Starting phenix.real_space_refine on Sat Sep 12 15:31:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbo_7846/09_2026/6dbo_7846_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbo_7846/09_2026/6dbo_7846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dbo_7846/09_2026/6dbo_7846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbo_7846/09_2026/6dbo_7846.map" model { file = "/net/cci-nas-00/data/ceres_data/6dbo_7846/09_2026/6dbo_7846_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbo_7846/09_2026/6dbo_7846_neut.cif" } resolution = 4.4 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 128 5.49 5 S 106 5.16 5 C 10178 2.51 5 N 2970 2.21 5 O 3432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16820 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4381 Classifications: {'peptide': 542} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 517} 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: 4381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4381 Classifications: {'peptide': 542} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 517} 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: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 654 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 658 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "G" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 654 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "H" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 658 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} 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 2053 SG CYS A 749 63.024 58.922 98.484 1.00128.59 S ATOM 2074 SG CYS A 752 61.101 58.576 101.316 1.00191.14 S ATOM 9148 SG CYS C 749 57.602 77.984 20.282 1.00123.25 S ATOM 9169 SG CYS C 752 55.168 79.056 17.849 1.00185.95 S Time building chain proxies: 3.49, per 1000 atoms: 0.21 Number of scatterers: 16820 At special positions: 0 Unit cell: (121.324, 143.608, 118.848, 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 128 15.00 O 3432 8.00 N 2970 7.00 C 10178 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: 1.43 Conformation dependent library (CDL) restraints added in 647.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " 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 752 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " Number of angles added : 4 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 34.5% alpha, 24.5% beta 56 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 577 through 589 Processing helix chain 'A' and resid 589 through 600 Processing helix chain 'A' and resid 686 through 705 removed outlier: 3.574A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix removed outlier: 3.534A pdb=" N MET A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 757 through 762 removed outlier: 3.590A pdb=" N GLN A 761 " --> pdb=" O ALA A 757 " (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 814 through 835 removed outlier: 3.803A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 862 removed outlier: 3.555A pdb=" N ARG A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 890 removed outlier: 3.688A pdb=" N VAL A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 917 Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 930 Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 955 through 964 Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.686A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1018 removed outlier: 4.230A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1027 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 519 through 527 removed outlier: 4.018A pdb=" N LYS C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 589 through 600 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.509A pdb=" N SER C 673 " --> pdb=" O SER C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.563A 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 738 Processing helix chain 'C' and resid 757 through 762 removed outlier: 3.628A pdb=" N GLN C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 757 through 762' Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 814 through 835 removed outlier: 3.969A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 862 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 889 removed outlier: 3.710A pdb=" N VAL C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 917 Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.637A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 4.265A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.733A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.733A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N MET A 647 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLN A 664 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 649 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.679A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N LEU B 55 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 345 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA B 8 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N TYR B 343 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.214A pdb=" N LEU B 106 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA7, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AA8, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AA9, first strand: chain 'B' and resid 277 through 279 Processing sheet with id=AB1, first strand: chain 'C' and resid 536 through 539 removed outlier: 3.524A pdb=" N PHE C 611 " --> pdb=" O SER C 719 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU C 617 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR C 727 " --> pdb=" O GLU C 617 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N CYS C 619 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU C 677 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 536 through 539 removed outlier: 3.524A pdb=" N PHE C 611 " --> pdb=" O SER C 719 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU C 617 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR C 727 " --> pdb=" O GLU C 617 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N CYS C 619 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N MET C 647 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLN C 664 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE C 649 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.689A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.060A pdb=" N LEU D 106 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB6, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB7, first strand: chain 'D' and resid 209 through 212 removed outlier: 3.573A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 263 through 265 Processing sheet with id=AB9, first strand: chain 'D' and resid 277 through 279 666 hydrogen bonds defined for protein. 1869 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 268 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 3.95 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3784 1.33 - 1.46: 5162 1.46 - 1.58: 8092 1.58 - 1.71: 250 1.71 - 1.84: 158 Bond restraints: 17446 Sorted by residual: bond pdb=" CA VAL A 965 " pdb=" CB VAL A 965 " ideal model delta sigma weight residual 1.539 1.569 -0.030 5.40e-03 3.43e+04 3.00e+01 bond pdb=" CA VAL C 965 " pdb=" CB VAL C 965 " ideal model delta sigma weight residual 1.539 1.567 -0.028 5.40e-03 3.43e+04 2.62e+01 bond pdb=" C1' DT H 9 " pdb=" N1 DT H 9 " ideal model delta sigma weight residual 1.468 1.539 -0.071 1.40e-02 5.10e+03 2.59e+01 bond pdb=" C1' DT F 9 " pdb=" N1 DT F 9 " ideal model delta sigma weight residual 1.468 1.537 -0.069 1.40e-02 5.10e+03 2.45e+01 bond pdb=" CA PRO D 70 " pdb=" C PRO D 70 " ideal model delta sigma weight residual 1.517 1.549 -0.032 6.70e-03 2.23e+04 2.33e+01 ... (remaining 17441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 22924 2.83 - 5.66: 1064 5.66 - 8.49: 111 8.49 - 11.32: 25 11.32 - 14.15: 6 Bond angle restraints: 24130 Sorted by residual: angle pdb=" C GLY A 512 " pdb=" N ARG A 513 " pdb=" CA ARG A 513 " ideal model delta sigma weight residual 121.70 132.72 -11.02 1.80e+00 3.09e-01 3.75e+01 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 127.00 141.15 -14.15 2.40e+00 1.74e-01 3.48e+01 angle pdb=" C GLY C 512 " pdb=" N ARG C 513 " pdb=" CA ARG C 513 " ideal model delta sigma weight residual 121.70 132.31 -10.61 1.80e+00 3.09e-01 3.47e+01 angle pdb=" O4' DG E 21 " pdb=" C1' DG E 21 " pdb=" N9 DG E 21 " ideal model delta sigma weight residual 108.00 112.11 -4.11 7.00e-01 2.04e+00 3.44e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CA PRO D 340 " ideal model delta sigma weight residual 127.00 140.80 -13.80 2.40e+00 1.74e-01 3.31e+01 ... (remaining 24125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.91: 8437 21.91 - 43.82: 1161 43.82 - 65.73: 537 65.73 - 87.64: 46 87.64 - 109.55: 3 Dihedral angle restraints: 10184 sinusoidal: 5014 harmonic: 5170 Sorted by residual: dihedral pdb=" CA ALA D 76 " pdb=" C ALA D 76 " pdb=" N ILE D 77 " pdb=" CA ILE D 77 " ideal model delta harmonic sigma weight residual -180.00 -150.75 -29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ALA A 509 " pdb=" C ALA A 509 " pdb=" N THR A 510 " pdb=" CA THR A 510 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLU A 617 " pdb=" C GLU A 617 " pdb=" N SER A 618 " pdb=" CA SER A 618 " ideal model delta harmonic sigma weight residual -180.00 -151.20 -28.80 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 10181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1788 0.064 - 0.128: 684 0.128 - 0.191: 139 0.191 - 0.255: 25 0.255 - 0.319: 4 Chirality restraints: 2640 Sorted by residual: chirality pdb=" CB VAL C 562 " pdb=" CA VAL C 562 " pdb=" CG1 VAL C 562 " pdb=" CG2 VAL C 562 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB VAL A 562 " pdb=" CA VAL A 562 " pdb=" CG1 VAL A 562 " pdb=" CG2 VAL A 562 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CG LEU A 653 " pdb=" CB LEU A 653 " pdb=" CD1 LEU A 653 " pdb=" CD2 LEU A 653 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2637 not shown) Planarity restraints: 2670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C1007 " -0.025 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C GLU C1007 " 0.087 2.00e-02 2.50e+03 pdb=" O GLU C1007 " -0.033 2.00e-02 2.50e+03 pdb=" N ASP C1008 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 713 " 0.024 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C VAL C 713 " -0.086 2.00e-02 2.50e+03 pdb=" O VAL C 713 " 0.033 2.00e-02 2.50e+03 pdb=" N GLY C 714 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 713 " -0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C VAL A 713 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL A 713 " -0.032 2.00e-02 2.50e+03 pdb=" N GLY A 714 " -0.029 2.00e-02 2.50e+03 ... (remaining 2667 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 158 2.48 - 3.08: 11500 3.08 - 3.69: 27296 3.69 - 4.29: 37822 4.29 - 4.90: 59597 Nonbonded interactions: 136373 Sorted by model distance: nonbonded pdb=" OE2 GLU A 617 " pdb=" NH1 ARG A 701 " model vdw 1.874 3.120 nonbonded pdb=" NH1 ARG A 860 " pdb=" C LYS A 864 " model vdw 1.951 3.350 nonbonded pdb=" OD2 ASP A 566 " pdb=" OH TYR B 138 " model vdw 1.964 3.040 nonbonded pdb=" O ILE C 975 " pdb=" N ALA C 977 " model vdw 1.990 3.120 nonbonded pdb=" O ARG C 783 " pdb=" OG SER D 67 " model vdw 2.006 3.040 ... (remaining 136368 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: 0.530 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.290 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.010 0.296 17454 Z= 0.579 Angle : 1.381 16.925 24134 Z= 0.837 Chirality : 0.068 0.319 2640 Planarity : 0.010 0.076 2670 Dihedral : 22.321 109.545 6856 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 25.37 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.82 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 26.24 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -4.15 (0.15), residues: 1774 helix: -2.79 (0.16), residues: 560 sheet: -2.10 (0.24), residues: 330 loop : -2.99 (0.15), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG C 577 TYR 0.043 0.005 TYR A 747 PHE 0.066 0.005 PHE C 576 TRP 0.036 0.004 TRP A 549 HIS 0.019 0.005 HIS C 964 Details of bonding type rmsd/Z covalent geometry : bond 0.00909 / 0.57 (17446) covalent geometry : angle 1.37369 / 0.84 (24130) hydrogen bonds : bond 0.15539 / 9.99 ( 763) hydrogen bonds : angle 7.69615 / 5.29 ( 2137) metal coordination : bond 0.16481 / 11.34 ( 8) metal coordination : angle 11.47429 / 5.53 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.692 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 GLN cc_start: 0.8454 (mt0) cc_final: 0.8042 (mt0) REVERT: A 594 MET cc_start: 0.9268 (mmm) cc_final: 0.8884 (mmm) REVERT: A 727 THR cc_start: 0.9328 (p) cc_final: 0.8944 (t) REVERT: A 738 GLU cc_start: 0.8356 (tp30) cc_final: 0.8109 (tp30) REVERT: A 743 SER cc_start: 0.8708 (t) cc_final: 0.8365 (p) REVERT: A 808 GLU cc_start: 0.9340 (tt0) cc_final: 0.8527 (tm-30) REVERT: A 905 MET cc_start: 0.9247 (tpp) cc_final: 0.8813 (mmm) REVERT: A 918 THR cc_start: 0.8973 (m) cc_final: 0.8744 (p) REVERT: A 1025 MET cc_start: 0.8302 (tpp) cc_final: 0.7928 (tpp) REVERT: B 185 ILE cc_start: 0.9404 (mt) cc_final: 0.9201 (tp) REVERT: C 499 GLN cc_start: 0.8237 (mt0) cc_final: 0.7816 (mp10) REVERT: C 733 MET cc_start: 0.8840 (ttm) cc_final: 0.8463 (tpp) REVERT: C 743 SER cc_start: 0.8697 (t) cc_final: 0.8494 (t) REVERT: C 782 TRP cc_start: 0.8801 (t-100) cc_final: 0.8336 (t-100) REVERT: C 794 LEU cc_start: 0.9599 (tp) cc_final: 0.8958 (tp) REVERT: C 808 GLU cc_start: 0.9340 (tt0) cc_final: 0.8825 (tm-30) REVERT: C 922 ARG cc_start: 0.9105 (ttp-170) cc_final: 0.8789 (ptm-80) REVERT: C 941 LEU cc_start: 0.9322 (tp) cc_final: 0.9007 (pp) REVERT: C 1006 LEU cc_start: 0.8486 (mt) cc_final: 0.8102 (mm) REVERT: C 1016 TYR cc_start: 0.8187 (t80) cc_final: 0.7707 (t80) REVERT: C 1024 PHE cc_start: 0.8945 (m-10) cc_final: 0.8699 (m-10) REVERT: D 185 ILE cc_start: 0.9505 (mt) cc_final: 0.9220 (tp) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.1489 time to fit residues: 82.3252 Evaluate side-chains 191 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 HIS ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 ASN A1013 HIS B 16 GLN ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN B 204 GLN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS C 492 ASN C 501 HIS C 514 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 ASN C1013 HIS ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 GLN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 213 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.058501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.042899 restraints weight = 93588.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.044404 restraints weight = 54027.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045441 restraints weight = 38036.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.046129 restraints weight = 30121.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.046551 restraints weight = 25860.894| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17454 Z= 0.218 Angle : 0.908 14.222 24134 Z= 0.487 Chirality : 0.051 0.232 2640 Planarity : 0.007 0.080 2670 Dihedral : 24.084 98.497 3364 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.38 % Allowed : 4.07 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -2.40 (0.17), residues: 1774 helix: -0.92 (0.20), residues: 556 sheet: -1.21 (0.26), residues: 332 loop : -2.19 (0.17), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 795 TYR 0.028 0.003 TYR C1020 PHE 0.018 0.002 PHE C 990 TRP 0.016 0.002 TRP D 317 HIS 0.014 0.002 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.22 (17446) covalent geometry : angle 0.90613 / 0.49 (24130) hydrogen bonds : bond 0.06807 / 4.57 ( 763) hydrogen bonds : angle 5.82021 / 4.00 ( 2137) metal coordination : bond 0.02396 / 1.71 ( 8) metal coordination : angle 4.08684 / 1.87 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 292 time to evaluate : 0.588 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: symmetry clash REVERT: A 486 CYS cc_start: 0.9291 (t) cc_final: 0.9073 (p) REVERT: A 522 LEU cc_start: 0.9678 (mp) cc_final: 0.9217 (mm) REVERT: A 575 ARG cc_start: 0.9148 (ptt90) cc_final: 0.8534 (ptm160) REVERT: A 598 ARG cc_start: 0.8802 (ppt170) cc_final: 0.8568 (ttp80) REVERT: A 666 GLN cc_start: 0.9142 (pm20) cc_final: 0.8877 (pm20) REVERT: A 700 GLU cc_start: 0.9021 (tt0) cc_final: 0.8622 (tm-30) REVERT: A 704 MET cc_start: 0.8687 (ptm) cc_final: 0.7824 (ptm) REVERT: A 727 THR cc_start: 0.9388 (p) cc_final: 0.9097 (t) REVERT: A 807 MET cc_start: 0.8745 (tpt) cc_final: 0.8496 (tpp) REVERT: A 912 LYS cc_start: 0.9545 (tmtt) cc_final: 0.9242 (tptt) REVERT: A 1016 TYR cc_start: 0.9362 (t80) cc_final: 0.8817 (t80) REVERT: A 1018 SER cc_start: 0.9435 (m) cc_final: 0.9031 (t) REVERT: B 56 LYS cc_start: 0.9116 (mmpt) cc_final: 0.8865 (tttp) REVERT: B 109 LEU cc_start: 0.9020 (tp) cc_final: 0.8749 (tp) REVERT: B 146 ASN cc_start: 0.8907 (p0) cc_final: 0.8707 (t0) REVERT: B 274 PHE cc_start: 0.8362 (m-10) cc_final: 0.7938 (m-10) REVERT: B 277 TYR cc_start: 0.8473 (m-80) cc_final: 0.8122 (m-10) REVERT: C 481 LEU cc_start: 0.8759 (pp) cc_final: 0.8276 (pp) REVERT: C 486 CYS cc_start: 0.8708 (p) cc_final: 0.8478 (p) REVERT: C 519 LEU cc_start: 0.9631 (mt) cc_final: 0.9404 (tp) REVERT: C 555 ASP cc_start: 0.9137 (p0) cc_final: 0.8905 (p0) REVERT: C 677 LEU cc_start: 0.9606 (tt) cc_final: 0.8063 (tp) REVERT: C 782 TRP cc_start: 0.9384 (t-100) cc_final: 0.8739 (t-100) REVERT: C 794 LEU cc_start: 0.9504 (tp) cc_final: 0.8849 (tp) REVERT: C 847 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9124 (mp0) REVERT: C 863 MET cc_start: 0.6308 (mtm) cc_final: 0.5989 (mtm) REVERT: C 922 ARG cc_start: 0.8903 (ttp-110) cc_final: 0.8545 (ptm-80) REVERT: C 941 LEU cc_start: 0.9240 (tp) cc_final: 0.8904 (pp) REVERT: C 945 MET cc_start: 0.8960 (tpt) cc_final: 0.8599 (tpp) REVERT: C 967 GLU cc_start: 0.9143 (mp0) cc_final: 0.8722 (pm20) REVERT: C 1010 LEU cc_start: 0.9692 (tp) cc_final: 0.9434 (tp) REVERT: C 1016 TYR cc_start: 0.9317 (t80) cc_final: 0.9000 (t80) REVERT: C 1018 SER cc_start: 0.9645 (m) cc_final: 0.9396 (t) REVERT: D 142 LEU cc_start: 0.9303 (tp) cc_final: 0.9087 (tp) REVERT: D 146 ASN cc_start: 0.9482 (p0) cc_final: 0.8849 (t0) REVERT: D 277 TYR cc_start: 0.8414 (m-80) cc_final: 0.7730 (m-80) outliers start: 6 outliers final: 3 residues processed: 298 average time/residue: 0.1488 time to fit residues: 64.7467 Evaluate side-chains 184 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 84 optimal weight: 8.9990 chunk 182 optimal weight: 50.0000 chunk 66 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 178 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS C 858 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 99 ASN D 213 GLN D 222 HIS ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.055950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.040952 restraints weight = 96069.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.042322 restraints weight = 56919.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.043271 restraints weight = 40448.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.043931 restraints weight = 32283.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.044340 restraints weight = 27706.649| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17454 Z= 0.275 Angle : 0.871 12.896 24134 Z= 0.467 Chirality : 0.049 0.221 2640 Planarity : 0.006 0.077 2670 Dihedral : 23.838 98.303 3364 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.13 % Allowed : 5.53 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -1.86 (0.18), residues: 1774 helix: -0.56 (0.20), residues: 570 sheet: -0.79 (0.28), residues: 332 loop : -1.85 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 523 TYR 0.019 0.002 TYR C 578 PHE 0.021 0.002 PHE C 611 TRP 0.011 0.002 TRP A1014 HIS 0.008 0.002 HIS B 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.27 (17446) covalent geometry : angle 0.86753 / 0.47 (24130) hydrogen bonds : bond 0.06646 / 4.45 ( 763) hydrogen bonds : angle 5.58510 / 3.84 ( 2137) metal coordination : bond 0.03451 / 2.50 ( 8) metal coordination : angle 5.74425 / 3.16 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 0.628 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: symmetry clash REVERT: A 486 CYS cc_start: 0.9160 (t) cc_final: 0.8876 (p) REVERT: A 522 LEU cc_start: 0.9673 (mp) cc_final: 0.9309 (mp) REVERT: A 530 LEU cc_start: 0.9650 (mm) cc_final: 0.9227 (pp) REVERT: A 578 TYR cc_start: 0.8261 (t80) cc_final: 0.7629 (t80) REVERT: A 704 MET cc_start: 0.8444 (ptm) cc_final: 0.7834 (ptt) REVERT: A 807 MET cc_start: 0.8968 (tpt) cc_final: 0.8591 (tpp) REVERT: A 912 LYS cc_start: 0.9507 (tmtt) cc_final: 0.9277 (tptt) REVERT: A 1016 TYR cc_start: 0.9197 (t80) cc_final: 0.8868 (t80) REVERT: A 1018 SER cc_start: 0.9598 (m) cc_final: 0.9227 (t) REVERT: B 24 LEU cc_start: 0.9538 (mt) cc_final: 0.9224 (mt) REVERT: B 56 LYS cc_start: 0.9148 (mmpt) cc_final: 0.8903 (tttp) REVERT: B 109 LEU cc_start: 0.9035 (tp) cc_final: 0.8691 (tp) REVERT: B 142 LEU cc_start: 0.9340 (tp) cc_final: 0.9092 (tp) REVERT: B 146 ASN cc_start: 0.8941 (p0) cc_final: 0.8525 (t0) REVERT: B 155 LEU cc_start: 0.9699 (tp) cc_final: 0.9200 (mm) REVERT: B 271 TYR cc_start: 0.9079 (m-80) cc_final: 0.8777 (m-80) REVERT: B 274 PHE cc_start: 0.8529 (m-10) cc_final: 0.8191 (m-10) REVERT: C 499 GLN cc_start: 0.9348 (mt0) cc_final: 0.9001 (mt0) REVERT: C 530 LEU cc_start: 0.9534 (mm) cc_final: 0.9201 (pp) REVERT: C 737 MET cc_start: 0.9408 (tpp) cc_final: 0.9019 (tpp) REVERT: C 738 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8732 (mm-30) REVERT: C 794 LEU cc_start: 0.9515 (tp) cc_final: 0.8965 (mt) REVERT: C 847 GLU cc_start: 0.9271 (mt-10) cc_final: 0.9031 (mp0) REVERT: C 922 ARG cc_start: 0.8854 (ttp-110) cc_final: 0.8560 (ptm-80) REVERT: C 941 LEU cc_start: 0.9302 (tp) cc_final: 0.8944 (pp) REVERT: C 945 MET cc_start: 0.9099 (tpt) cc_final: 0.8674 (tpp) REVERT: C 967 GLU cc_start: 0.9151 (mp0) cc_final: 0.8810 (mp0) REVERT: C 1010 LEU cc_start: 0.9739 (tp) cc_final: 0.9534 (tp) REVERT: C 1016 TYR cc_start: 0.9242 (t80) cc_final: 0.8206 (t80) REVERT: C 1018 SER cc_start: 0.9634 (m) cc_final: 0.9372 (t) REVERT: D 33 GLN cc_start: 0.8551 (pt0) cc_final: 0.8310 (pm20) REVERT: D 109 LEU cc_start: 0.9122 (tp) cc_final: 0.8795 (tp) REVERT: D 142 LEU cc_start: 0.9249 (tp) cc_final: 0.8994 (tp) REVERT: D 285 MET cc_start: 0.8746 (mmp) cc_final: 0.8198 (tpp) outliers start: 2 outliers final: 1 residues processed: 236 average time/residue: 0.1301 time to fit residues: 47.1038 Evaluate side-chains 165 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 141 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 165 optimal weight: 30.0000 chunk 161 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS C 514 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 213 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.057454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.042149 restraints weight = 93657.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.043575 restraints weight = 55511.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.044573 restraints weight = 39365.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.045223 restraints weight = 31235.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.045708 restraints weight = 26808.353| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17454 Z= 0.201 Angle : 0.803 12.068 24134 Z= 0.431 Chirality : 0.049 0.212 2640 Planarity : 0.005 0.096 2670 Dihedral : 23.710 99.875 3364 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.19 % Allowed : 3.56 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -1.53 (0.18), residues: 1774 helix: -0.17 (0.20), residues: 572 sheet: -0.63 (0.28), residues: 338 loop : -1.75 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 600 TYR 0.019 0.002 TYR C1020 PHE 0.022 0.002 PHE A 681 TRP 0.016 0.002 TRP C 560 HIS 0.012 0.002 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 (17446) covalent geometry : angle 0.79878 / 0.43 (24130) hydrogen bonds : bond 0.05980 / 4.03 ( 763) hydrogen bonds : angle 5.29722 / 3.65 ( 2137) metal coordination : bond 0.01953 / 1.33 ( 8) metal coordination : angle 6.07290 / 2.96 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 220 time to evaluate : 0.636 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 522 LEU cc_start: 0.9673 (mp) cc_final: 0.9308 (mp) REVERT: A 530 LEU cc_start: 0.9638 (mm) cc_final: 0.9189 (pp) REVERT: A 622 MET cc_start: 0.8136 (mtt) cc_final: 0.7672 (mtt) REVERT: A 705 MET cc_start: 0.8875 (mpp) cc_final: 0.8602 (mpp) REVERT: A 738 GLU cc_start: 0.8752 (tp30) cc_final: 0.8405 (tp30) REVERT: A 794 LEU cc_start: 0.9232 (mt) cc_final: 0.8871 (mt) REVERT: A 825 GLU cc_start: 0.9365 (tp30) cc_final: 0.9158 (tp30) REVERT: A 905 MET cc_start: 0.9329 (tpt) cc_final: 0.8603 (tpt) REVERT: A 912 LYS cc_start: 0.9477 (tmtt) cc_final: 0.9119 (tptp) REVERT: B 24 LEU cc_start: 0.9434 (mt) cc_final: 0.9214 (tp) REVERT: B 56 LYS cc_start: 0.9137 (mmpt) cc_final: 0.8896 (tttm) REVERT: B 79 HIS cc_start: 0.8788 (OUTLIER) cc_final: 0.8496 (t-90) REVERT: B 109 LEU cc_start: 0.8943 (tp) cc_final: 0.8409 (pp) REVERT: B 146 ASN cc_start: 0.8992 (p0) cc_final: 0.8513 (t0) REVERT: B 271 TYR cc_start: 0.9004 (m-80) cc_final: 0.8738 (m-80) REVERT: B 274 PHE cc_start: 0.8523 (m-10) cc_final: 0.8168 (m-10) REVERT: B 277 TYR cc_start: 0.8420 (m-80) cc_final: 0.7874 (m-80) REVERT: C 530 LEU cc_start: 0.9508 (mm) cc_final: 0.9138 (pp) REVERT: C 622 MET cc_start: 0.8571 (mtt) cc_final: 0.8341 (mtt) REVERT: C 700 GLU cc_start: 0.8588 (pt0) cc_final: 0.7852 (pt0) REVERT: C 737 MET cc_start: 0.9406 (tpp) cc_final: 0.8586 (tpp) REVERT: C 738 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8319 (tp30) REVERT: C 782 TRP cc_start: 0.9337 (t-100) cc_final: 0.8945 (t-100) REVERT: C 922 ARG cc_start: 0.8797 (ttp-110) cc_final: 0.8462 (ptm-80) REVERT: C 941 LEU cc_start: 0.9258 (tp) cc_final: 0.8910 (pp) REVERT: C 945 MET cc_start: 0.8982 (tpt) cc_final: 0.8523 (tpp) REVERT: C 967 GLU cc_start: 0.9122 (mp0) cc_final: 0.8763 (mp0) REVERT: C 1008 ASP cc_start: 0.8905 (m-30) cc_final: 0.8691 (m-30) REVERT: C 1010 LEU cc_start: 0.9728 (tp) cc_final: 0.9501 (tp) REVERT: C 1016 TYR cc_start: 0.8915 (t80) cc_final: 0.8612 (t80) REVERT: C 1018 SER cc_start: 0.9637 (m) cc_final: 0.9331 (t) REVERT: D 33 GLN cc_start: 0.8500 (pt0) cc_final: 0.8271 (pm20) REVERT: D 142 LEU cc_start: 0.9269 (tp) cc_final: 0.9015 (tp) REVERT: D 236 LEU cc_start: 0.9497 (pp) cc_final: 0.9084 (mp) REVERT: D 285 MET cc_start: 0.8680 (mmp) cc_final: 0.8024 (tpp) outliers start: 3 outliers final: 1 residues processed: 223 average time/residue: 0.1390 time to fit residues: 47.2427 Evaluate side-chains 158 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 90 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 185 optimal weight: 50.0000 chunk 27 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN D 99 ASN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.056924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.041397 restraints weight = 97769.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.042758 restraints weight = 60368.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.043693 restraints weight = 44145.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.044303 restraints weight = 35921.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.044678 restraints weight = 31381.224| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17454 Z= 0.224 Angle : 0.782 11.244 24134 Z= 0.424 Chirality : 0.047 0.215 2640 Planarity : 0.006 0.101 2670 Dihedral : 23.625 100.515 3364 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -1.43 (0.19), residues: 1774 helix: -0.17 (0.20), residues: 578 sheet: -0.49 (0.28), residues: 338 loop : -1.67 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 600 TYR 0.016 0.002 TYR C1020 PHE 0.034 0.002 PHE C 724 TRP 0.029 0.002 TRP A 560 HIS 0.011 0.002 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.22 (17446) covalent geometry : angle 0.78033 / 0.42 (24130) hydrogen bonds : bond 0.05886 / 3.94 ( 763) hydrogen bonds : angle 5.21749 / 3.60 ( 2137) metal coordination : bond 0.02330 / 1.38 ( 8) metal coordination : angle 4.40462 / 1.97 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.621 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 522 LEU cc_start: 0.9496 (mp) cc_final: 0.9263 (mp) REVERT: A 530 LEU cc_start: 0.9659 (mm) cc_final: 0.9243 (pp) REVERT: A 622 MET cc_start: 0.7841 (mtt) cc_final: 0.7589 (mtt) REVERT: A 737 MET cc_start: 0.9095 (ttm) cc_final: 0.8872 (ttm) REVERT: A 738 GLU cc_start: 0.8718 (tp30) cc_final: 0.8360 (tp30) REVERT: A 782 TRP cc_start: 0.9232 (t-100) cc_final: 0.9013 (t-100) REVERT: A 1016 TYR cc_start: 0.9117 (t80) cc_final: 0.8883 (t80) REVERT: B 56 LYS cc_start: 0.9140 (mmpt) cc_final: 0.8852 (tttp) REVERT: B 69 LEU cc_start: 0.9234 (tp) cc_final: 0.9032 (tp) REVERT: B 109 LEU cc_start: 0.9008 (tp) cc_final: 0.8461 (pp) REVERT: B 146 ASN cc_start: 0.9020 (p0) cc_final: 0.8475 (t0) REVERT: B 271 TYR cc_start: 0.9028 (m-80) cc_final: 0.8802 (m-80) REVERT: B 277 TYR cc_start: 0.8336 (m-80) cc_final: 0.7817 (m-80) REVERT: C 530 LEU cc_start: 0.9562 (mm) cc_final: 0.9194 (pp) REVERT: C 737 MET cc_start: 0.9483 (tpp) cc_final: 0.8769 (tpp) REVERT: C 738 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8308 (tp30) REVERT: C 794 LEU cc_start: 0.9485 (tp) cc_final: 0.9133 (mt) REVERT: C 941 LEU cc_start: 0.9199 (tp) cc_final: 0.8857 (pp) REVERT: C 945 MET cc_start: 0.9025 (tpt) cc_final: 0.8617 (tpp) REVERT: C 967 GLU cc_start: 0.9164 (mp0) cc_final: 0.8824 (mp0) REVERT: C 1018 SER cc_start: 0.9635 (m) cc_final: 0.9389 (t) REVERT: C 1025 MET cc_start: 0.9099 (tpp) cc_final: 0.8894 (tmm) REVERT: D 142 LEU cc_start: 0.9267 (tp) cc_final: 0.9021 (tp) REVERT: D 285 MET cc_start: 0.8772 (mmp) cc_final: 0.8213 (tpp) outliers start: 1 outliers final: 0 residues processed: 210 average time/residue: 0.1364 time to fit residues: 43.6552 Evaluate side-chains 149 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 159 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 185 optimal weight: 50.0000 chunk 129 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 501 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.057663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042188 restraints weight = 96167.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.043550 restraints weight = 59580.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.044495 restraints weight = 43684.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.045111 restraints weight = 35518.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045484 restraints weight = 31052.088| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17454 Z= 0.170 Angle : 0.742 10.533 24134 Z= 0.402 Chirality : 0.047 0.205 2640 Planarity : 0.005 0.053 2670 Dihedral : 23.522 101.729 3364 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.13 % Allowed : 2.41 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -1.24 (0.19), residues: 1774 helix: -0.05 (0.20), residues: 574 sheet: -0.30 (0.28), residues: 338 loop : -1.57 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 701 TYR 0.020 0.002 TYR C 578 PHE 0.012 0.001 PHE A 787 TRP 0.011 0.001 TRP D 317 HIS 0.008 0.001 HIS C 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (17446) covalent geometry : angle 0.74101 / 0.40 (24130) hydrogen bonds : bond 0.05400 / 3.64 ( 763) hydrogen bonds : angle 5.04126 / 3.47 ( 2137) metal coordination : bond 0.02264 / 1.45 ( 8) metal coordination : angle 2.50654 / 1.28 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 0.722 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: symmetry clash revert: symmetry clash REVERT: A 522 LEU cc_start: 0.9588 (mp) cc_final: 0.9224 (mp) REVERT: A 530 LEU cc_start: 0.9607 (mm) cc_final: 0.9207 (pp) REVERT: A 622 MET cc_start: 0.7595 (mtt) cc_final: 0.6695 (mtt) REVERT: A 700 GLU cc_start: 0.9126 (pm20) cc_final: 0.8656 (mp0) REVERT: A 704 MET cc_start: 0.8650 (ptp) cc_final: 0.8402 (ptp) REVERT: A 705 MET cc_start: 0.8916 (mpp) cc_final: 0.8584 (mpp) REVERT: A 733 MET cc_start: 0.9407 (tpp) cc_final: 0.8963 (tpt) REVERT: A 738 GLU cc_start: 0.8694 (tp30) cc_final: 0.8240 (tp30) REVERT: A 825 GLU cc_start: 0.9375 (tp30) cc_final: 0.9159 (tp30) REVERT: A 905 MET cc_start: 0.9227 (tpt) cc_final: 0.8523 (tpt) REVERT: B 56 LYS cc_start: 0.9139 (mmpt) cc_final: 0.8863 (tttp) REVERT: B 109 LEU cc_start: 0.9018 (tp) cc_final: 0.8553 (pp) REVERT: B 146 ASN cc_start: 0.9069 (p0) cc_final: 0.8502 (t0) REVERT: B 271 TYR cc_start: 0.9030 (m-80) cc_final: 0.8814 (m-80) REVERT: B 274 PHE cc_start: 0.8604 (m-80) cc_final: 0.8203 (m-80) REVERT: B 277 TYR cc_start: 0.8419 (m-80) cc_final: 0.7764 (m-80) REVERT: C 530 LEU cc_start: 0.9472 (mm) cc_final: 0.8984 (pp) REVERT: C 737 MET cc_start: 0.9496 (tpp) cc_final: 0.9143 (tpp) REVERT: C 794 LEU cc_start: 0.9547 (tp) cc_final: 0.9046 (mt) REVERT: C 807 MET cc_start: 0.8622 (tpt) cc_final: 0.8387 (tpp) REVERT: C 905 MET cc_start: 0.9200 (tpt) cc_final: 0.8707 (tpt) REVERT: C 941 LEU cc_start: 0.9156 (tp) cc_final: 0.8825 (pp) REVERT: C 945 MET cc_start: 0.9038 (tpt) cc_final: 0.8714 (tpp) REVERT: C 967 GLU cc_start: 0.9146 (mp0) cc_final: 0.8783 (mp0) REVERT: C 1016 TYR cc_start: 0.8932 (t80) cc_final: 0.8530 (t80) REVERT: C 1018 SER cc_start: 0.9648 (m) cc_final: 0.9402 (t) REVERT: D 100 ASN cc_start: 0.8486 (t0) cc_final: 0.8278 (t0) REVERT: D 142 LEU cc_start: 0.9286 (tp) cc_final: 0.9057 (tp) REVERT: D 285 MET cc_start: 0.8819 (mmp) cc_final: 0.8239 (tpp) outliers start: 2 outliers final: 1 residues processed: 222 average time/residue: 0.1315 time to fit residues: 45.3392 Evaluate side-chains 164 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 99 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 180 optimal weight: 50.0000 chunk 159 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 176 optimal weight: 0.0770 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 501 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.056530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.041273 restraints weight = 96995.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.042608 restraints weight = 60383.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.043490 restraints weight = 44333.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044103 restraints weight = 36251.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.044464 restraints weight = 31724.239| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17454 Z= 0.222 Angle : 0.767 10.040 24134 Z= 0.414 Chirality : 0.047 0.239 2640 Planarity : 0.005 0.058 2670 Dihedral : 23.484 102.094 3364 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.06 % Allowed : 1.40 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -1.27 (0.19), residues: 1774 helix: -0.17 (0.20), residues: 582 sheet: -0.26 (0.28), residues: 370 loop : -1.58 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 701 TYR 0.016 0.002 TYR C 931 PHE 0.046 0.002 PHE A 681 TRP 0.014 0.002 TRP A 782 HIS 0.008 0.002 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 (17446) covalent geometry : angle 0.76560 / 0.41 (24130) hydrogen bonds : bond 0.05595 / 3.75 ( 763) hydrogen bonds : angle 5.00503 / 3.45 ( 2137) metal coordination : bond 0.02293 / 1.62 ( 8) metal coordination : angle 3.30263 / 1.80 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.689 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 522 LEU cc_start: 0.9590 (mp) cc_final: 0.9200 (mp) REVERT: A 530 LEU cc_start: 0.9635 (mm) cc_final: 0.9204 (pp) REVERT: A 733 MET cc_start: 0.9513 (tpp) cc_final: 0.8825 (tpp) REVERT: A 738 GLU cc_start: 0.8807 (tp30) cc_final: 0.8370 (tp30) REVERT: A 825 GLU cc_start: 0.9351 (tp30) cc_final: 0.9143 (tp30) REVERT: A 905 MET cc_start: 0.9237 (tpt) cc_final: 0.8564 (tpt) REVERT: A 1016 TYR cc_start: 0.9197 (t80) cc_final: 0.8911 (t80) REVERT: B 56 LYS cc_start: 0.9124 (mmpt) cc_final: 0.8840 (tttp) REVERT: B 69 LEU cc_start: 0.9224 (tp) cc_final: 0.8949 (tp) REVERT: B 109 LEU cc_start: 0.9005 (tp) cc_final: 0.8560 (pp) REVERT: B 146 ASN cc_start: 0.9019 (p0) cc_final: 0.8510 (t0) REVERT: B 274 PHE cc_start: 0.8674 (m-80) cc_final: 0.8110 (m-80) REVERT: B 277 TYR cc_start: 0.8420 (m-80) cc_final: 0.7848 (m-80) REVERT: C 530 LEU cc_start: 0.9506 (mm) cc_final: 0.9042 (pp) REVERT: C 598 ARG cc_start: 0.9308 (ppt170) cc_final: 0.8948 (ttp80) REVERT: C 737 MET cc_start: 0.9582 (tpp) cc_final: 0.9013 (tpp) REVERT: C 738 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8216 (tp30) REVERT: C 794 LEU cc_start: 0.9570 (tp) cc_final: 0.9144 (mt) REVERT: C 871 MET cc_start: 0.8944 (tpp) cc_final: 0.8628 (tpp) REVERT: C 905 MET cc_start: 0.9322 (tpt) cc_final: 0.8895 (tpt) REVERT: C 922 ARG cc_start: 0.8833 (ttp-110) cc_final: 0.8401 (ttp80) REVERT: C 941 LEU cc_start: 0.9191 (tp) cc_final: 0.8849 (pp) REVERT: C 945 MET cc_start: 0.9123 (tpt) cc_final: 0.8701 (tpp) REVERT: C 967 GLU cc_start: 0.9169 (mp0) cc_final: 0.8884 (mp0) REVERT: C 1010 LEU cc_start: 0.9683 (tp) cc_final: 0.9481 (tp) REVERT: C 1016 TYR cc_start: 0.8957 (t80) cc_final: 0.8404 (t80) REVERT: D 142 LEU cc_start: 0.9284 (tp) cc_final: 0.9068 (tp) REVERT: D 285 MET cc_start: 0.8902 (mmp) cc_final: 0.8538 (mmp) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.1302 time to fit residues: 41.9189 Evaluate side-chains 155 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 88 optimal weight: 6.9990 chunk 188 optimal weight: 50.0000 chunk 71 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 180 optimal weight: 50.0000 chunk 78 optimal weight: 10.0000 chunk 75 optimal weight: 0.0670 chunk 149 optimal weight: 10.0000 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 501 HIS C 544 ASN C 858 GLN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.057468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.042119 restraints weight = 97555.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.043473 restraints weight = 60708.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.044403 restraints weight = 44489.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045020 restraints weight = 36267.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045436 restraints weight = 31695.303| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17454 Z= 0.168 Angle : 0.736 10.959 24134 Z= 0.395 Chirality : 0.046 0.213 2640 Planarity : 0.005 0.050 2670 Dihedral : 23.419 103.442 3364 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.13 % Allowed : 1.40 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -1.14 (0.19), residues: 1774 helix: -0.05 (0.20), residues: 582 sheet: -0.20 (0.28), residues: 370 loop : -1.51 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 795 TYR 0.018 0.002 TYR C 578 PHE 0.026 0.002 PHE A 681 TRP 0.036 0.002 TRP A 782 HIS 0.006 0.001 HIS D 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (17446) covalent geometry : angle 0.73458 / 0.40 (24130) hydrogen bonds : bond 0.05176 / 3.48 ( 763) hydrogen bonds : angle 4.89925 / 3.36 ( 2137) metal coordination : bond 0.01392 / 1.05 ( 8) metal coordination : angle 3.43418 / 1.70 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.488 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 522 LEU cc_start: 0.9623 (mp) cc_final: 0.9260 (mp) REVERT: A 530 LEU cc_start: 0.9615 (mm) cc_final: 0.9208 (pp) REVERT: A 705 MET cc_start: 0.8972 (mpp) cc_final: 0.8526 (mpp) REVERT: A 738 GLU cc_start: 0.8679 (tp30) cc_final: 0.8218 (tp30) REVERT: A 794 LEU cc_start: 0.9443 (pp) cc_final: 0.9076 (pp) REVERT: A 825 GLU cc_start: 0.9256 (tp30) cc_final: 0.9004 (tp30) REVERT: A 905 MET cc_start: 0.9189 (tpt) cc_final: 0.8491 (tpt) REVERT: A 1025 MET cc_start: 0.9049 (tpp) cc_final: 0.8826 (tpp) REVERT: B 56 LYS cc_start: 0.9183 (mmpt) cc_final: 0.8779 (tttp) REVERT: B 100 ASN cc_start: 0.8565 (t0) cc_final: 0.8365 (t0) REVERT: B 109 LEU cc_start: 0.8977 (tp) cc_final: 0.8558 (pp) REVERT: B 146 ASN cc_start: 0.9308 (p0) cc_final: 0.8372 (t0) REVERT: B 274 PHE cc_start: 0.8471 (m-80) cc_final: 0.8005 (m-80) REVERT: B 277 TYR cc_start: 0.8434 (m-80) cc_final: 0.8012 (m-80) REVERT: C 530 LEU cc_start: 0.9480 (mm) cc_final: 0.9008 (pp) REVERT: C 598 ARG cc_start: 0.9292 (ppt170) cc_final: 0.9002 (ttp80) REVERT: C 737 MET cc_start: 0.9622 (tpp) cc_final: 0.9090 (tpp) REVERT: C 782 TRP cc_start: 0.9200 (t-100) cc_final: 0.8976 (t-100) REVERT: C 871 MET cc_start: 0.8930 (tpp) cc_final: 0.8654 (tpp) REVERT: C 905 MET cc_start: 0.9291 (tpt) cc_final: 0.8849 (tpt) REVERT: C 922 ARG cc_start: 0.8823 (ttp-110) cc_final: 0.8455 (ptm-80) REVERT: C 941 LEU cc_start: 0.9125 (tp) cc_final: 0.8803 (pp) REVERT: C 945 MET cc_start: 0.9077 (tpt) cc_final: 0.8633 (tpp) REVERT: C 967 GLU cc_start: 0.9099 (mp0) cc_final: 0.8771 (mp0) REVERT: C 1016 TYR cc_start: 0.8819 (t80) cc_final: 0.8256 (t80) REVERT: C 1018 SER cc_start: 0.9637 (m) cc_final: 0.9407 (t) REVERT: D 108 MET cc_start: 0.8943 (ppp) cc_final: 0.8738 (ppp) REVERT: D 109 LEU cc_start: 0.9338 (pp) cc_final: 0.9090 (pp) REVERT: D 142 LEU cc_start: 0.9252 (tp) cc_final: 0.9033 (tp) REVERT: D 236 LEU cc_start: 0.9477 (pp) cc_final: 0.9120 (mp) REVERT: D 285 MET cc_start: 0.8850 (mmp) cc_final: 0.8374 (mmp) outliers start: 2 outliers final: 0 residues processed: 219 average time/residue: 0.1207 time to fit residues: 40.9871 Evaluate side-chains 161 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 141 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 chunk 149 optimal weight: 0.4980 chunk 107 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 501 HIS ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** 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 = 0.3328 r_free = 0.3328 target = 0.057827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.042458 restraints weight = 97477.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.043826 restraints weight = 60993.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.044753 restraints weight = 44764.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045322 restraints weight = 36592.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.045761 restraints weight = 32185.118| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17454 Z= 0.160 Angle : 0.738 9.241 24134 Z= 0.397 Chirality : 0.046 0.210 2640 Planarity : 0.005 0.054 2670 Dihedral : 23.340 104.542 3364 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.06 % Allowed : 0.76 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: 1774 helix: 0.03 (0.21), residues: 582 sheet: -0.08 (0.28), residues: 370 loop : -1.51 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 577 TYR 0.023 0.002 TYR B 271 PHE 0.022 0.001 PHE A 681 TRP 0.026 0.002 TRP A 782 HIS 0.008 0.001 HIS C 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (17446) covalent geometry : angle 0.73697 / 0.40 (24130) hydrogen bonds : bond 0.05032 / 3.41 ( 763) hydrogen bonds : angle 4.79612 / 3.28 ( 2137) metal coordination : bond 0.01178 / 0.83 ( 8) metal coordination : angle 3.35302 / 1.66 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.456 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 522 LEU cc_start: 0.9647 (mp) cc_final: 0.9291 (mp) REVERT: A 530 LEU cc_start: 0.9607 (mm) cc_final: 0.9192 (pp) REVERT: A 700 GLU cc_start: 0.9028 (pt0) cc_final: 0.8482 (pt0) REVERT: A 705 MET cc_start: 0.9042 (mpp) cc_final: 0.8722 (mpp) REVERT: A 738 GLU cc_start: 0.8623 (tp30) cc_final: 0.8141 (tp30) REVERT: A 825 GLU cc_start: 0.9282 (tp30) cc_final: 0.9014 (tp30) REVERT: A 905 MET cc_start: 0.9207 (tpt) cc_final: 0.8584 (tpt) REVERT: A 1005 GLU cc_start: 0.9211 (tt0) cc_final: 0.8727 (pt0) REVERT: A 1016 TYR cc_start: 0.9075 (t80) cc_final: 0.8846 (t80) REVERT: A 1025 MET cc_start: 0.9057 (tpp) cc_final: 0.8845 (tpp) REVERT: B 56 LYS cc_start: 0.9206 (mmpt) cc_final: 0.8700 (tttp) REVERT: B 69 LEU cc_start: 0.9164 (tp) cc_final: 0.8757 (tp) REVERT: B 109 LEU cc_start: 0.8977 (tp) cc_final: 0.8595 (pp) REVERT: B 146 ASN cc_start: 0.9303 (p0) cc_final: 0.8332 (t0) REVERT: B 271 TYR cc_start: 0.9115 (m-80) cc_final: 0.8787 (m-80) REVERT: B 274 PHE cc_start: 0.8482 (m-80) cc_final: 0.8023 (m-80) REVERT: B 277 TYR cc_start: 0.8454 (m-80) cc_final: 0.8160 (m-80) REVERT: C 530 LEU cc_start: 0.9538 (mm) cc_final: 0.8963 (pp) REVERT: C 700 GLU cc_start: 0.8980 (pt0) cc_final: 0.8309 (pt0) REVERT: C 733 MET cc_start: 0.9299 (tpp) cc_final: 0.9007 (tpt) REVERT: C 737 MET cc_start: 0.9621 (tpp) cc_final: 0.9197 (tpp) REVERT: C 738 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8556 (mp0) REVERT: C 794 LEU cc_start: 0.9441 (tp) cc_final: 0.9179 (mt) REVERT: C 871 MET cc_start: 0.8900 (tpp) cc_final: 0.8639 (tpp) REVERT: C 905 MET cc_start: 0.9294 (tpt) cc_final: 0.8879 (tpt) REVERT: C 922 ARG cc_start: 0.8817 (ttp-110) cc_final: 0.8453 (ptm-80) REVERT: C 945 MET cc_start: 0.9117 (tpt) cc_final: 0.8778 (tpp) REVERT: C 967 GLU cc_start: 0.9146 (mp0) cc_final: 0.8774 (mp0) REVERT: C 1018 SER cc_start: 0.9626 (m) cc_final: 0.9385 (t) REVERT: D 142 LEU cc_start: 0.9284 (tp) cc_final: 0.9070 (tp) REVERT: D 236 LEU cc_start: 0.9489 (pp) cc_final: 0.9147 (mp) REVERT: D 285 MET cc_start: 0.8901 (mmp) cc_final: 0.8463 (mmp) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1166 time to fit residues: 38.9542 Evaluate side-chains 156 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 117 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 187 optimal weight: 50.0000 chunk 126 optimal weight: 0.5980 chunk 123 optimal weight: 9.9990 chunk 160 optimal weight: 0.5980 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 501 HIS ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** 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 = 0.3318 r_free = 0.3318 target = 0.057359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.042124 restraints weight = 98165.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.043493 restraints weight = 61182.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.044412 restraints weight = 44885.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045018 restraints weight = 36668.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.045392 restraints weight = 32134.848| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17454 Z= 0.173 Angle : 0.738 9.097 24134 Z= 0.397 Chirality : 0.046 0.211 2640 Planarity : 0.005 0.053 2670 Dihedral : 23.294 105.391 3364 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.06 % Allowed : 0.19 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -1.03 (0.19), residues: 1774 helix: 0.07 (0.21), residues: 580 sheet: -0.01 (0.28), residues: 370 loop : -1.54 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 523 TYR 0.020 0.002 TYR B 271 PHE 0.019 0.002 PHE A 681 TRP 0.017 0.001 TRP A 782 HIS 0.008 0.001 HIS C 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (17446) covalent geometry : angle 0.73682 / 0.40 (24130) hydrogen bonds : bond 0.05071 / 3.42 ( 763) hydrogen bonds : angle 4.82794 / 3.29 ( 2137) metal coordination : bond 0.01333 / 0.97 ( 8) metal coordination : angle 3.79530 / 1.92 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.602 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 522 LEU cc_start: 0.9652 (mp) cc_final: 0.9295 (mp) REVERT: A 530 LEU cc_start: 0.9606 (mm) cc_final: 0.9183 (pp) REVERT: A 638 LYS cc_start: 0.9110 (ptpt) cc_final: 0.8849 (ptpp) REVERT: A 700 GLU cc_start: 0.9113 (pt0) cc_final: 0.8718 (pt0) REVERT: A 705 MET cc_start: 0.9060 (mpp) cc_final: 0.8791 (mpp) REVERT: A 738 GLU cc_start: 0.8734 (tp30) cc_final: 0.7524 (tp30) REVERT: A 825 GLU cc_start: 0.9278 (tp30) cc_final: 0.9028 (tp30) REVERT: A 871 MET cc_start: 0.7963 (tpp) cc_final: 0.7455 (tpp) REVERT: A 905 MET cc_start: 0.9211 (tpt) cc_final: 0.8589 (tpt) REVERT: A 1016 TYR cc_start: 0.9120 (t80) cc_final: 0.8812 (t80) REVERT: B 56 LYS cc_start: 0.9211 (mmpt) cc_final: 0.8711 (tttp) REVERT: B 69 LEU cc_start: 0.9219 (tp) cc_final: 0.8965 (tp) REVERT: B 109 LEU cc_start: 0.9062 (tp) cc_final: 0.8576 (pp) REVERT: B 146 ASN cc_start: 0.9303 (p0) cc_final: 0.8327 (t0) REVERT: C 530 LEU cc_start: 0.9509 (mm) cc_final: 0.8879 (pp) REVERT: C 594 MET cc_start: 0.9117 (mmt) cc_final: 0.8841 (mpp) REVERT: C 622 MET cc_start: 0.7762 (mmt) cc_final: 0.7461 (mmt) REVERT: C 737 MET cc_start: 0.9714 (tpp) cc_final: 0.9239 (tpp) REVERT: C 871 MET cc_start: 0.8933 (tpp) cc_final: 0.8661 (tpp) REVERT: C 905 MET cc_start: 0.9291 (tpt) cc_final: 0.8896 (tpt) REVERT: C 922 ARG cc_start: 0.8919 (ttp-110) cc_final: 0.8532 (ptm-80) REVERT: C 945 MET cc_start: 0.9123 (tpt) cc_final: 0.8806 (tpp) REVERT: C 967 GLU cc_start: 0.9161 (mp0) cc_final: 0.8787 (mp0) REVERT: C 1010 LEU cc_start: 0.9692 (tp) cc_final: 0.9484 (tp) REVERT: C 1018 SER cc_start: 0.9628 (m) cc_final: 0.9389 (t) REVERT: D 236 LEU cc_start: 0.9506 (pp) cc_final: 0.9172 (mp) REVERT: D 285 MET cc_start: 0.8869 (mmp) cc_final: 0.8219 (tpt) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.1157 time to fit residues: 37.2866 Evaluate side-chains 160 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 184 optimal weight: 40.0000 chunk 66 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.058249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.042897 restraints weight = 95685.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.044296 restraints weight = 59441.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.045238 restraints weight = 43354.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.045860 restraints weight = 35230.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.046282 restraints weight = 30763.180| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17454 Z= 0.142 Angle : 0.728 9.000 24134 Z= 0.389 Chirality : 0.046 0.213 2640 Planarity : 0.004 0.054 2670 Dihedral : 23.219 107.081 3364 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -0.95 (0.19), residues: 1774 helix: 0.15 (0.21), residues: 580 sheet: 0.09 (0.28), residues: 380 loop : -1.55 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 302 TYR 0.027 0.002 TYR C1020 PHE 0.022 0.001 PHE C1024 TRP 0.035 0.002 TRP C 782 HIS 0.012 0.001 HIS C 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (17446) covalent geometry : angle 0.72631 / 0.39 (24130) hydrogen bonds : bond 0.04863 / 3.31 ( 763) hydrogen bonds : angle 4.72763 / 3.22 ( 2137) metal coordination : bond 0.00645 / 0.47 ( 8) metal coordination : angle 3.49831 / 1.69 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2326.02 seconds wall clock time: 41 minutes 27.44 seconds (2487.44 seconds total)