Starting phenix.real_space_refine on Tue Nov 18 19:55:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbu_7850/11_2025/6dbu_7850_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbu_7850/11_2025/6dbu_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_7850/11_2025/6dbu_7850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbu_7850/11_2025/6dbu_7850.map" model { file = "/net/cci-nas-00/data/ceres_data/6dbu_7850/11_2025/6dbu_7850_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbu_7850/11_2025/6dbu_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-2.0-5881/lib/python3.9/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: 4.20, per 1000 atoms: 0.25 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: 1.52 Conformation dependent library (CDL) restraints added in 666.3 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: 1.97 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: 3.93 Time building geometry restraints manager: 2.02 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: 2656 0.173 - 0.346: 13 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: 1.510 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.650 Find NCS groups from input model: 0.230 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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= 0.350 Angle : 1.198 59.160 24448 Z= 0.710 Chirality : 0.049 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 covalent geometry : bond 0.00670 (17658) covalent geometry : angle 1.19831 (24448) hydrogen bonds : bond 0.11984 ( 754) hydrogen bonds : angle 6.96781 ( 2034) metal coordination : bond 0.22311 ( 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 : 0.518 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: 0.9230 (mt) cc_final: 0.8952 (tp) REVERT: A 808 GLU cc_start: 0.9271 (tt0) cc_final: 0.9024 (tt0) REVERT: A 829 ILE cc_start: 0.9001 (mt) cc_final: 0.8767 (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: 0.7425 (tpm170) REVERT: A 869 MET cc_start: 0.6668 (pp-130) cc_final: 0.6183 (ppp) REVERT: A 870 ARG cc_start: 0.7751 (ptt90) cc_final: 0.7224 (ptt180) REVERT: A 922 ARG cc_start: 0.7651 (ttt-90) cc_final: 0.7400 (mtp85) REVERT: B 210 LEU cc_start: 0.8489 (mt) cc_final: 0.8238 (mp) REVERT: B 213 GLN cc_start: 0.7882 (tp40) cc_final: 0.7652 (tm-30) REVERT: B 214 ASP cc_start: 0.7816 (p0) cc_final: 0.7412 (p0) REVERT: C 808 GLU cc_start: 0.9261 (tt0) cc_final: 0.8895 (tt0) REVERT: C 870 ARG cc_start: 0.7320 (ptt90) cc_final: 0.7115 (ptt180) REVERT: C 905 MET cc_start: 0.7456 (tpp) cc_final: 0.7246 (tpp) REVERT: C 922 ARG cc_start: 0.7605 (ttt-90) cc_final: 0.7383 (mtp85) REVERT: D 177 ASP cc_start: 0.8363 (m-30) cc_final: 0.8157 (m-30) REVERT: D 210 LEU cc_start: 0.8548 (mt) cc_final: 0.8252 (mp) REVERT: D 214 ASP cc_start: 0.7607 (p0) cc_final: 0.7263 (p0) outliers start: 2 outliers final: 1 residues processed: 383 average time/residue: 0.1588 time to fit residues: 85.9166 Evaluate side-chains 203 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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: 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: 8.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN A 831 GLN A 910 GLN A 936 GLN A 964 HIS ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN 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 761 GLN C 766 HIS C 910 GLN C 934 ASN C 936 GLN C 937 GLN ** C 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.108919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.081942 restraints weight = 49361.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082745 restraints weight = 35872.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083653 restraints weight = 25088.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083790 restraints weight = 21883.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083921 restraints weight = 20444.869| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17664 Z= 0.187 Angle : 0.753 10.582 24448 Z= 0.406 Chirality : 0.044 0.217 2672 Planarity : 0.006 0.058 2682 Dihedral : 24.664 156.090 3447 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 8.76 % Allowed : 22.72 % Favored : 68.53 % 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: -2.73 (0.18), residues: 1776 helix: -0.93 (0.20), residues: 542 sheet: -1.67 (0.27), residues: 354 loop : -2.46 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 845 TYR 0.038 0.002 TYR A 908 PHE 0.015 0.001 PHE A 787 TRP 0.015 0.002 TRP C 538 HIS 0.010 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00412 (17658) covalent geometry : angle 0.75312 (24448) hydrogen bonds : bond 0.04764 ( 754) hydrogen bonds : angle 5.47460 ( 2034) metal coordination : bond 0.01677 ( 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 355 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 217 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8756 (mtpp) REVERT: A 602 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7887 (tp) REVERT: A 661 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8756 (p) REVERT: A 681 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8832 (m-10) REVERT: A 694 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9144 (mp) REVERT: A 870 ARG cc_start: 0.7374 (ptt90) cc_final: 0.7138 (ptt180) REVERT: A 905 MET cc_start: 0.7294 (tpp) cc_final: 0.6906 (tpp) REVERT: A 922 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7341 (mtp85) REVERT: A 992 ARG cc_start: 0.8143 (tpt170) cc_final: 0.7746 (ttt90) REVERT: A 996 MET cc_start: 0.8702 (mtt) cc_final: 0.8419 (mtm) REVERT: B 86 LYS cc_start: 0.7544 (tppt) cc_final: 0.7215 (tppp) REVERT: B 106 LEU cc_start: 0.8919 (tt) cc_final: 0.8601 (pp) REVERT: B 107 TYR cc_start: 0.8517 (m-80) cc_final: 0.8233 (m-80) REVERT: B 189 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.6819 (m-80) REVERT: B 213 GLN cc_start: 0.7436 (tp40) cc_final: 0.7171 (tm-30) REVERT: C 500 TYR cc_start: 0.8235 (t80) cc_final: 0.7956 (t80) REVERT: C 589 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8380 (mp) REVERT: C 602 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7766 (tp) REVERT: C 661 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8714 (p) REVERT: C 733 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8354 (tpp) REVERT: C 808 GLU cc_start: 0.8471 (tt0) cc_final: 0.8189 (tt0) REVERT: C 922 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7449 (mtp85) REVERT: D 9 VAL cc_start: 0.5085 (OUTLIER) cc_final: 0.4779 (p) REVERT: D 108 MET cc_start: 0.7852 (ptm) cc_final: 0.7634 (ptt) REVERT: D 127 LYS cc_start: 0.9021 (tppt) cc_final: 0.8768 (tppt) REVERT: D 189 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6920 (m-80) REVERT: D 210 LEU cc_start: 0.8828 (mt) cc_final: 0.8505 (mp) REVERT: D 308 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7503 (m) outliers start: 138 outliers final: 44 residues processed: 327 average time/residue: 0.1386 time to fit residues: 66.7591 Evaluate side-chains 245 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 186 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 507 VAL Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 681 PHE 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 A residue 922 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 150 LYS 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 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 589 LEU Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 617 GLU 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 750 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 809 THR 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 928 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1006 LEU 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 189 PHE 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: chunk 96 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 84 optimal weight: 0.4980 chunk 69 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 GLN A 983 ASN B 4 GLN B 65 ASN B 146 ASN B 173 ASN B 347 GLN C 983 ASN C 997 ASN D 4 GLN D 65 ASN D 146 ASN D 347 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.110357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.082244 restraints weight = 49611.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.084113 restraints weight = 29085.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.085263 restraints weight = 21392.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.085917 restraints weight = 17991.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.086316 restraints weight = 16343.880| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17664 Z= 0.145 Angle : 0.689 8.945 24448 Z= 0.374 Chirality : 0.043 0.192 2672 Planarity : 0.005 0.050 2682 Dihedral : 24.317 154.635 3446 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 6.03 % Allowed : 23.67 % Favored : 70.30 % 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: -1.97 (0.19), residues: 1776 helix: -0.26 (0.21), residues: 544 sheet: -1.20 (0.28), residues: 354 loop : -2.04 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 852 TYR 0.017 0.002 TYR A 933 PHE 0.016 0.001 PHE B 274 TRP 0.015 0.001 TRP A 915 HIS 0.021 0.002 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00312 (17658) covalent geometry : angle 0.68938 (24448) hydrogen bonds : bond 0.03953 ( 754) hydrogen bonds : angle 5.05735 ( 2034) metal coordination : bond 0.00273 ( 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 309 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 214 time to evaluate : 0.419 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 587 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8710 (mtpp) REVERT: A 661 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8739 (p) REVERT: A 672 LEU cc_start: 0.8738 (mp) cc_final: 0.8481 (mt) REVERT: A 681 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8654 (m-10) REVERT: A 694 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9171 (mp) REVERT: A 717 LEU cc_start: 0.8944 (pp) cc_final: 0.8669 (pp) REVERT: A 829 ILE cc_start: 0.8890 (mt) cc_final: 0.8629 (mt) REVERT: A 870 ARG cc_start: 0.7257 (ptt90) cc_final: 0.6930 (ptt180) REVERT: A 871 MET cc_start: 0.8382 (mmp) cc_final: 0.7986 (mmp) REVERT: A 905 MET cc_start: 0.7158 (tpp) cc_final: 0.6746 (tpp) REVERT: A 922 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7295 (mtp85) REVERT: A 992 ARG cc_start: 0.8131 (tpt170) cc_final: 0.7896 (ttt90) REVERT: B 73 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7905 (ttp80) REVERT: B 189 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6804 (m-80) REVERT: B 213 GLN cc_start: 0.7427 (tp40) cc_final: 0.7162 (tm-30) REVERT: C 587 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8537 (mtpp) REVERT: C 589 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8281 (mp) REVERT: C 661 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8715 (p) REVERT: C 672 LEU cc_start: 0.8753 (mp) cc_final: 0.8272 (mt) REVERT: C 690 LEU cc_start: 0.9435 (tp) cc_final: 0.9143 (tt) REVERT: C 717 LEU cc_start: 0.8901 (pp) cc_final: 0.8619 (pp) REVERT: C 808 GLU cc_start: 0.8424 (tt0) cc_final: 0.8125 (tt0) REVERT: C 825 GLU cc_start: 0.8346 (tp30) cc_final: 0.8115 (tp30) REVERT: C 870 ARG cc_start: 0.7147 (ptt180) cc_final: 0.6435 (ptt180) REVERT: C 871 MET cc_start: 0.8273 (mmp) cc_final: 0.7808 (mmp) REVERT: C 905 MET cc_start: 0.6874 (tpp) cc_final: 0.6645 (tpp) REVERT: C 922 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7243 (mtp85) REVERT: D 189 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6848 (m-80) REVERT: D 210 LEU cc_start: 0.8869 (mt) cc_final: 0.8616 (mp) outliers start: 95 outliers final: 38 residues processed: 288 average time/residue: 0.1332 time to fit residues: 57.5327 Evaluate side-chains 238 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 587 LYS 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 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 1024 PHE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 146 ASN 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 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 313 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 ILE 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 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 989 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 116 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 95 optimal weight: 0.0070 chunk 13 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.8604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 146 ASN B 347 GLN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** D 83 GLN ** 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 = 0.3858 r_free = 0.3858 target = 0.110853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082892 restraints weight = 49830.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.084905 restraints weight = 28341.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086130 restraints weight = 20380.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.086835 restraints weight = 16905.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.087213 restraints weight = 15284.668| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17664 Z= 0.139 Angle : 0.660 9.038 24448 Z= 0.357 Chirality : 0.041 0.149 2672 Planarity : 0.005 0.066 2682 Dihedral : 24.096 154.998 3446 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.76 % Allowed : 24.18 % Favored : 71.07 % 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: -1.59 (0.19), residues: 1776 helix: 0.08 (0.22), residues: 550 sheet: -0.99 (0.28), residues: 352 loop : -1.84 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 992 TYR 0.018 0.001 TYR A 908 PHE 0.010 0.001 PHE C 990 TRP 0.013 0.001 TRP B 317 HIS 0.011 0.001 HIS C 817 Details of bonding type rmsd covalent geometry : bond 0.00304 (17658) covalent geometry : angle 0.65992 (24448) hydrogen bonds : bond 0.03690 ( 754) hydrogen bonds : angle 4.89941 ( 2034) metal coordination : bond 0.00336 ( 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 279 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 204 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8797 (p) REVERT: A 681 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8768 (m-10) REVERT: A 694 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9149 (mp) REVERT: A 717 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8624 (pp) REVERT: A 825 GLU cc_start: 0.8513 (tp30) cc_final: 0.7417 (tm-30) REVERT: A 829 ILE cc_start: 0.8838 (mt) cc_final: 0.8273 (mt) REVERT: A 922 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7169 (mtp85) REVERT: B 73 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7850 (ttp80) REVERT: B 189 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.6796 (m-80) REVERT: C 587 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8563 (mtpp) REVERT: C 589 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8202 (mp) REVERT: C 661 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8707 (p) REVERT: C 672 LEU cc_start: 0.8623 (mp) cc_final: 0.8420 (mt) REVERT: C 690 LEU cc_start: 0.9471 (tp) cc_final: 0.9240 (tt) REVERT: C 717 LEU cc_start: 0.8869 (pp) cc_final: 0.8580 (pp) REVERT: C 782 TRP cc_start: 0.9216 (OUTLIER) cc_final: 0.8910 (t-100) REVERT: C 808 GLU cc_start: 0.8383 (tt0) cc_final: 0.8132 (tt0) REVERT: C 849 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.7076 (tpt90) REVERT: C 911 MET cc_start: 0.8643 (mtp) cc_final: 0.7556 (mtt) REVERT: C 915 TRP cc_start: 0.8008 (p90) cc_final: 0.7058 (p90) REVERT: C 922 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7130 (mtp85) REVERT: C 950 TYR cc_start: 0.7625 (m-10) cc_final: 0.7334 (m-10) REVERT: D 127 LYS cc_start: 0.9101 (tppt) cc_final: 0.8774 (tppt) REVERT: D 189 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.6787 (m-80) REVERT: D 210 LEU cc_start: 0.8881 (mt) cc_final: 0.8626 (mp) outliers start: 75 outliers final: 28 residues processed: 260 average time/residue: 0.1359 time to fit residues: 52.7865 Evaluate side-chains 225 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 892 VAL Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 928 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 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 560 TRP Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 589 LEU 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 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 1018 SER Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 133 VAL 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: chunk 94 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 89 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 106 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 83 GLN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.112271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.084305 restraints weight = 49234.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086293 restraints weight = 28166.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.087504 restraints weight = 20415.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.087968 restraints weight = 17015.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.088517 restraints weight = 15632.933| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17664 Z= 0.131 Angle : 0.648 8.759 24448 Z= 0.349 Chirality : 0.041 0.147 2672 Planarity : 0.005 0.055 2682 Dihedral : 23.838 155.294 3446 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.76 % Allowed : 23.86 % Favored : 71.38 % 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: -1.29 (0.19), residues: 1776 helix: 0.33 (0.22), residues: 548 sheet: -0.81 (0.29), residues: 352 loop : -1.64 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 756 TYR 0.017 0.001 TYR A 933 PHE 0.018 0.001 PHE C 990 TRP 0.013 0.001 TRP B 317 HIS 0.010 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00282 (17658) covalent geometry : angle 0.64848 (24448) hydrogen bonds : bond 0.03418 ( 754) hydrogen bonds : angle 4.74967 ( 2034) metal coordination : bond 0.00197 ( 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 283 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 208 time to evaluate : 0.579 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 606 MET cc_start: 0.6292 (tpt) cc_final: 0.5860 (ttt) REVERT: A 661 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8793 (p) REVERT: A 681 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8776 (m-10) REVERT: A 717 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8585 (pp) REVERT: A 825 GLU cc_start: 0.8521 (tp30) cc_final: 0.7508 (tm-30) REVERT: A 871 MET cc_start: 0.8367 (mmp) cc_final: 0.8013 (mmp) REVERT: A 880 MET cc_start: 0.7430 (mtt) cc_final: 0.6464 (ppp) REVERT: A 905 MET cc_start: 0.6831 (tpp) cc_final: 0.6585 (tpp) REVERT: A 922 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7153 (mtp85) REVERT: A 1021 LEU cc_start: 0.8901 (mt) cc_final: 0.8558 (mp) REVERT: B 1 MET cc_start: 0.6654 (tpp) cc_final: 0.6432 (tpp) REVERT: B 73 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7793 (ttp80) REVERT: B 189 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: C 587 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8571 (mtpp) REVERT: C 589 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8260 (mp) REVERT: C 606 MET cc_start: 0.6798 (tpt) cc_final: 0.6126 (ttt) REVERT: C 661 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8738 (p) REVERT: C 717 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8474 (pp) REVERT: C 782 TRP cc_start: 0.9172 (OUTLIER) cc_final: 0.8778 (t-100) REVERT: C 808 GLU cc_start: 0.8251 (tt0) cc_final: 0.7986 (tt0) REVERT: C 871 MET cc_start: 0.8307 (mmp) cc_final: 0.7764 (mmp) REVERT: C 911 MET cc_start: 0.8768 (mtp) cc_final: 0.8532 (mtt) REVERT: C 922 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7078 (mtp85) REVERT: D 210 LEU cc_start: 0.8861 (mt) cc_final: 0.8636 (mp) outliers start: 75 outliers final: 33 residues processed: 263 average time/residue: 0.1394 time to fit residues: 54.3723 Evaluate side-chains 230 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 ILE 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 717 LEU Chi-restraints excluded: chain A residue 748 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 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 617 GLU 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 817 HIS Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 168 THR 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: chunk 155 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 94 optimal weight: 0.3980 chunk 141 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 34 optimal weight: 0.3980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 ASN B 65 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.111063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082996 restraints weight = 49618.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.084922 restraints weight = 28735.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.086078 restraints weight = 20982.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.086695 restraints weight = 17564.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.087116 restraints weight = 15991.346| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17664 Z= 0.149 Angle : 0.650 14.770 24448 Z= 0.347 Chirality : 0.040 0.192 2672 Planarity : 0.005 0.054 2682 Dihedral : 23.748 156.225 3446 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.01 % Allowed : 23.98 % Favored : 71.00 % 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: -1.13 (0.20), residues: 1776 helix: 0.47 (0.22), residues: 548 sheet: -0.54 (0.29), residues: 362 loop : -1.66 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 992 TYR 0.018 0.001 TYR A 933 PHE 0.010 0.001 PHE D 218 TRP 0.010 0.001 TRP B 317 HIS 0.006 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00330 (17658) covalent geometry : angle 0.65000 (24448) hydrogen bonds : bond 0.03445 ( 754) hydrogen bonds : angle 4.62504 ( 2034) metal coordination : bond 0.00452 ( 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 270 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 191 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8163 (mp) REVERT: A 606 MET cc_start: 0.6377 (tpt) cc_final: 0.6150 (ttt) REVERT: A 661 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8774 (p) REVERT: A 681 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8807 (m-10) REVERT: A 717 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8614 (pp) REVERT: A 782 TRP cc_start: 0.9147 (OUTLIER) cc_final: 0.8819 (t-100) REVERT: A 796 ASP cc_start: 0.8270 (p0) cc_final: 0.8001 (p0) REVERT: A 825 GLU cc_start: 0.8518 (tp30) cc_final: 0.7514 (tm-30) REVERT: A 871 MET cc_start: 0.8265 (mmp) cc_final: 0.7601 (mmp) REVERT: A 880 MET cc_start: 0.7254 (mtt) cc_final: 0.6979 (ppp) REVERT: A 922 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7027 (mtp85) REVERT: A 1021 LEU cc_start: 0.8943 (mt) cc_final: 0.8593 (mp) REVERT: B 73 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7749 (ttp80) REVERT: B 189 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: C 587 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8570 (mtpp) REVERT: C 606 MET cc_start: 0.6638 (tpt) cc_final: 0.6046 (ttt) REVERT: C 661 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8752 (p) REVERT: C 690 LEU cc_start: 0.9452 (tp) cc_final: 0.9241 (tt) REVERT: C 717 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8512 (pp) REVERT: C 782 TRP cc_start: 0.9203 (OUTLIER) cc_final: 0.8862 (t-100) REVERT: C 808 GLU cc_start: 0.8225 (tt0) cc_final: 0.7938 (tt0) REVERT: C 871 MET cc_start: 0.8246 (mmp) cc_final: 0.7557 (mmp) REVERT: C 877 ARG cc_start: 0.8473 (ptt180) cc_final: 0.8171 (ptt90) REVERT: C 911 MET cc_start: 0.8767 (mtp) cc_final: 0.8508 (mtt) REVERT: C 922 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7108 (mtp85) REVERT: D 1 MET cc_start: 0.6817 (tpp) cc_final: 0.6186 (tpp) REVERT: D 109 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8751 (tt) outliers start: 79 outliers final: 40 residues processed: 247 average time/residue: 0.1317 time to fit residues: 49.1100 Evaluate side-chains 230 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 661 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 681 PHE 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 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 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 248 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS 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 649 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 771 SER Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 817 HIS 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 1018 SER Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 168 THR 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: chunk 97 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.111163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082876 restraints weight = 49346.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.084824 restraints weight = 28716.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.086000 restraints weight = 20974.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.086688 restraints weight = 17535.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.087077 restraints weight = 15885.574| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17664 Z= 0.145 Angle : 0.650 10.638 24448 Z= 0.346 Chirality : 0.040 0.157 2672 Planarity : 0.005 0.058 2682 Dihedral : 23.649 156.734 3446 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.44 % Allowed : 24.68 % 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: -1.01 (0.20), residues: 1776 helix: 0.58 (0.23), residues: 546 sheet: -0.51 (0.28), residues: 372 loop : -1.57 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 992 TYR 0.023 0.001 TYR A 908 PHE 0.013 0.001 PHE A 681 TRP 0.013 0.001 TRP C 915 HIS 0.006 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00322 (17658) covalent geometry : angle 0.64989 (24448) hydrogen bonds : bond 0.03393 ( 754) hydrogen bonds : angle 4.58615 ( 2034) metal coordination : bond 0.00418 ( 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 262 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 192 time to evaluate : 0.596 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 589 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8173 (mp) REVERT: A 661 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8797 (p) REVERT: A 681 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8772 (m-10) REVERT: A 717 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8618 (pp) REVERT: A 782 TRP cc_start: 0.9141 (OUTLIER) cc_final: 0.8817 (t-100) REVERT: A 796 ASP cc_start: 0.8328 (p0) cc_final: 0.8073 (p0) REVERT: A 871 MET cc_start: 0.8138 (mmp) cc_final: 0.7735 (mmp) REVERT: A 922 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.6985 (mtp85) REVERT: B 73 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7983 (ttp80) REVERT: B 189 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6599 (m-80) REVERT: C 587 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8541 (mtpp) REVERT: C 606 MET cc_start: 0.6561 (tpt) cc_final: 0.6219 (ttt) REVERT: C 661 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8862 (p) REVERT: C 690 LEU cc_start: 0.9487 (tp) cc_final: 0.9234 (tt) REVERT: C 717 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8529 (pp) REVERT: C 782 TRP cc_start: 0.9212 (OUTLIER) cc_final: 0.8870 (t-100) REVERT: C 871 MET cc_start: 0.8265 (mmp) cc_final: 0.7569 (mmp) REVERT: C 911 MET cc_start: 0.8770 (mtp) cc_final: 0.7700 (mtt) REVERT: C 915 TRP cc_start: 0.7960 (p90) cc_final: 0.7011 (p90) REVERT: C 922 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7026 (mtp85) REVERT: C 1021 LEU cc_start: 0.8864 (mt) cc_final: 0.8395 (mp) REVERT: D 109 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8776 (tt) REVERT: D 189 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6793 (m-80) outliers start: 70 outliers final: 40 residues processed: 241 average time/residue: 0.1312 time to fit residues: 47.4672 Evaluate side-chains 236 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 661 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 681 PHE 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 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 133 VAL 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 201 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS 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 717 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 817 HIS 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 3 LEU Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 153 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 23 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 53 optimal weight: 0.0370 chunk 178 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 6 optimal weight: 0.0020 overall best weight: 0.7268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.112231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.084133 restraints weight = 49556.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.086066 restraints weight = 29190.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.087216 restraints weight = 21379.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.087870 restraints weight = 17946.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088186 restraints weight = 16310.145| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17664 Z= 0.134 Angle : 0.655 8.839 24448 Z= 0.350 Chirality : 0.040 0.171 2672 Planarity : 0.005 0.063 2682 Dihedral : 23.527 156.501 3446 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.93 % Allowed : 25.19 % 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: -0.97 (0.20), residues: 1776 helix: 0.53 (0.23), residues: 548 sheet: -0.45 (0.28), residues: 372 loop : -1.50 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 849 TYR 0.023 0.001 TYR A 933 PHE 0.011 0.001 PHE A 990 TRP 0.012 0.001 TRP C 915 HIS 0.006 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00285 (17658) covalent geometry : angle 0.65475 (24448) hydrogen bonds : bond 0.03307 ( 754) hydrogen bonds : angle 4.57926 ( 2034) metal coordination : bond 0.00204 ( 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 254 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 192 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: A 503 MET cc_start: 0.8329 (tmm) cc_final: 0.8105 (tmm) REVERT: A 589 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8115 (mp) REVERT: A 661 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8799 (p) REVERT: A 681 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8697 (m-10) REVERT: A 717 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8613 (pp) REVERT: A 782 TRP cc_start: 0.9068 (OUTLIER) cc_final: 0.8732 (t-100) REVERT: A 796 ASP cc_start: 0.8363 (p0) cc_final: 0.8081 (p0) REVERT: A 871 MET cc_start: 0.7692 (mmp) cc_final: 0.7166 (mmp) REVERT: A 922 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6992 (mtp85) REVERT: A 992 ARG cc_start: 0.8097 (ttt90) cc_final: 0.7787 (ttt90) REVERT: B 73 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7954 (ttp80) REVERT: B 189 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6695 (m-80) REVERT: C 587 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8597 (mtpp) REVERT: C 661 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8876 (p) REVERT: C 690 LEU cc_start: 0.9496 (tp) cc_final: 0.9291 (tt) REVERT: C 717 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8515 (pp) REVERT: C 782 TRP cc_start: 0.9152 (OUTLIER) cc_final: 0.8817 (t-100) REVERT: C 911 MET cc_start: 0.8771 (mtp) cc_final: 0.7755 (mtt) REVERT: C 915 TRP cc_start: 0.7898 (p90) cc_final: 0.6936 (p90) REVERT: C 922 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7009 (mtp85) outliers start: 62 outliers final: 38 residues processed: 234 average time/residue: 0.1324 time to fit residues: 46.8811 Evaluate side-chains 223 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 717 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 782 TRP 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 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 248 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS 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 679 LEU Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 771 SER Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 892 VAL 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 107 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 248 THR 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: chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 178 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 96 optimal weight: 0.0000 chunk 73 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN A 534 HIS ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN C 956 ASN ** D 4 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 = 0.3818 r_free = 0.3818 target = 0.108646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080238 restraints weight = 49612.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082128 restraints weight = 28833.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.083264 restraints weight = 21034.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083946 restraints weight = 17594.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.084274 restraints weight = 15929.572| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17664 Z= 0.230 Angle : 0.725 10.631 24448 Z= 0.387 Chirality : 0.043 0.155 2672 Planarity : 0.006 0.085 2682 Dihedral : 23.596 157.947 3446 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.19 % Allowed : 25.51 % Favored : 70.30 % 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: -1.06 (0.19), residues: 1776 helix: 0.60 (0.22), residues: 546 sheet: -0.54 (0.28), residues: 372 loop : -1.65 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 878 TYR 0.032 0.002 TYR A 908 PHE 0.013 0.002 PHE B 62 TRP 0.015 0.002 TRP C 915 HIS 0.005 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00510 (17658) covalent geometry : angle 0.72537 (24448) hydrogen bonds : bond 0.04321 ( 754) hydrogen bonds : angle 4.75625 ( 2034) metal coordination : bond 0.00876 ( 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 246 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 180 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8868 (p) REVERT: A 681 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8934 (m-80) REVERT: A 717 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8757 (pp) REVERT: A 825 GLU cc_start: 0.8612 (tp30) cc_final: 0.7559 (tm-30) REVERT: A 871 MET cc_start: 0.8124 (mmp) cc_final: 0.7764 (mmp) REVERT: A 905 MET cc_start: 0.7147 (tpp) cc_final: 0.6815 (tpp) REVERT: A 922 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6911 (mtp85) REVERT: B 73 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8084 (ttp80) REVERT: B 189 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6723 (m-80) REVERT: C 587 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8533 (mtpp) REVERT: C 661 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8916 (p) REVERT: C 690 LEU cc_start: 0.9569 (tp) cc_final: 0.9310 (tt) REVERT: C 717 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8731 (pp) REVERT: C 871 MET cc_start: 0.8369 (mmp) cc_final: 0.7819 (mmp) REVERT: C 911 MET cc_start: 0.8780 (mtp) cc_final: 0.8564 (mtt) REVERT: C 922 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7136 (mtp85) REVERT: D 1 MET cc_start: 0.7057 (tpp) cc_final: 0.5955 (tpp) REVERT: D 127 LYS cc_start: 0.9028 (tppt) cc_final: 0.8705 (mmtm) REVERT: D 189 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6947 (m-80) outliers start: 66 outliers final: 47 residues processed: 226 average time/residue: 0.1295 time to fit residues: 44.3982 Evaluate side-chains 229 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 681 PHE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 817 HIS 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 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 248 THR Chi-restraints excluded: chain B residue 290 VAL 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 526 GLU Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 590 GLU Chi-restraints excluded: chain C residue 617 GLU 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 717 LEU 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 880 MET 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 65 ASN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 153 CYS 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 290 VAL 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: chunk 169 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 62 optimal weight: 0.0770 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** C 534 HIS ** 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 = 0.3858 r_free = 0.3858 target = 0.111039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082857 restraints weight = 49047.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084702 restraints weight = 29075.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.085813 restraints weight = 21492.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.086481 restraints weight = 18070.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086722 restraints weight = 16403.605| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17664 Z= 0.140 Angle : 0.695 12.077 24448 Z= 0.366 Chirality : 0.042 0.302 2672 Planarity : 0.005 0.083 2682 Dihedral : 23.460 156.840 3446 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.49 % Allowed : 26.40 % 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: -0.92 (0.20), residues: 1776 helix: 0.65 (0.23), residues: 546 sheet: -0.42 (0.28), residues: 372 loop : -1.54 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 778 TYR 0.026 0.002 TYR A 933 PHE 0.012 0.001 PHE A 681 TRP 0.013 0.001 TRP C 915 HIS 0.006 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00311 (17658) covalent geometry : angle 0.69487 (24448) hydrogen bonds : bond 0.03371 ( 754) hydrogen bonds : angle 4.63312 ( 2034) metal coordination : bond 0.00245 ( 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 248 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 193 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 MET cc_start: 0.7956 (mmm) cc_final: 0.7674 (mmt) REVERT: A 661 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8869 (p) REVERT: A 681 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8718 (m-10) REVERT: A 717 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8670 (pp) REVERT: A 829 ILE cc_start: 0.8737 (mt) cc_final: 0.8476 (mt) REVERT: A 870 ARG cc_start: 0.7186 (ptt180) cc_final: 0.6799 (ptt180) REVERT: A 922 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.6935 (mtp85) REVERT: B 69 LEU cc_start: 0.8968 (tp) cc_final: 0.8580 (tp) REVERT: B 73 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7999 (ttp80) REVERT: B 189 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6614 (m-80) REVERT: C 587 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8639 (mtpp) REVERT: C 661 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8877 (p) REVERT: C 690 LEU cc_start: 0.9520 (tp) cc_final: 0.9232 (tt) REVERT: C 717 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8596 (pp) REVERT: C 825 GLU cc_start: 0.8025 (tp30) cc_final: 0.7682 (tp30) REVERT: C 871 MET cc_start: 0.8345 (mmp) cc_final: 0.7792 (mmp) REVERT: C 911 MET cc_start: 0.8726 (mtp) cc_final: 0.8519 (mtt) REVERT: C 922 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7052 (mtp85) REVERT: C 992 ARG cc_start: 0.7967 (tpp80) cc_final: 0.7634 (tpp80) REVERT: C 1025 MET cc_start: 0.7331 (ttm) cc_final: 0.6992 (ttm) REVERT: D 108 MET cc_start: 0.8251 (ppp) cc_final: 0.7906 (ppp) REVERT: D 227 ASP cc_start: 0.7943 (t0) cc_final: 0.7722 (t0) outliers start: 55 outliers final: 37 residues processed: 229 average time/residue: 0.1300 time to fit residues: 45.4681 Evaluate side-chains 232 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 717 LEU Chi-restraints excluded: chain A residue 748 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 65 ASN 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 248 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 311 ILE 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 662 ILE Chi-restraints excluded: chain C residue 717 LEU 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 880 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 892 VAL 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 3 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 140 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 179 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.111050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083021 restraints weight = 49065.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084903 restraints weight = 29021.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.086042 restraints weight = 21322.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086702 restraints weight = 17850.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.087012 restraints weight = 16147.598| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 17664 Z= 0.237 Angle : 0.865 59.195 24448 Z= 0.497 Chirality : 0.044 0.638 2672 Planarity : 0.005 0.078 2682 Dihedral : 23.463 156.828 3446 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.36 % Allowed : 26.78 % Favored : 69.86 % Cbeta Deviations : 0.06 % 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: -0.92 (0.20), residues: 1776 helix: 0.66 (0.23), residues: 546 sheet: -0.42 (0.28), residues: 372 loop : -1.55 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 849 TYR 0.022 0.001 TYR A 933 PHE 0.012 0.001 PHE A 681 TRP 0.013 0.001 TRP C 915 HIS 0.008 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00491 (17658) covalent geometry : angle 0.86495 (24448) hydrogen bonds : bond 0.03382 ( 754) hydrogen bonds : angle 4.63843 ( 2034) metal coordination : bond 0.00288 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2793.74 seconds wall clock time: 49 minutes 9.82 seconds (2949.82 seconds total)