ASP 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 696 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 672 GLN Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 71 optimal weight: 0.9990 chunk 225 optimal weight: 5.9990 chunk 213 optimal weight: 10.0000 chunk 330 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 270 optimal weight: 0.7980 chunk 273 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 672 GLN H 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.148952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.123786 restraints weight = 52178.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.122407 restraints weight = 105757.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.121276 restraints weight = 94752.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.120605 restraints weight = 90338.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.119869 restraints weight = 85611.498| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.3378 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= 0.178 Angle : 0.572 10.524 36996 Z= 0.295 Chirality : 0.046 0.180 4180 Planarity : 0.004 0.054 4779 Dihedral : 4.580 25.246 3628 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 1.38 % Allowed : 8.24 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.14), residues: 3316 helix: 1.78 (0.21), residues: 616 sheet: 0.05 (0.20), residues: 621 loop : -1.12 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 38 TYR 0.025 0.001 TYR A 262 PHE 0.035 0.001 PHE C 90 TRP 0.014 0.001 TRP B 350 HIS 0.004 0.001 HIS B1080 Details of bonding type rmsd covalent geometry : bond 0.00428 (27148) covalent geometry : angle 0.56877 (36934) SS BOND : bond 0.00311 ( 31) SS BOND : angle 1.55310 ( 62) hydrogen bonds : bond 0.04182 ( 971) hydrogen bonds : angle 5.56888 ( 2721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 122 THR cc_start: 0.8366 (p) cc_final: 0.8027 (t) REVERT: A 184 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7728 (tp) REVERT: A 317 VAL cc_start: 0.7595 (OUTLIER) cc_final: 0.7139 (m) REVERT: A 658 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6479 (tt0) REVERT: B 579 LEU cc_start: 0.7691 (mt) cc_final: 0.7446 (mt) REVERT: B 696 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8226 (mp) REVERT: C 163 PHE cc_start: -0.0619 (OUTLIER) cc_final: -0.1823 (m-10) REVERT: C 302 SER cc_start: 0.8817 (t) cc_final: 0.8401 (p) REVERT: C 915 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: C 1081 ASP cc_start: 0.7363 (p0) cc_final: 0.6857 (p0) REVERT: H 4 LEU cc_start: 0.8229 (mm) cc_final: 0.7910 (mp) REVERT: H 43 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7756 (ttmm) REVERT: H 46 GLU cc_start: 0.7058 (pm20) cc_final: 0.6668 (pm20) REVERT: H 100 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6192 (p90) outliers start: 41 outliers final: 30 residues processed: 243 average time/residue: 0.1623 time to fit residues: 63.7972 Evaluate side-chains 246 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1122 ASN Chi-restraints excluded: chain B residue 78 ASP 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 696 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 672 GLN Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 137 optimal weight: 9.9990 chunk 184 optimal weight: 0.5980 chunk 281 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 169 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 175 optimal weight: 0.3980 chunk 163 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 GLN H 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.154286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.130823 restraints weight = 50160.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128062 restraints weight = 96113.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.126120 restraints weight = 81192.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124311 restraints weight = 91028.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.123551 restraints weight = 99522.290| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27179 Z= 0.141 Angle : 0.550 11.068 36996 Z= 0.284 Chirality : 0.045 0.178 4180 Planarity : 0.004 0.054 4779 Dihedral : 4.502 24.536 3628 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 1.31 % Allowed : 8.47 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.14), residues: 3316 helix: 1.82 (0.22), residues: 616 sheet: 0.03 (0.20), residues: 636 loop : -1.07 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 38 TYR 0.022 0.001 TYR A1064 PHE 0.033 0.001 PHE C 90 TRP 0.014 0.001 TRP B 350 HIS 0.003 0.001 HIS C1055 Details of bonding type rmsd covalent geometry : bond 0.00333 (27148) covalent geometry : angle 0.54790 (36934) SS BOND : bond 0.00274 ( 31) SS BOND : angle 1.40771 ( 62) hydrogen bonds : bond 0.03968 ( 971) hydrogen bonds : angle 5.48044 ( 2721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 THR cc_start: 0.8348 (p) cc_final: 0.8081 (t) REVERT: A 184 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7742 (tp) REVERT: A 317 VAL cc_start: 0.7483 (OUTLIER) cc_final: 0.7059 (m) REVERT: A 658 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6469 (tt0) REVERT: B 579 LEU cc_start: 0.7718 (mt) cc_final: 0.7471 (mt) REVERT: B 696 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8236 (mp) REVERT: C 163 PHE cc_start: -0.0667 (OUTLIER) cc_final: -0.1937 (m-80) REVERT: C 302 SER cc_start: 0.8794 (t) cc_final: 0.8429 (p) REVERT: C 915 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: C 1081 ASP cc_start: 0.7296 (p0) cc_final: 0.6780 (p0) REVERT: H 4 LEU cc_start: 0.8242 (mm) cc_final: 0.7854 (mp) REVERT: H 43 LYS cc_start: 0.8098 (mmtm) cc_final: 0.7797 (ttmt) REVERT: H 46 GLU cc_start: 0.7055 (pm20) cc_final: 0.6826 (pm20) REVERT: H 100 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.6183 (p90) outliers start: 39 outliers final: 29 residues processed: 240 average time/residue: 0.1615 time to fit residues: 62.9486 Evaluate side-chains 233 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1122 ASN Chi-restraints excluded: chain B residue 78 ASP 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 587 CYS Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 672 GLN Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 194 optimal weight: 0.5980 chunk 200 optimal weight: 0.5980 chunk 301 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 293 optimal weight: 0.4980 chunk 169 optimal weight: 0.7980 chunk 69 optimal weight: 0.0980 chunk 275 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 144 optimal weight: 0.0370 chunk 72 optimal weight: 0.6980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 GLN H 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.147349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.121663 restraints weight = 53197.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.119268 restraints weight = 107363.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.118784 restraints weight = 111931.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.117581 restraints weight = 90202.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.117339 restraints weight = 98712.387| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27179 Z= 0.104 Angle : 0.528 10.920 36996 Z= 0.273 Chirality : 0.044 0.175 4180 Planarity : 0.004 0.055 4779 Dihedral : 4.330 22.524 3628 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 1.08 % Allowed : 8.64 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.14), residues: 3316 helix: 1.97 (0.22), residues: 623 sheet: 0.13 (0.19), residues: 660 loop : -1.02 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 38 TYR 0.020 0.001 TYR A1064 PHE 0.033 0.001 PHE C 90 TRP 0.014 0.001 TRP B 350 HIS 0.002 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00230 (27148) covalent geometry : angle 0.52575 (36934) SS BOND : bond 0.00245 ( 31) SS BOND : angle 1.21263 ( 62) hydrogen bonds : bond 0.03641 ( 971) hydrogen bonds : angle 5.30229 ( 2721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4415.84 seconds wall clock time: 77 minutes 37.45 seconds (4657.45 seconds total)