Starting phenix.real_space_refine on Sun Oct 25 11:49:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbu_7850/10_2026/6dbu_7850_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbu_7850/10_2026/6dbu_7850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dbu_7850/10_2026/6dbu_7850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbu_7850/10_2026/6dbu_7850.map" model { file = "/net/cci-nas-00/data/ceres_data/6dbu_7850/10_2026/6dbu_7850_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbu_7850/10_2026/6dbu_7850_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 2 6.06 5 P 136 5.49 5 S 106 5.16 5 C 10272 2.51 5 N 3004 2.21 5 O 3486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17010 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4394 Classifications: {'peptide': 543} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 519} Chain breaks: 1 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "C" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4394 Classifications: {'peptide': 543} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 519} Chain breaks: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "F" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "G" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "H" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2075 SG CYS A 749 106.444 97.375 60.497 1.00 43.54 S ATOM 9183 SG CYS C 749 48.329 32.009 60.495 1.00 42.97 S Time building chain proxies: 3.13, per 1000 atoms: 0.18 Number of scatterers: 17010 At special positions: 0 Unit cell: (155.82, 130.38, 115.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 4 19.99 S 106 16.00 P 136 15.00 O 3486 8.00 N 3004 7.00 C 10272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 624.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 18 sheets defined 33.3% alpha, 21.9% beta 66 base pairs and 119 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 497 through 511 removed outlier: 3.547A pdb=" N SER A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 527 Processing helix chain 'A' and resid 577 through 600 removed outlier: 4.892A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 705 removed outlier: 3.712A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.687A pdb=" N ALA A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 819 through 835 removed outlier: 4.327A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 863 Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 890 removed outlier: 3.636A pdb=" N GLU A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 917 removed outlier: 3.859A pdb=" N GLU A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 924 through 945 removed outlier: 3.885A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.546A pdb=" N HIS A 959 " --> pdb=" O THR A 955 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A 964 " --> pdb=" O LYS A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 973 Processing helix chain 'A' and resid 975 through 979 removed outlier: 3.517A pdb=" N ALA A 979 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 4.154A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 991 " --> pdb=" O ASN A 987 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1017 removed outlier: 4.290A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1024 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 497 through 511 removed outlier: 3.574A pdb=" N SER C 511 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 527 Processing helix chain 'C' and resid 577 through 600 removed outlier: 4.921A pdb=" N GLU C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.757A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix Processing helix chain 'C' and resid 730 through 739 Processing helix chain 'C' and resid 755 through 762 removed outlier: 3.679A pdb=" N ALA C 759 " --> pdb=" O THR C 755 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 819 through 835 removed outlier: 4.371A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 863 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 890 removed outlier: 3.570A pdb=" N GLU C 890 " --> pdb=" O GLU C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 917 removed outlier: 3.855A pdb=" N GLU C 899 " --> pdb=" O GLU C 895 " (cutoff:3.500A) Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 924 through 945 removed outlier: 3.879A pdb=" N LEU C 928 " --> pdb=" O CYS C 924 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER C 932 " --> pdb=" O LEU C 928 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR C 933 " --> pdb=" O CYS C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 964 removed outlier: 3.548A pdb=" N HIS C 959 " --> pdb=" O THR C 955 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 960 " --> pdb=" O ASN C 956 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 964 " --> pdb=" O LYS C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 975 through 979 Processing helix chain 'C' and resid 980 through 997 removed outlier: 4.429A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET C 996 " --> pdb=" O ARG C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1017 removed outlier: 4.179A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1024 Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 537 through 539 removed outlier: 6.951A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 539 removed outlier: 6.951A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 651 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR A 661 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 5.862A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8 removed outlier: 6.786A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 80 removed outlier: 6.801A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB1, first strand: chain 'C' and resid 537 through 539 removed outlier: 6.957A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 537 through 539 removed outlier: 6.957A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 651 " --> pdb=" O THR C 661 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR C 661 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 5 removed outlier: 5.853A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 7 through 8 removed outlier: 6.782A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 80 removed outlier: 6.810A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB7, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB8, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AB9, first strand: chain 'D' and resid 263 through 265 624 hydrogen bonds defined for protein. 1698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 168 hydrogen bonds 336 hydrogen bond angles 0 basepair planarities 66 basepair parallelities 119 stacking parallelities Total time for adding SS restraints: 4.16 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 81 1.23 - 1.37: 5748 1.37 - 1.52: 7554 1.52 - 1.67: 4115 1.67 - 1.82: 160 Bond restraints: 17658 Sorted by residual: bond pdb=" CA HIS D 222 " pdb=" CB HIS D 222 " ideal model delta sigma weight residual 1.534 1.314 0.220 2.33e-02 1.84e+03 8.94e+01 bond pdb=" CA HIS B 222 " pdb=" CB HIS B 222 " ideal model delta sigma weight residual 1.534 1.315 0.219 2.33e-02 1.84e+03 8.84e+01 bond pdb=" CG ASN D 10 " pdb=" OD1 ASN D 10 " ideal model delta sigma weight residual 1.231 1.080 0.151 1.90e-02 2.77e+03 6.28e+01 bond pdb=" CG GLN D 282 " pdb=" CD GLN D 282 " ideal model delta sigma weight residual 1.516 1.708 -0.192 2.50e-02 1.60e+03 5.88e+01 bond pdb=" CG GLN B 282 " pdb=" CD GLN B 282 " ideal model delta sigma weight residual 1.516 1.692 -0.176 2.50e-02 1.60e+03 4.96e+01 ... (remaining 17653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.83: 24414 11.83 - 23.66: 22 23.66 - 35.50: 10 35.50 - 47.33: 1 47.33 - 59.16: 1 Bond angle restraints: 24448 Sorted by residual: angle pdb=" CG GLN C 910 " pdb=" CD GLN C 910 " pdb=" OE1 GLN C 910 " ideal model delta sigma weight residual 120.80 179.96 -59.16 2.00e+00 2.50e-01 8.75e+02 angle pdb=" CG GLN C 910 " pdb=" CD GLN C 910 " pdb=" NE2 GLN C 910 " ideal model delta sigma weight residual 116.40 75.43 40.97 1.50e+00 4.44e-01 7.46e+02 angle pdb=" CB HIS C 687 " pdb=" CG HIS C 687 " pdb=" CD2 HIS C 687 " ideal model delta sigma weight residual 131.20 97.36 33.84 1.30e+00 5.92e-01 6.78e+02 angle pdb=" OE1 GLN C 910 " pdb=" CD GLN C 910 " pdb=" NE2 GLN C 910 " ideal model delta sigma weight residual 122.60 104.60 18.00 1.00e+00 1.00e+00 3.24e+02 angle pdb=" CB ASN B 10 " pdb=" CG ASN B 10 " pdb=" ND2 ASN B 10 " ideal model delta sigma weight residual 116.40 90.28 26.12 1.50e+00 4.44e-01 3.03e+02 ... (remaining 24443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.11: 9168 32.11 - 64.21: 1066 64.21 - 96.32: 42 96.32 - 128.43: 0 128.43 - 160.53: 2 Dihedral angle restraints: 10278 sinusoidal: 5102 harmonic: 5176 Sorted by residual: dihedral pdb=" C HIS B 222 " pdb=" N HIS B 222 " pdb=" CA HIS B 222 " pdb=" CB HIS B 222 " ideal model delta harmonic sigma weight residual -122.60 -86.55 -36.05 0 2.50e+00 1.60e-01 2.08e+02 dihedral pdb=" C HIS D 222 " pdb=" N HIS D 222 " pdb=" CA HIS D 222 " pdb=" CB HIS D 222 " ideal model delta harmonic sigma weight residual -122.60 -86.75 -35.85 0 2.50e+00 1.60e-01 2.06e+02 dihedral pdb=" C GLN B 282 " pdb=" N GLN B 282 " pdb=" CA GLN B 282 " pdb=" CB GLN B 282 " ideal model delta harmonic sigma weight residual -122.60 -94.39 -28.21 0 2.50e+00 1.60e-01 1.27e+02 ... (remaining 10275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 2655 0.173 - 0.346: 14 0.346 - 0.519: 2 0.519 - 0.692: 0 0.692 - 0.864: 1 Chirality restraints: 2672 Sorted by residual: chirality pdb=" CA HIS C 687 " pdb=" N HIS C 687 " pdb=" C HIS C 687 " pdb=" CB HIS C 687 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.87e+01 chirality pdb=" CB VAL D 48 " pdb=" CA VAL D 48 " pdb=" CG1 VAL D 48 " pdb=" CG2 VAL D 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CA GLN B 282 " pdb=" N GLN B 282 " pdb=" C GLN B 282 " pdb=" CB GLN B 282 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 2669 not shown) Planarity restraints: 2682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 687 " -0.155 2.00e-02 2.50e+03 1.41e-01 3.00e+02 pdb=" CG HIS C 687 " 0.252 2.00e-02 2.50e+03 pdb=" ND1 HIS C 687 " -0.103 2.00e-02 2.50e+03 pdb=" CD2 HIS C 687 " 0.087 2.00e-02 2.50e+03 pdb=" CE1 HIS C 687 " 0.032 2.00e-02 2.50e+03 pdb=" NE2 HIS C 687 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 936 " -0.085 2.00e-02 2.50e+03 1.73e-01 2.99e+02 pdb=" CD GLN C 936 " 0.297 2.00e-02 2.50e+03 pdb=" OE1 GLN C 936 " -0.135 2.00e-02 2.50e+03 pdb=" NE2 GLN C 936 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 936 " 0.085 2.00e-02 2.50e+03 1.73e-01 2.98e+02 pdb=" CD GLN A 936 " -0.296 2.00e-02 2.50e+03 pdb=" OE1 GLN A 936 " 0.136 2.00e-02 2.50e+03 pdb=" NE2 GLN A 936 " 0.075 2.00e-02 2.50e+03 ... (remaining 2679 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 103 2.40 - 3.02: 10150 3.02 - 3.65: 27107 3.65 - 4.27: 38341 4.27 - 4.90: 59878 Nonbonded interactions: 135579 Sorted by model distance: nonbonded pdb=" OE2 GLU A 789 " pdb=" NH1 ARG A 797 " model vdw 1.769 3.120 nonbonded pdb=" OD2 ASP A 588 " pdb=" OG SER A1018 " model vdw 1.914 3.040 nonbonded pdb=" OD2 ASP C 588 " pdb=" OG SER C1018 " model vdw 1.920 3.040 nonbonded pdb=" OE2 GLU C 789 " pdb=" NH1 ARG C 797 " model vdw 1.956 3.120 nonbonded pdb=" O ASN D 10 " pdb=" ND2 ASN D 10 " model vdw 1.966 3.120 ... (remaining 135574 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 19.300 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.008 0.309 17664 Z= 0.454 Angle : 1.231 59.160 24448 Z= 0.794 Chirality : 0.052 0.864 2672 Planarity : 0.011 0.173 2682 Dihedral : 22.114 160.535 6946 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 23.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.84 % Favored : 90.93 % Rotamer: Outliers : 0.13 % Allowed : 29.19 % Favored : 70.69 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.16), residues: 1776 helix: -2.36 (0.17), residues: 552 sheet: -2.11 (0.26), residues: 340 loop : -3.34 (0.17), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG C 922 TYR 0.018 0.002 TYR C 747 PHE 0.078 0.002 PHE B 62 TRP 0.049 0.002 TRP C 538 HIS 0.209 0.008 HIS D 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.43 (17658) covalent geometry : angle 1.23103 / 0.79 (24448) hydrogen bonds : bond 0.11984 / 8.05 ( 754) hydrogen bonds : angle 6.96781 / 4.82 ( 2034) metal coordination : bond 0.22311 / 12.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 381 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9231 (mt) cc_final: 0.8948 (tp) REVERT: A 808 GLU cc_start: 0.9271 (tt0) cc_final: 0.9023 (tt0) REVERT: A 829 ILE cc_start: 0.9001 (mt) cc_final: 0.8769 (mt) REVERT: A 836 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6827 (pm20) REVERT: A 849 ARG cc_start: 0.7797 (mmt180) cc_final: 0.7431 (tpm170) REVERT: A 869 MET cc_start: 0.6668 (pp-130) cc_final: 0.6380 (tmm) REVERT: A 870 ARG cc_start: 0.7751 (ptt90) cc_final: 0.7315 (ptt180) REVERT: A 922 ARG cc_start: 0.7651 (ttt-90) cc_final: 0.7405 (mtp85) REVERT: B 210 LEU cc_start: 0.8489 (mt) cc_final: 0.8240 (mp) REVERT: B 213 GLN cc_start: 0.7882 (tp40) cc_final: 0.7654 (tm-30) REVERT: B 214 ASP cc_start: 0.7816 (p0) cc_final: 0.7413 (p0) REVERT: C 808 GLU cc_start: 0.9261 (tt0) cc_final: 0.8892 (tt0) REVERT: C 870 ARG cc_start: 0.7320 (ptt90) cc_final: 0.7114 (ptt180) REVERT: C 905 MET cc_start: 0.7455 (tpp) cc_final: 0.7231 (tpp) REVERT: C 922 ARG cc_start: 0.7605 (ttt-90) cc_final: 0.7387 (mtp85) REVERT: D 177 ASP cc_start: 0.8363 (m-30) cc_final: 0.8159 (m-30) REVERT: D 210 LEU cc_start: 0.8548 (mt) cc_final: 0.8254 (mp) REVERT: D 214 ASP cc_start: 0.7607 (p0) cc_final: 0.7262 (p0) outliers start: 2 outliers final: 1 residues processed: 383 average time/residue: 0.1573 time to fit residues: 86.5687 Evaluate side-chains 205 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 ASN A 910 GLN A 936 GLN A 937 GLN A 964 HIS ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN B 171 ASN B 222 HIS B 282 GLN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS C 687 HIS C 761 GLN C 766 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 GLN C 934 ASN C 936 GLN C 937 GLN ** C 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 146 ASN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS D 282 GLN D 347 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.110038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083332 restraints weight = 49897.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084721 restraints weight = 36302.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084763 restraints weight = 25527.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084987 restraints weight = 23598.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.085092 restraints weight = 22659.288| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17664 Z= 0.174 Angle : 0.797 9.954 24448 Z= 0.429 Chirality : 0.049 0.380 2672 Planarity : 0.006 0.069 2682 Dihedral : 24.930 160.153 3447 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.20 % Rotamer: Outliers : 8.31 % Allowed : 21.89 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.18), residues: 1776 helix: -1.04 (0.20), residues: 542 sheet: -1.62 (0.27), residues: 354 loop : -2.48 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 232 TYR 0.038 0.002 TYR A 908 PHE 0.019 0.001 PHE A 787 TRP 0.013 0.002 TRP C 915 HIS 0.018 0.002 HIS C 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (17658) covalent geometry : angle 0.79701 / 0.43 (24448) hydrogen bonds : bond 0.04982 / 3.28 ( 754) hydrogen bonds : angle 5.59496 / 3.90 ( 2034) metal coordination : bond 0.02042 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 225 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8695 (p) REVERT: A 694 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9108 (mp) REVERT: A 733 MET cc_start: 0.8569 (tpp) cc_final: 0.8196 (tpp) REVERT: A 829 ILE cc_start: 0.8891 (mt) cc_final: 0.8679 (mt) REVERT: A 905 MET cc_start: 0.7169 (tpp) cc_final: 0.6842 (tpp) REVERT: A 922 ARG cc_start: 0.7865 (ttt-90) cc_final: 0.7339 (mtp85) REVERT: B 86 LYS cc_start: 0.7528 (tppt) cc_final: 0.7230 (tppp) REVERT: B 189 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6804 (m-80) REVERT: B 213 GLN cc_start: 0.7424 (tp40) cc_final: 0.7166 (tm-30) REVERT: C 500 TYR cc_start: 0.8208 (t80) cc_final: 0.7931 (t80) REVERT: C 602 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7814 (tp) REVERT: C 661 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8687 (p) REVERT: C 733 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8458 (tpp) REVERT: C 808 GLU cc_start: 0.8420 (tt0) cc_final: 0.8161 (tt0) REVERT: C 922 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7451 (mtp85) REVERT: D 9 VAL cc_start: 0.4908 (OUTLIER) cc_final: 0.4587 (p) REVERT: D 127 LYS cc_start: 0.9055 (tppt) cc_final: 0.8743 (tppt) REVERT: D 210 LEU cc_start: 0.8732 (mt) cc_final: 0.8449 (mp) REVERT: D 308 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7506 (m) outliers start: 131 outliers final: 36 residues processed: 329 average time/residue: 0.1378 time to fit residues: 67.6653 Evaluate side-chains 235 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 886 GLU Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 311 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [96, 97, 189, 84, 69, 170, 100, 35, 104, 117, 175] chunk 96 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 189 optimal weight: 40.0000 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 831 GLN ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 146 ASN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 997 ASN D 65 ASN D 83 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.109515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.082771 restraints weight = 50423.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083770 restraints weight = 33894.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.083998 restraints weight = 25094.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.084185 restraints weight = 23538.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.084278 restraints weight = 22535.749| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17664 Z= 0.166 Angle : 0.739 9.507 24448 Z= 0.400 Chirality : 0.048 0.375 2672 Planarity : 0.006 0.056 2682 Dihedral : 24.755 160.082 3446 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 6.47 % Allowed : 23.54 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % 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 are not related in a simple way. whole: -2.15 (0.19), residues: 1776 helix: -0.43 (0.21), residues: 540 sheet: -1.35 (0.27), residues: 366 loop : -2.10 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 232 TYR 0.029 0.002 TYR A 908 PHE 0.017 0.001 PHE C 787 TRP 0.008 0.001 TRP A 915 HIS 0.015 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (17658) covalent geometry : angle 0.73896 / 0.40 (24448) hydrogen bonds : bond 0.04468 / 2.91 ( 754) hydrogen bonds : angle 5.26226 / 3.66 ( 2034) metal coordination : bond 0.00614 / 0.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 196 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8740 (p) REVERT: A 694 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9165 (mp) REVERT: A 829 ILE cc_start: 0.8895 (mt) cc_final: 0.8686 (mt) REVERT: A 831 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.5875 (mt0) REVERT: A 871 MET cc_start: 0.8371 (mmp) cc_final: 0.7942 (mmp) REVERT: A 915 TRP cc_start: 0.8041 (p90) cc_final: 0.7827 (p-90) REVERT: A 922 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7349 (mtp85) REVERT: B 73 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8049 (ttp80) REVERT: B 189 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.6906 (m-80) REVERT: B 213 GLN cc_start: 0.7457 (tp40) cc_final: 0.7163 (tm-30) REVERT: C 587 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8502 (mtpp) REVERT: C 661 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8730 (p) REVERT: C 690 LEU cc_start: 0.9449 (tp) cc_final: 0.9221 (tt) REVERT: C 733 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8431 (tpp) REVERT: C 808 GLU cc_start: 0.8327 (tt0) cc_final: 0.8042 (tt0) REVERT: C 825 GLU cc_start: 0.8239 (tp30) cc_final: 0.8007 (tp30) REVERT: C 871 MET cc_start: 0.8298 (mmp) cc_final: 0.7766 (mmp) REVERT: C 922 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7412 (mtp85) REVERT: D 38 LYS cc_start: 0.7640 (mmmm) cc_final: 0.7354 (mmtp) REVERT: D 189 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.6952 (m-80) REVERT: D 210 LEU cc_start: 0.8799 (mt) cc_final: 0.8506 (mp) outliers start: 102 outliers final: 47 residues processed: 274 average time/residue: 0.1316 time to fit residues: 54.5410 Evaluate side-chains 233 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 175 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 831 GLN Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1024 PHE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 771 SER Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 311 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [98, 3, 139, 116, 67, 28, 132, 95, 13, 29, 143] chunk 98 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN B 4 GLN B 65 ASN B 347 GLN C 766 HIS C 983 ASN D 65 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.109969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081946 restraints weight = 50000.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.083830 restraints weight = 29226.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.084949 restraints weight = 21363.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.085602 restraints weight = 17862.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.085883 restraints weight = 16185.840| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17664 Z= 0.144 Angle : 0.709 9.632 24448 Z= 0.382 Chirality : 0.047 0.387 2672 Planarity : 0.005 0.066 2682 Dihedral : 24.565 161.053 3446 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.57 % Allowed : 24.56 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % 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 are not related in a simple way. whole: -1.77 (0.19), residues: 1776 helix: -0.07 (0.22), residues: 544 sheet: -1.19 (0.27), residues: 366 loop : -1.88 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 756 TYR 0.025 0.001 TYR C 908 PHE 0.012 0.001 PHE C 787 TRP 0.009 0.001 TRP C 978 HIS 0.013 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (17658) covalent geometry : angle 0.70936 / 0.38 (24448) hydrogen bonds : bond 0.04088 / 2.67 ( 754) hydrogen bonds : angle 5.07118 / 3.53 ( 2034) metal coordination : bond 0.00471 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 201 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8751 (p) REVERT: A 694 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9007 (mp) REVERT: A 717 LEU cc_start: 0.8984 (pp) cc_final: 0.8704 (pp) REVERT: A 829 ILE cc_start: 0.8866 (mt) cc_final: 0.8627 (mt) REVERT: A 871 MET cc_start: 0.8313 (mmp) cc_final: 0.7886 (mmp) REVERT: A 905 MET cc_start: 0.6987 (tpp) cc_final: 0.6623 (tpp) REVERT: A 922 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7252 (mtp85) REVERT: B 73 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7936 (ttp80) REVERT: B 189 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6782 (m-80) REVERT: B 213 GLN cc_start: 0.7392 (tp40) cc_final: 0.7167 (tm-30) REVERT: C 587 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8377 (mtpp) REVERT: C 602 LEU cc_start: 0.7859 (mm) cc_final: 0.7625 (tp) REVERT: C 661 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8698 (p) REVERT: C 690 LEU cc_start: 0.9474 (tp) cc_final: 0.9157 (tt) REVERT: C 808 GLU cc_start: 0.8308 (tt0) cc_final: 0.7966 (tt0) REVERT: C 849 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7094 (tpt90) REVERT: C 905 MET cc_start: 0.5951 (tpt) cc_final: 0.5393 (tpp) REVERT: C 911 MET cc_start: 0.8596 (mtp) cc_final: 0.8366 (mtt) REVERT: C 922 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7245 (mtp85) REVERT: C 950 TYR cc_start: 0.7642 (m-10) cc_final: 0.7370 (m-10) REVERT: D 38 LYS cc_start: 0.7530 (mmmm) cc_final: 0.7273 (mmtp) REVERT: D 189 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6772 (m-80) REVERT: D 210 LEU cc_start: 0.8859 (mt) cc_final: 0.8613 (mp) outliers start: 72 outliers final: 36 residues processed: 256 average time/residue: 0.1335 time to fit residues: 51.2804 Evaluate side-chains 224 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1024 PHE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 771 SER Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 849 ARG Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 311 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [94, 139, 15, 50, 17, 89, 151, 85, 40, 106, 90] chunk 94 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN B 173 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN D 173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.110075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.082118 restraints weight = 49306.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083986 restraints weight = 28930.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.085102 restraints weight = 21064.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.085764 restraints weight = 17622.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.086127 restraints weight = 15969.514| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17664 Z= 0.142 Angle : 0.689 10.059 24448 Z= 0.371 Chirality : 0.046 0.395 2672 Planarity : 0.005 0.057 2682 Dihedral : 24.361 161.046 3446 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.01 % Allowed : 23.41 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % 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 are not related in a simple way. whole: -1.55 (0.19), residues: 1776 helix: 0.18 (0.22), residues: 548 sheet: -1.00 (0.28), residues: 356 loop : -1.85 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 232 TYR 0.020 0.001 TYR A 908 PHE 0.013 0.001 PHE D 218 TRP 0.009 0.001 TRP A 915 HIS 0.013 0.001 HIS C 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (17658) covalent geometry : angle 0.68889 / 0.37 (24448) hydrogen bonds : bond 0.03918 / 2.55 ( 754) hydrogen bonds : angle 4.94366 / 3.44 ( 2034) metal coordination : bond 0.00469 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 194 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8781 (p) REVERT: A 681 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8759 (m-10) REVERT: A 694 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8952 (mp) REVERT: A 717 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8682 (pp) REVERT: A 829 ILE cc_start: 0.8852 (mt) cc_final: 0.8622 (mt) REVERT: A 880 MET cc_start: 0.7309 (mtt) cc_final: 0.6782 (ppp) REVERT: A 905 MET cc_start: 0.7082 (tpp) cc_final: 0.6787 (tpp) REVERT: A 915 TRP cc_start: 0.8053 (p90) cc_final: 0.7140 (p90) REVERT: A 922 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7179 (mtp85) REVERT: B 73 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7999 (ttp80) REVERT: B 189 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: C 587 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8430 (mtpp) REVERT: C 661 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8872 (p) REVERT: C 717 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8640 (pp) REVERT: C 782 TRP cc_start: 0.9253 (OUTLIER) cc_final: 0.8937 (t-100) REVERT: C 849 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.7036 (tpt90) REVERT: C 871 MET cc_start: 0.8250 (mmp) cc_final: 0.7700 (mmp) REVERT: C 911 MET cc_start: 0.8693 (mtp) cc_final: 0.8442 (mtt) REVERT: C 922 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7241 (mtp85) REVERT: D 38 LYS cc_start: 0.7533 (mmmm) cc_final: 0.7277 (mmtp) REVERT: D 127 LYS cc_start: 0.9056 (tppt) cc_final: 0.8744 (tppt) REVERT: D 189 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6773 (m-80) REVERT: D 210 LEU cc_start: 0.8881 (mt) cc_final: 0.8647 (mp) outliers start: 79 outliers final: 43 residues processed: 252 average time/residue: 0.1278 time to fit residues: 49.1476 Evaluate side-chains 235 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 681 PHE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1024 PHE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 849 ARG Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 311 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [155, 172, 83, 71, 57, 146, 182, 94, 141, 187, 34] chunk 155 optimal weight: 7.9990 chunk 172 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 187 optimal weight: 40.0000 chunk 34 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.110186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081989 restraints weight = 49219.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083880 restraints weight = 28911.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084999 restraints weight = 21209.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.085656 restraints weight = 17792.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.085970 restraints weight = 16152.786| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17664 Z= 0.147 Angle : 0.679 13.236 24448 Z= 0.364 Chirality : 0.045 0.393 2672 Planarity : 0.005 0.057 2682 Dihedral : 24.213 161.086 3446 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.08 % Allowed : 23.67 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % 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 are not related in a simple way. whole: -1.37 (0.19), residues: 1776 helix: 0.33 (0.22), residues: 548 sheet: -0.82 (0.29), residues: 356 loop : -1.76 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 232 TYR 0.019 0.002 TYR A 933 PHE 0.013 0.001 PHE D 218 TRP 0.009 0.001 TRP C 915 HIS 0.009 0.001 HIS C 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (17658) covalent geometry : angle 0.67864 / 0.36 (24448) hydrogen bonds : bond 0.03855 / 2.51 ( 754) hydrogen bonds : angle 4.81330 / 3.36 ( 2034) metal coordination : bond 0.00453 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 195 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 661 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8851 (p) REVERT: A 681 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8746 (m-10) REVERT: A 694 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.8980 (mp) REVERT: A 717 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8681 (pp) REVERT: A 782 TRP cc_start: 0.9226 (OUTLIER) cc_final: 0.8894 (t-100) REVERT: A 825 GLU cc_start: 0.8479 (tp30) cc_final: 0.7236 (tm-30) REVERT: A 829 ILE cc_start: 0.8848 (mt) cc_final: 0.8277 (mt) REVERT: A 870 ARG cc_start: 0.7228 (ptt180) cc_final: 0.6488 (ptt180) REVERT: A 871 MET cc_start: 0.8416 (mmp) cc_final: 0.7975 (mmp) REVERT: A 922 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7205 (mtp85) REVERT: B 1 MET cc_start: 0.6658 (tpp) cc_final: 0.6252 (tpp) REVERT: B 73 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8005 (ttp80) REVERT: B 189 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.6772 (m-80) REVERT: C 587 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8421 (mtpp) REVERT: C 661 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8912 (p) REVERT: C 717 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8611 (pp) REVERT: C 782 TRP cc_start: 0.9248 (OUTLIER) cc_final: 0.8919 (t-100) REVERT: C 849 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.7031 (tpt90) REVERT: C 871 MET cc_start: 0.8287 (mmp) cc_final: 0.7776 (mmp) REVERT: C 911 MET cc_start: 0.8747 (mtp) cc_final: 0.8494 (mtt) REVERT: C 922 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7229 (mtp85) REVERT: C 992 ARG cc_start: 0.8275 (ttt90) cc_final: 0.7951 (tpt90) REVERT: D 1 MET cc_start: 0.6719 (tpp) cc_final: 0.6123 (tpp) REVERT: D 189 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.6879 (m-80) REVERT: D 240 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6583 (mp) outliers start: 80 outliers final: 45 residues processed: 254 average time/residue: 0.1290 time to fit residues: 49.6217 Evaluate side-chains 238 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 176 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 681 PHE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 782 TRP Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1024 PHE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 849 ARG Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 311 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [97, 188, 3, 13, 47, 21, 20, 103, 60, 64, 86] chunk 97 optimal weight: 8.9990 chunk 188 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 HIS ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN C 492 ASN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.107210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.078727 restraints weight = 49354.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.080567 restraints weight = 29297.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081662 restraints weight = 21583.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.082318 restraints weight = 18163.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082535 restraints weight = 16484.429| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17664 Z= 0.260 Angle : 0.761 9.994 24448 Z= 0.404 Chirality : 0.048 0.396 2672 Planarity : 0.006 0.060 2682 Dihedral : 24.254 163.426 3446 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.71 % Allowed : 24.18 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % 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 are not related in a simple way. whole: -1.44 (0.19), residues: 1776 helix: 0.36 (0.22), residues: 544 sheet: -0.86 (0.29), residues: 356 loop : -1.86 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 212 TYR 0.026 0.002 TYR A 908 PHE 0.015 0.002 PHE A 644 TRP 0.012 0.002 TRP C 915 HIS 0.005 0.001 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 (17658) covalent geometry : angle 0.76096 / 0.40 (24448) hydrogen bonds : bond 0.04711 / 3.10 ( 754) hydrogen bonds : angle 4.97864 / 3.47 ( 2034) metal coordination : bond 0.01084 / 0.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 171 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8344 (mp) REVERT: A 661 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8943 (p) REVERT: A 680 MET cc_start: 0.8671 (ptp) cc_final: 0.8380 (ptp) REVERT: A 681 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8845 (m-10) REVERT: A 700 GLU cc_start: 0.7373 (tt0) cc_final: 0.7091 (mt-10) REVERT: A 782 TRP cc_start: 0.9298 (OUTLIER) cc_final: 0.9036 (t-100) REVERT: A 825 GLU cc_start: 0.8514 (tp30) cc_final: 0.7351 (tm-30) REVERT: A 871 MET cc_start: 0.8308 (mmp) cc_final: 0.7671 (mmp) REVERT: A 886 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8598 (mm-30) REVERT: A 905 MET cc_start: 0.6926 (tpp) cc_final: 0.6473 (tpp) REVERT: A 915 TRP cc_start: 0.8138 (p90) cc_final: 0.7259 (p90) REVERT: A 922 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7176 (mtp85) REVERT: B 73 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8118 (ttp80) REVERT: B 106 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8808 (pp) REVERT: B 189 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6774 (m-80) REVERT: C 587 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8435 (mtpp) REVERT: C 661 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8987 (p) REVERT: C 871 MET cc_start: 0.8309 (mmp) cc_final: 0.7835 (mmp) REVERT: C 880 MET cc_start: 0.8153 (tmm) cc_final: 0.7346 (ppp) REVERT: C 911 MET cc_start: 0.8792 (mtp) cc_final: 0.8531 (mtt) REVERT: C 922 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7139 (mtp85) REVERT: C 992 ARG cc_start: 0.8218 (ttt90) cc_final: 0.7844 (ttt90) REVERT: D 189 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.6942 (m-80) REVERT: D 306 GLN cc_start: 0.5451 (OUTLIER) cc_final: 0.4736 (pm20) outliers start: 90 outliers final: 61 residues processed: 243 average time/residue: 0.1245 time to fit residues: 46.4857 Evaluate side-chains 237 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 163 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 681 PHE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 782 TRP Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1024 PHE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 771 SER Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 311 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [23, 128, 14, 1, 81, 43, 106, 53, 178, 162, 6] chunk 23 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 14 optimal weight: 0.0970 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 178 optimal weight: 40.0000 chunk 162 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 ASN A 983 ASN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.108673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.080273 restraints weight = 49217.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.082088 restraints weight = 29303.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.083186 restraints weight = 21684.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083843 restraints weight = 18291.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.084030 restraints weight = 16647.438| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17664 Z= 0.168 Angle : 0.708 10.149 24448 Z= 0.377 Chirality : 0.046 0.388 2672 Planarity : 0.005 0.063 2682 Dihedral : 24.132 163.925 3446 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.76 % Allowed : 25.76 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % 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 are not related in a simple way. whole: -1.37 (0.19), residues: 1776 helix: 0.39 (0.22), residues: 546 sheet: -0.85 (0.28), residues: 356 loop : -1.80 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 232 TYR 0.018 0.002 TYR A 933 PHE 0.016 0.001 PHE B 274 TRP 0.012 0.001 TRP C 915 HIS 0.006 0.001 HIS C 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (17658) covalent geometry : angle 0.70829 / 0.38 (24448) hydrogen bonds : bond 0.04001 / 2.62 ( 754) hydrogen bonds : angle 4.90283 / 3.43 ( 2034) metal coordination : bond 0.00585 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 178 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.8379 (tmm) cc_final: 0.8171 (tmm) REVERT: A 589 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8246 (mp) REVERT: A 606 MET cc_start: 0.6316 (tpt) cc_final: 0.5770 (ttt) REVERT: A 661 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8893 (p) REVERT: A 680 MET cc_start: 0.8709 (ptp) cc_final: 0.8396 (ptp) REVERT: A 681 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8781 (m-10) REVERT: A 700 GLU cc_start: 0.7358 (tt0) cc_final: 0.7140 (mt-10) REVERT: A 871 MET cc_start: 0.8347 (mmp) cc_final: 0.7799 (mmp) REVERT: A 915 TRP cc_start: 0.8034 (p90) cc_final: 0.7152 (p90) REVERT: A 922 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7123 (mtp85) REVERT: A 992 ARG cc_start: 0.8073 (ttt90) cc_final: 0.7638 (ttt90) REVERT: B 73 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8016 (ttp80) REVERT: B 189 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: C 587 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8567 (mtpp) REVERT: C 661 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8936 (p) REVERT: C 871 MET cc_start: 0.8307 (mmp) cc_final: 0.7839 (mmp) REVERT: C 911 MET cc_start: 0.8772 (mtp) cc_final: 0.8546 (mtt) REVERT: C 922 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7065 (mtp85) REVERT: C 992 ARG cc_start: 0.8200 (ttt90) cc_final: 0.7762 (tpt90) REVERT: D 189 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6987 (m-80) REVERT: D 306 GLN cc_start: 0.5428 (OUTLIER) cc_final: 0.4716 (pm20) outliers start: 75 outliers final: 49 residues processed: 235 average time/residue: 0.1255 time to fit residues: 45.3119 Evaluate side-chains 226 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 166 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 681 PHE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1024 PHE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 771 SER Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 311 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [64, 67, 79, 49, 93, 178, 42, 170, 96, 73, 149] chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 178 optimal weight: 40.0000 chunk 42 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 ASN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.108661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080433 restraints weight = 48945.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.082309 restraints weight = 28389.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.083432 restraints weight = 20680.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.084065 restraints weight = 17279.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.084433 restraints weight = 15631.334| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17664 Z= 0.166 Angle : 0.711 11.718 24448 Z= 0.376 Chirality : 0.046 0.395 2672 Planarity : 0.005 0.064 2682 Dihedral : 23.975 164.351 3446 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.31 % Allowed : 26.14 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % 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 are not related in a simple way. whole: -1.30 (0.19), residues: 1776 helix: 0.44 (0.23), residues: 548 sheet: -0.82 (0.28), residues: 356 loop : -1.74 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 123 TYR 0.020 0.002 TYR A 933 PHE 0.014 0.001 PHE B 274 TRP 0.012 0.001 TRP C 915 HIS 0.005 0.001 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (17658) covalent geometry : angle 0.71059 / 0.38 (24448) hydrogen bonds : bond 0.03924 / 2.57 ( 754) hydrogen bonds : angle 4.81029 / 3.37 ( 2034) metal coordination : bond 0.00617 / 0.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 175 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.8376 (tmm) cc_final: 0.8175 (tmm) REVERT: A 589 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8224 (mp) REVERT: A 606 MET cc_start: 0.6523 (tpt) cc_final: 0.5850 (ttt) REVERT: A 661 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8887 (p) REVERT: A 680 MET cc_start: 0.8724 (ptp) cc_final: 0.8386 (ptp) REVERT: A 681 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8787 (m-10) REVERT: A 700 GLU cc_start: 0.7343 (tt0) cc_final: 0.7109 (mt-10) REVERT: A 871 MET cc_start: 0.8321 (mmp) cc_final: 0.7718 (mmp) REVERT: A 886 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8591 (mm-30) REVERT: A 915 TRP cc_start: 0.8052 (p90) cc_final: 0.7246 (p90) REVERT: A 922 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7094 (mtp85) REVERT: A 992 ARG cc_start: 0.8039 (ttt90) cc_final: 0.7637 (ttt90) REVERT: B 73 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8073 (ttp80) REVERT: B 189 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6703 (m-80) REVERT: C 587 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8526 (mtpp) REVERT: C 661 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8947 (p) REVERT: C 871 MET cc_start: 0.8307 (mmp) cc_final: 0.7805 (mmp) REVERT: C 880 MET cc_start: 0.8213 (tmm) cc_final: 0.7842 (tmm) REVERT: C 911 MET cc_start: 0.8795 (mtp) cc_final: 0.8551 (mtt) REVERT: C 922 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7066 (mtp85) REVERT: C 992 ARG cc_start: 0.8198 (ttt90) cc_final: 0.7757 (tpt90) REVERT: C 1025 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7349 (ttm) REVERT: D 65 ASN cc_start: 0.7689 (p0) cc_final: 0.7445 (p0) REVERT: D 189 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7006 (m-80) REVERT: D 306 GLN cc_start: 0.5437 (OUTLIER) cc_final: 0.4707 (pm20) outliers start: 68 outliers final: 51 residues processed: 224 average time/residue: 0.1276 time to fit residues: 43.9379 Evaluate side-chains 237 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 174 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 681 PHE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1024 PHE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 771 SER Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain C residue 1025 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 311 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [169, 124, 104, 36, 112, 42, 62, 80, 31, 138, 100] chunk 169 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN C 492 ASN C 956 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.110217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081965 restraints weight = 48737.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083850 restraints weight = 28693.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.084977 restraints weight = 20940.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.085531 restraints weight = 17527.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.085919 restraints weight = 15977.922| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17664 Z= 0.131 Angle : 0.692 13.033 24448 Z= 0.365 Chirality : 0.045 0.387 2672 Planarity : 0.005 0.066 2682 Dihedral : 23.810 164.070 3446 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.68 % Allowed : 26.90 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % 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 are not related in a simple way. whole: -1.19 (0.19), residues: 1776 helix: 0.51 (0.23), residues: 548 sheet: -0.73 (0.28), residues: 376 loop : -1.69 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 232 TYR 0.021 0.001 TYR A 933 PHE 0.013 0.001 PHE A 990 TRP 0.019 0.001 TRP D 317 HIS 0.006 0.001 HIS C 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (17658) covalent geometry : angle 0.69213 / 0.36 (24448) hydrogen bonds : bond 0.03591 / 2.33 ( 754) hydrogen bonds : angle 4.79018 / 3.38 ( 2034) metal coordination : bond 0.00247 / 0.12 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.8336 (tmm) cc_final: 0.8136 (tmm) REVERT: A 565 ASP cc_start: 0.8528 (p0) cc_final: 0.8174 (p0) REVERT: A 589 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8167 (mp) REVERT: A 606 MET cc_start: 0.6577 (tpt) cc_final: 0.5993 (ttt) REVERT: A 661 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8855 (p) REVERT: A 680 MET cc_start: 0.8679 (ptp) cc_final: 0.8313 (ptp) REVERT: A 681 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8738 (m-10) REVERT: A 700 GLU cc_start: 0.7450 (tt0) cc_final: 0.7239 (mt-10) REVERT: A 733 MET cc_start: 0.8637 (tpp) cc_final: 0.8375 (tpp) REVERT: A 796 ASP cc_start: 0.8106 (m-30) cc_final: 0.7887 (m-30) REVERT: A 871 MET cc_start: 0.8349 (mmp) cc_final: 0.7757 (mmp) REVERT: A 886 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8567 (mm-30) REVERT: A 905 MET cc_start: 0.6523 (tpp) cc_final: 0.6262 (tpp) REVERT: A 922 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7071 (mtp85) REVERT: A 992 ARG cc_start: 0.8057 (ttt90) cc_final: 0.7627 (ttt90) REVERT: B 73 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8088 (ttp80) REVERT: B 189 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: C 587 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8529 (mtpp) REVERT: C 661 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8910 (p) REVERT: C 871 MET cc_start: 0.8276 (mmp) cc_final: 0.7775 (mmp) REVERT: C 880 MET cc_start: 0.8209 (tmm) cc_final: 0.7830 (tmm) REVERT: C 911 MET cc_start: 0.8763 (mtp) cc_final: 0.7784 (mtt) REVERT: C 915 TRP cc_start: 0.7920 (p90) cc_final: 0.6933 (p90) REVERT: C 922 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7052 (mtp85) REVERT: C 992 ARG cc_start: 0.8235 (ttt90) cc_final: 0.7913 (tpt90) REVERT: C 1025 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6955 (ttm) REVERT: D 65 ASN cc_start: 0.7755 (p0) cc_final: 0.7505 (p0) REVERT: D 189 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.7004 (m-80) REVERT: D 253 HIS cc_start: 0.7147 (p-80) cc_final: 0.6669 (p90) outliers start: 58 outliers final: 37 residues processed: 228 average time/residue: 0.1265 time to fit residues: 44.2163 Evaluate side-chains 225 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 681 PHE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1024 PHE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 771 SER Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain C residue 1025 MET Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 311 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [140, 0, 164, 87, 40, 61, 35, 111, 116, 57, 179] chunk 140 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 116 optimal weight: 0.0870 chunk 57 optimal weight: 0.8980 chunk 179 optimal weight: 30.0000 overall best weight: 1.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.110173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081885 restraints weight = 48891.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083768 restraints weight = 28760.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084879 restraints weight = 21102.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085531 restraints weight = 17711.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.085806 restraints weight = 16061.947| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.269 17664 Z= 0.246 Angle : 0.845 59.200 24448 Z= 0.479 Chirality : 0.045 0.388 2672 Planarity : 0.005 0.066 2682 Dihedral : 23.812 164.048 3446 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.36 % Allowed : 27.35 % Favored : 69.29 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % 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 are not related in a simple way. whole: -1.19 (0.19), residues: 1776 helix: 0.51 (0.23), residues: 548 sheet: -0.72 (0.28), residues: 376 loop : -1.69 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 232 TYR 0.019 0.001 TYR A 933 PHE 0.011 0.001 PHE B 274 TRP 0.017 0.001 TRP D 317 HIS 0.006 0.001 HIS C 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.25 (17658) covalent geometry : angle 0.84502 / 0.48 (24448) hydrogen bonds : bond 0.03596 / 2.34 ( 754) hydrogen bonds : angle 4.78729 / 3.38 ( 2034) metal coordination : bond 0.00292 / 0.15 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2699.14 seconds wall clock time: 47 minutes 44.30 seconds (2864.30 seconds total)