Starting phenix.real_space_refine on Sat Oct 11 18:20:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbo_7846/10_2025/6dbo_7846_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbo_7846/10_2025/6dbo_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 { model { file = "/net/cci-nas-00/data/ceres_data/6dbo_7846/10_2025/6dbo_7846_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbo_7846/10_2025/6dbo_7846_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dbo_7846/10_2025/6dbo_7846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbo_7846/10_2025/6dbo_7846.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/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: 4.11, per 1000 atoms: 0.24 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: 1.51 Conformation dependent library (CDL) restraints added in 622.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.30 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: 3.96 Time building geometry restraints manager: 1.99 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=" 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 bond pdb=" N LEU C 751 " pdb=" CA LEU C 751 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.35e-02 5.49e+03 8.35e+00 bond pdb=" C CYS A 674 " pdb=" N ARG A 675 " ideal model delta sigma weight residual 1.331 1.378 -0.047 1.63e-02 3.76e+03 8.22e+00 ... (remaining 17441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 22980 2.83 - 5.66: 1008 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=" 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 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CD PRO B 340 " ideal model delta sigma weight residual 120.60 109.21 11.39 2.20e+00 2.07e-01 2.68e+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: 1852 0.064 - 0.128: 623 0.128 - 0.191: 136 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: 0.470 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.300 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 0.009 0.296 17454 Z= 0.423 Angle : 1.354 16.925 24134 Z= 0.743 Chirality : 0.067 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 aren 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 covalent geometry : bond 0.00864 (17446) covalent geometry : angle 1.34592 (24130) hydrogen bonds : bond 0.15539 ( 763) hydrogen bonds : angle 7.69615 ( 2137) metal coordination : bond 0.16481 ( 8) metal coordination : angle 11.47429 ( 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 : 0.644 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: 0.8089 (mp10) REVERT: A 594 MET cc_start: 0.9268 (mmm) cc_final: 0.8885 (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: 0.8108 (tp30) REVERT: A 743 SER cc_start: 0.8708 (t) cc_final: 0.8448 (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: 0.8811 (mmm) REVERT: A 918 THR cc_start: 0.8973 (m) cc_final: 0.8741 (p) REVERT: A 1025 MET cc_start: 0.8302 (tpp) cc_final: 0.7917 (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: 0.7878 (mp10) REVERT: C 733 MET cc_start: 0.8840 (ttm) cc_final: 0.8465 (tpp) REVERT: C 743 SER cc_start: 0.8697 (t) cc_final: 0.8252 (p) 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: 0.8960 (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: 0.8794 (ptm-80) REVERT: C 941 LEU cc_start: 0.9322 (tp) cc_final: 0.9006 (pp) REVERT: C 1006 LEU cc_start: 0.8486 (mt) cc_final: 0.8094 (mm) REVERT: C 1016 TYR cc_start: 0.8187 (t80) cc_final: 0.7705 (t80) REVERT: C 1024 PHE cc_start: 0.8945 (m-10) cc_final: 0.8697 (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: 0.1499 time to fit residues: 82.1004 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 : 0.618 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 GLN A 956 ASN ** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 HIS B 16 GLN ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN C 956 ASN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 GLN D 79 HIS D 99 ASN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.058532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.042830 restraints weight = 93596.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.044345 restraints weight = 55107.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.045320 restraints weight = 39159.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.046038 restraints weight = 31483.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.046474 restraints weight = 27148.624| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17454 Z= 0.202 Angle : 0.821 13.896 24134 Z= 0.442 Chirality : 0.046 0.203 2640 Planarity : 0.007 0.097 2670 Dihedral : 23.860 103.147 3364 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.32 % Allowed : 3.68 % Favored : 96.00 % 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 aren not related in a simple way. whole: -2.16 (0.18), residues: 1774 helix: -0.63 (0.20), residues: 558 sheet: -1.24 (0.26), residues: 342 loop : -2.04 (0.18), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 39 TYR 0.025 0.002 TYR A 747 PHE 0.016 0.002 PHE C 990 TRP 0.018 0.002 TRP D 317 HIS 0.010 0.002 HIS A1013 Details of bonding type rmsd covalent geometry : bond 0.00425 (17446) covalent geometry : angle 0.81905 (24130) hydrogen bonds : bond 0.05966 ( 763) hydrogen bonds : angle 5.61024 ( 2137) metal coordination : bond 0.01650 ( 8) metal coordination : angle 4.05110 ( 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 297 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 292 time to evaluate : 0.616 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: A 486 CYS cc_start: 0.9349 (t) cc_final: 0.9113 (p) REVERT: A 522 LEU cc_start: 0.9665 (mp) cc_final: 0.9077 (mm) REVERT: A 598 ARG cc_start: 0.8908 (ppt170) cc_final: 0.8672 (ttp80) REVERT: A 666 GLN cc_start: 0.9118 (pm20) cc_final: 0.8872 (pm20) REVERT: A 700 GLU cc_start: 0.8962 (tt0) cc_final: 0.8692 (tm-30) REVERT: A 704 MET cc_start: 0.8634 (ptm) cc_final: 0.7600 (ptt) REVERT: A 727 THR cc_start: 0.9370 (p) cc_final: 0.9073 (t) REVERT: A 733 MET cc_start: 0.9388 (tpp) cc_final: 0.8855 (tpp) REVERT: A 905 MET cc_start: 0.9371 (tpp) cc_final: 0.8971 (tpt) REVERT: A 912 LYS cc_start: 0.9534 (tmtt) cc_final: 0.9213 (tptt) REVERT: A 997 ASN cc_start: 0.9079 (m-40) cc_final: 0.8823 (m-40) REVERT: A 1013 HIS cc_start: 0.9502 (t-90) cc_final: 0.9223 (t-170) REVERT: A 1016 TYR cc_start: 0.9359 (t80) cc_final: 0.9054 (t80) REVERT: B 142 LEU cc_start: 0.9397 (tp) cc_final: 0.9179 (tp) REVERT: B 146 ASN cc_start: 0.9011 (p0) cc_final: 0.8702 (t0) REVERT: B 200 LEU cc_start: 0.9192 (mp) cc_final: 0.8963 (mp) REVERT: B 236 LEU cc_start: 0.9521 (pp) cc_final: 0.9198 (mp) REVERT: B 274 PHE cc_start: 0.8477 (m-10) cc_final: 0.8148 (m-10) REVERT: B 277 TYR cc_start: 0.8540 (m-80) cc_final: 0.8297 (m-10) REVERT: C 481 LEU cc_start: 0.8817 (pp) cc_final: 0.8331 (pp) REVERT: C 486 CYS cc_start: 0.8768 (p) cc_final: 0.8531 (p) REVERT: C 487 LEU cc_start: 0.9765 (tp) cc_final: 0.9531 (tp) REVERT: C 496 SER cc_start: 0.8962 (m) cc_final: 0.8730 (t) REVERT: C 499 GLN cc_start: 0.9317 (mt0) cc_final: 0.9028 (mt0) REVERT: C 594 MET cc_start: 0.9381 (mmt) cc_final: 0.9164 (mmt) REVERT: C 677 LEU cc_start: 0.9627 (tt) cc_final: 0.8591 (tp) REVERT: C 794 LEU cc_start: 0.9500 (tp) cc_final: 0.8923 (mt) REVERT: C 847 GLU cc_start: 0.9350 (mt-10) cc_final: 0.9092 (mp0) REVERT: C 863 MET cc_start: 0.6337 (mtm) cc_final: 0.6075 (mtm) REVERT: C 905 MET cc_start: 0.9232 (tpt) cc_final: 0.8845 (tpt) REVERT: C 922 ARG cc_start: 0.8885 (ttp-110) cc_final: 0.8530 (ptm-80) REVERT: C 941 LEU cc_start: 0.9234 (tp) cc_final: 0.8907 (pp) REVERT: C 945 MET cc_start: 0.8955 (tpt) cc_final: 0.8660 (tpp) REVERT: C 967 GLU cc_start: 0.9154 (mp0) cc_final: 0.8707 (pm20) REVERT: C 989 LEU cc_start: 0.9463 (mm) cc_final: 0.9254 (mm) REVERT: C 1010 LEU cc_start: 0.9707 (tp) cc_final: 0.9432 (tp) REVERT: C 1013 HIS cc_start: 0.9499 (t70) cc_final: 0.8927 (t-170) REVERT: C 1016 TYR cc_start: 0.9337 (t80) cc_final: 0.9090 (t80) REVERT: C 1018 SER cc_start: 0.9626 (m) cc_final: 0.9384 (t) REVERT: D 34 LYS cc_start: 0.9233 (mmmt) cc_final: 0.8935 (mmmm) REVERT: D 109 LEU cc_start: 0.9122 (tp) cc_final: 0.8789 (tp) REVERT: D 142 LEU cc_start: 0.9335 (tp) cc_final: 0.9105 (tp) REVERT: D 146 ASN cc_start: 0.9569 (p0) cc_final: 0.8912 (t0) REVERT: D 277 TYR cc_start: 0.8409 (m-80) cc_final: 0.8026 (m-80) outliers start: 5 outliers final: 4 residues processed: 297 average time/residue: 0.1676 time to fit residues: 71.6930 Evaluate side-chains 188 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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: 20.0000 chunk 182 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 HIS A 761 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** 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 501 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS C 858 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3281 r_free = 0.3281 target = 0.055401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.040348 restraints weight = 96485.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.041674 restraints weight = 58194.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.042596 restraints weight = 41936.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.043238 restraints weight = 33669.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.043648 restraints weight = 29047.106| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17454 Z= 0.273 Angle : 0.809 12.354 24134 Z= 0.434 Chirality : 0.045 0.207 2640 Planarity : 0.006 0.086 2670 Dihedral : 23.563 101.998 3364 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.06 % Allowed : 5.97 % Favored : 93.96 % 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 aren not related in a simple way. whole: -1.55 (0.18), residues: 1774 helix: -0.17 (0.21), residues: 574 sheet: -0.74 (0.28), residues: 334 loop : -1.72 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 675 TYR 0.020 0.002 TYR C1020 PHE 0.020 0.002 PHE C 611 TRP 0.010 0.002 TRP C 560 HIS 0.009 0.002 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00561 (17446) covalent geometry : angle 0.79930 (24130) hydrogen bonds : bond 0.06167 ( 763) hydrogen bonds : angle 5.33526 ( 2137) metal coordination : bond 0.02401 ( 8) metal coordination : angle 9.78496 ( 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 227 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.639 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: A 486 CYS cc_start: 0.9318 (t) cc_final: 0.9093 (t) REVERT: A 522 LEU cc_start: 0.9686 (mp) cc_final: 0.9251 (mp) REVERT: A 530 LEU cc_start: 0.9661 (mm) cc_final: 0.9175 (pp) REVERT: A 578 TYR cc_start: 0.8180 (t80) cc_final: 0.7677 (t80) REVERT: A 622 MET cc_start: 0.7865 (mtt) cc_final: 0.7461 (mtt) REVERT: A 700 GLU cc_start: 0.9035 (tt0) cc_final: 0.8763 (tm-30) REVERT: A 733 MET cc_start: 0.9609 (tpp) cc_final: 0.9124 (tpp) REVERT: A 736 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8844 (mt-10) REVERT: A 738 GLU cc_start: 0.8893 (tp30) cc_final: 0.8669 (tp30) REVERT: A 912 LYS cc_start: 0.9454 (tmtt) cc_final: 0.9094 (tptp) REVERT: A 1025 MET cc_start: 0.9154 (tpp) cc_final: 0.8924 (tpp) REVERT: B 79 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.8592 (t-90) REVERT: B 109 LEU cc_start: 0.8989 (tp) cc_final: 0.8619 (mp) REVERT: B 142 LEU cc_start: 0.9373 (tp) cc_final: 0.9074 (tp) REVERT: B 146 ASN cc_start: 0.9008 (p0) cc_final: 0.8390 (t0) REVERT: B 274 PHE cc_start: 0.8543 (m-10) cc_final: 0.8207 (m-10) REVERT: B 277 TYR cc_start: 0.8527 (m-80) cc_final: 0.7960 (m-80) REVERT: C 496 SER cc_start: 0.8909 (m) cc_final: 0.8241 (t) REVERT: C 499 GLN cc_start: 0.9319 (mt0) cc_final: 0.9102 (mt0) REVERT: C 588 ASP cc_start: 0.8995 (t70) cc_final: 0.8782 (t0) REVERT: C 598 ARG cc_start: 0.9131 (ppt170) cc_final: 0.8924 (ttp80) REVERT: C 677 LEU cc_start: 0.9186 (tt) cc_final: 0.8513 (tt) REVERT: C 678 CYS cc_start: 0.8415 (m) cc_final: 0.7552 (m) REVERT: C 737 MET cc_start: 0.9564 (tpp) cc_final: 0.9009 (tpp) REVERT: C 922 ARG cc_start: 0.8797 (ttp-110) cc_final: 0.8355 (ttp80) REVERT: C 941 LEU cc_start: 0.9283 (tp) cc_final: 0.8913 (pp) REVERT: C 945 MET cc_start: 0.9058 (tpt) cc_final: 0.8687 (tpp) REVERT: C 967 GLU cc_start: 0.9149 (mp0) cc_final: 0.8779 (mp0) REVERT: C 1010 LEU cc_start: 0.9716 (tp) cc_final: 0.9459 (tp) REVERT: C 1013 HIS cc_start: 0.9480 (t70) cc_final: 0.8781 (t-170) REVERT: C 1016 TYR cc_start: 0.9215 (t80) cc_final: 0.8446 (t80) REVERT: D 34 LYS cc_start: 0.9322 (mmmt) cc_final: 0.9085 (mmmm) REVERT: D 109 LEU cc_start: 0.9031 (tp) cc_final: 0.8704 (tp) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1449 time to fit residues: 49.4145 Evaluate side-chains 161 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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: 0.8980 chunk 86 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 0.0970 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 overall best weight: 1.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 858 GLN ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** 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 482 HIS ** C 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 810 GLN C 858 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3344 r_free = 0.3344 target = 0.058119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.042414 restraints weight = 91442.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.043884 restraints weight = 54449.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.044874 restraints weight = 38837.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.045569 restraints weight = 30943.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.046013 restraints weight = 26538.472| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17454 Z= 0.155 Angle : 0.719 11.089 24134 Z= 0.385 Chirality : 0.044 0.200 2640 Planarity : 0.005 0.069 2670 Dihedral : 23.352 107.968 3364 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.25 % Allowed : 3.24 % Favored : 96.51 % 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 aren not related in a simple way. whole: -1.26 (0.18), residues: 1774 helix: 0.10 (0.21), residues: 576 sheet: -0.42 (0.28), residues: 332 loop : -1.65 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 600 TYR 0.019 0.002 TYR D 268 PHE 0.019 0.001 PHE D 62 TRP 0.014 0.001 TRP D 317 HIS 0.008 0.001 HIS C 959 Details of bonding type rmsd covalent geometry : bond 0.00332 (17446) covalent geometry : angle 0.71677 (24130) hydrogen bonds : bond 0.04953 ( 763) hydrogen bonds : angle 4.92359 ( 2137) metal coordination : bond 0.00928 ( 8) metal coordination : angle 4.06520 ( 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 241 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 237 time to evaluate : 0.627 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: 0.9346 (t) cc_final: 0.9077 (t) REVERT: A 522 LEU cc_start: 0.9673 (mp) cc_final: 0.9164 (mp) REVERT: A 530 LEU cc_start: 0.9609 (mm) cc_final: 0.9147 (pp) REVERT: A 578 TYR cc_start: 0.8345 (t80) cc_final: 0.7848 (t80) REVERT: A 622 MET cc_start: 0.7485 (mtt) cc_final: 0.7086 (mtt) REVERT: A 711 ILE cc_start: 0.9572 (pt) cc_final: 0.9168 (mp) REVERT: A 733 MET cc_start: 0.9513 (tpp) cc_final: 0.8301 (tpp) REVERT: A 738 GLU cc_start: 0.8838 (tp30) cc_final: 0.8476 (tp30) REVERT: A 794 LEU cc_start: 0.9295 (mt) cc_final: 0.8817 (mt) REVERT: A 912 LYS cc_start: 0.9450 (tmtt) cc_final: 0.9015 (tptp) REVERT: A 1015 LEU cc_start: 0.9436 (tp) cc_final: 0.9231 (tp) REVERT: B 56 LYS cc_start: 0.9053 (mmpt) cc_final: 0.8560 (tttp) REVERT: B 69 LEU cc_start: 0.9224 (tp) cc_final: 0.8807 (tp) REVERT: B 109 LEU cc_start: 0.9009 (tp) cc_final: 0.8619 (pp) REVERT: B 142 LEU cc_start: 0.9403 (tp) cc_final: 0.9102 (tp) REVERT: B 146 ASN cc_start: 0.8899 (p0) cc_final: 0.8377 (t0) REVERT: B 277 TYR cc_start: 0.8322 (m-80) cc_final: 0.7867 (m-80) REVERT: C 496 SER cc_start: 0.8849 (m) cc_final: 0.8183 (t) REVERT: C 598 ARG cc_start: 0.9093 (ppt170) cc_final: 0.8891 (ttp80) REVERT: C 700 GLU cc_start: 0.8799 (pt0) cc_final: 0.8079 (pt0) REVERT: C 731 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8441 (mt-10) REVERT: C 733 MET cc_start: 0.9463 (tpp) cc_final: 0.9098 (tpt) REVERT: C 737 MET cc_start: 0.9637 (tpp) cc_final: 0.9161 (tpp) REVERT: C 794 LEU cc_start: 0.9449 (tp) cc_final: 0.9182 (mt) REVERT: C 922 ARG cc_start: 0.8804 (ttp-110) cc_final: 0.8460 (ptm-80) REVERT: C 941 LEU cc_start: 0.9197 (tp) cc_final: 0.8848 (pp) REVERT: C 945 MET cc_start: 0.9051 (tpt) cc_final: 0.8717 (tpp) REVERT: C 967 GLU cc_start: 0.9153 (mp0) cc_final: 0.8800 (mp0) REVERT: C 1010 LEU cc_start: 0.9739 (tp) cc_final: 0.9495 (tp) REVERT: C 1013 HIS cc_start: 0.9350 (t70) cc_final: 0.8511 (t-90) REVERT: C 1016 TYR cc_start: 0.9012 (t80) cc_final: 0.8762 (t80) REVERT: D 34 LYS cc_start: 0.9310 (mmmt) cc_final: 0.9007 (mmmm) REVERT: D 142 LEU cc_start: 0.9314 (tp) cc_final: 0.9066 (tp) REVERT: D 285 MET cc_start: 0.8355 (mmp) cc_final: 0.7927 (tpp) outliers start: 4 outliers final: 0 residues processed: 241 average time/residue: 0.1342 time to fit residues: 48.5383 Evaluate side-chains 162 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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: 7.9990 chunk 69 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 761 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** 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 501 HIS ** 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** C 937 GLN ** C1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 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 = 0.3292 r_free = 0.3292 target = 0.056084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.040745 restraints weight = 98687.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.042049 restraints weight = 61713.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.042944 restraints weight = 45518.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.043520 restraints weight = 37366.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.043874 restraints weight = 32897.185| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17454 Z= 0.256 Angle : 0.758 10.430 24134 Z= 0.409 Chirality : 0.044 0.195 2640 Planarity : 0.005 0.066 2670 Dihedral : 23.311 103.759 3364 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.06 % Allowed : 2.41 % Favored : 97.52 % 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 aren not related in a simple way. whole: -1.26 (0.19), residues: 1774 helix: 0.08 (0.20), residues: 584 sheet: -0.52 (0.27), residues: 370 loop : -1.63 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 600 TYR 0.022 0.002 TYR C1020 PHE 0.020 0.002 PHE B 274 TRP 0.010 0.002 TRP D 317 HIS 0.009 0.002 HIS C 959 Details of bonding type rmsd covalent geometry : bond 0.00527 (17446) covalent geometry : angle 0.75392 (24130) hydrogen bonds : bond 0.05685 ( 763) hydrogen bonds : angle 4.96093 ( 2137) metal coordination : bond 0.02213 ( 8) metal coordination : angle 5.80027 ( 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 201 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.642 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: A 486 CYS cc_start: 0.9212 (t) cc_final: 0.8970 (t) REVERT: A 522 LEU cc_start: 0.9689 (mp) cc_final: 0.9281 (mp) REVERT: A 530 LEU cc_start: 0.9658 (mm) cc_final: 0.9234 (pp) REVERT: A 700 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8529 (tm-30) REVERT: A 737 MET cc_start: 0.8985 (ttm) cc_final: 0.8751 (tmm) REVERT: A 738 GLU cc_start: 0.8702 (tp30) cc_final: 0.8388 (tp30) REVERT: A 794 LEU cc_start: 0.9282 (mt) cc_final: 0.9039 (mt) REVERT: A 912 LYS cc_start: 0.9443 (tmtt) cc_final: 0.9004 (tptp) REVERT: B 56 LYS cc_start: 0.9196 (mmpt) cc_final: 0.8788 (tttp) REVERT: B 69 LEU cc_start: 0.9251 (tp) cc_final: 0.9032 (tp) REVERT: B 109 LEU cc_start: 0.8931 (tp) cc_final: 0.8559 (pp) REVERT: B 146 ASN cc_start: 0.8978 (p0) cc_final: 0.8289 (t0) REVERT: B 271 TYR cc_start: 0.9126 (m-80) cc_final: 0.8733 (m-80) REVERT: B 274 PHE cc_start: 0.8602 (m-80) cc_final: 0.8259 (m-80) REVERT: B 277 TYR cc_start: 0.8433 (m-80) cc_final: 0.7862 (m-80) REVERT: C 496 SER cc_start: 0.9012 (m) cc_final: 0.7961 (t) REVERT: C 598 ARG cc_start: 0.9148 (ppt170) cc_final: 0.8890 (ttp80) REVERT: C 700 GLU cc_start: 0.8806 (pt0) cc_final: 0.8131 (pt0) REVERT: C 733 MET cc_start: 0.9496 (tpp) cc_final: 0.9186 (tpp) REVERT: C 737 MET cc_start: 0.9613 (tpp) cc_final: 0.9148 (tpp) REVERT: C 794 LEU cc_start: 0.9478 (tp) cc_final: 0.9265 (mt) REVERT: C 905 MET cc_start: 0.9298 (tpt) cc_final: 0.8820 (tpt) REVERT: C 922 ARG cc_start: 0.8853 (ttp-110) cc_final: 0.8444 (ttp80) REVERT: C 945 MET cc_start: 0.9136 (tpt) cc_final: 0.8850 (tpp) REVERT: C 967 GLU cc_start: 0.9147 (mp0) cc_final: 0.8805 (mp0) REVERT: C 1010 LEU cc_start: 0.9677 (tp) cc_final: 0.9445 (tp) REVERT: C 1013 HIS cc_start: 0.9255 (t70) cc_final: 0.8895 (t-90) REVERT: C 1016 TYR cc_start: 0.8969 (t80) cc_final: 0.8521 (t80) REVERT: D 100 ASN cc_start: 0.8389 (t0) cc_final: 0.8077 (t0) REVERT: D 142 LEU cc_start: 0.9249 (tp) cc_final: 0.9047 (tp) REVERT: D 285 MET cc_start: 0.8509 (mmp) cc_final: 0.7999 (tpp) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.1308 time to fit residues: 40.6612 Evaluate side-chains 148 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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: 8.9990 chunk 131 optimal weight: 0.4980 chunk 168 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 278 GLN C 501 HIS C 514 GLN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.056372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.040964 restraints weight = 97645.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.042263 restraints weight = 61357.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043149 restraints weight = 45364.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.043698 restraints weight = 37326.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044118 restraints weight = 32915.928| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17454 Z= 0.216 Angle : 0.720 9.808 24134 Z= 0.387 Chirality : 0.043 0.194 2640 Planarity : 0.005 0.067 2670 Dihedral : 23.289 108.341 3364 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.06 % Allowed : 2.41 % Favored : 97.52 % 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 aren not related in a simple way. whole: -1.13 (0.19), residues: 1774 helix: 0.14 (0.20), residues: 582 sheet: -0.33 (0.27), residues: 380 loop : -1.60 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 302 TYR 0.020 0.002 TYR C1020 PHE 0.013 0.002 PHE A 724 TRP 0.011 0.002 TRP B 317 HIS 0.007 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00449 (17446) covalent geometry : angle 0.71525 (24130) hydrogen bonds : bond 0.05040 ( 763) hydrogen bonds : angle 4.79292 ( 2137) metal coordination : bond 0.01695 ( 8) metal coordination : angle 6.69546 ( 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 205 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.655 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: 0.9257 (t) cc_final: 0.8967 (t) REVERT: A 522 LEU cc_start: 0.9673 (mp) cc_final: 0.9194 (mp) REVERT: A 530 LEU cc_start: 0.9649 (mm) cc_final: 0.9241 (pp) REVERT: A 622 MET cc_start: 0.7257 (mtt) cc_final: 0.6870 (mtt) REVERT: A 737 MET cc_start: 0.8997 (ttm) cc_final: 0.8787 (tmm) REVERT: A 738 GLU cc_start: 0.8710 (tp30) cc_final: 0.7969 (tp30) REVERT: B 56 LYS cc_start: 0.9161 (mmpt) cc_final: 0.8739 (tttp) REVERT: B 109 LEU cc_start: 0.9072 (tp) cc_final: 0.8617 (pp) REVERT: B 146 ASN cc_start: 0.8977 (p0) cc_final: 0.8426 (t0) REVERT: B 213 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7678 (tp-100) REVERT: B 277 TYR cc_start: 0.8396 (m-80) cc_final: 0.7940 (m-80) REVERT: B 278 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8605 (pp30) REVERT: B 285 MET cc_start: 0.8064 (mmp) cc_final: 0.7853 (tpp) REVERT: C 496 SER cc_start: 0.8865 (m) cc_final: 0.7609 (t) REVERT: C 598 ARG cc_start: 0.9146 (ppt170) cc_final: 0.8889 (ttp80) REVERT: C 700 GLU cc_start: 0.8827 (pt0) cc_final: 0.8111 (pt0) REVERT: C 733 MET cc_start: 0.9518 (tpp) cc_final: 0.9227 (tpp) REVERT: C 737 MET cc_start: 0.9675 (tpp) cc_final: 0.9117 (tpp) REVERT: C 794 LEU cc_start: 0.9464 (tp) cc_final: 0.9232 (mt) REVERT: C 905 MET cc_start: 0.9354 (tpt) cc_final: 0.8904 (tpt) REVERT: C 922 ARG cc_start: 0.8887 (ttp-110) cc_final: 0.8500 (ptm-80) REVERT: C 945 MET cc_start: 0.9154 (tpt) cc_final: 0.8841 (tpp) REVERT: C 967 GLU cc_start: 0.9180 (mp0) cc_final: 0.8927 (mp0) REVERT: C 1010 LEU cc_start: 0.9669 (tp) cc_final: 0.9444 (tp) REVERT: C 1016 TYR cc_start: 0.8935 (t80) cc_final: 0.8518 (t80) REVERT: D 285 MET cc_start: 0.8593 (mmp) cc_final: 0.8043 (tpp) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.1337 time to fit residues: 41.9296 Evaluate side-chains 151 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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: 0.6980 chunk 170 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 176 optimal weight: 0.4980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 HIS ** 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 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.057380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.041975 restraints weight = 96597.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.043315 restraints weight = 60922.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.044217 restraints weight = 45089.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044813 restraints weight = 37006.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045181 restraints weight = 32543.488| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17454 Z= 0.167 Angle : 0.703 9.773 24134 Z= 0.377 Chirality : 0.043 0.190 2640 Planarity : 0.004 0.061 2670 Dihedral : 23.243 109.455 3364 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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 aren not related in a simple way. whole: -1.03 (0.19), residues: 1774 helix: 0.22 (0.20), residues: 578 sheet: -0.17 (0.28), residues: 370 loop : -1.57 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 58 TYR 0.026 0.002 TYR B 271 PHE 0.010 0.001 PHE A1024 TRP 0.011 0.001 TRP A1014 HIS 0.006 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00355 (17446) covalent geometry : angle 0.70019 (24130) hydrogen bonds : bond 0.04800 ( 763) hydrogen bonds : angle 4.69951 ( 2137) metal coordination : bond 0.00945 ( 8) metal coordination : angle 4.73242 ( 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 204 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.545 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 486 CYS cc_start: 0.9214 (t) cc_final: 0.8971 (t) REVERT: A 503 MET cc_start: 0.9425 (ttp) cc_final: 0.8998 (tmm) REVERT: A 522 LEU cc_start: 0.9693 (mp) cc_final: 0.9244 (mp) REVERT: A 530 LEU cc_start: 0.9628 (mm) cc_final: 0.9192 (pp) REVERT: A 592 ASP cc_start: 0.9681 (m-30) cc_final: 0.9004 (m-30) REVERT: A 733 MET cc_start: 0.9270 (tpp) cc_final: 0.9019 (tpp) REVERT: A 738 GLU cc_start: 0.8774 (tp30) cc_final: 0.7424 (tp30) REVERT: A 794 LEU cc_start: 0.9391 (mt) cc_final: 0.8919 (mt) REVERT: B 56 LYS cc_start: 0.9185 (mmpt) cc_final: 0.8690 (tttp) REVERT: B 69 LEU cc_start: 0.9250 (tp) cc_final: 0.8858 (tp) REVERT: B 109 LEU cc_start: 0.9054 (tp) cc_final: 0.8645 (pp) REVERT: B 146 ASN cc_start: 0.8991 (p0) cc_final: 0.8385 (t0) REVERT: B 213 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7585 (tp-100) REVERT: B 274 PHE cc_start: 0.8554 (m-80) cc_final: 0.8254 (m-80) REVERT: B 277 TYR cc_start: 0.8422 (m-80) cc_final: 0.8013 (m-80) REVERT: C 496 SER cc_start: 0.8856 (m) cc_final: 0.7449 (t) REVERT: C 598 ARG cc_start: 0.9138 (ppt170) cc_final: 0.8843 (ttp80) REVERT: C 700 GLU cc_start: 0.8803 (pt0) cc_final: 0.8031 (pt0) REVERT: C 733 MET cc_start: 0.9540 (tpp) cc_final: 0.9254 (tpp) REVERT: C 737 MET cc_start: 0.9696 (tpp) cc_final: 0.9249 (tpp) REVERT: C 794 LEU cc_start: 0.9446 (tp) cc_final: 0.9205 (mt) REVERT: C 871 MET cc_start: 0.8956 (tpp) cc_final: 0.8747 (tpp) REVERT: C 905 MET cc_start: 0.9339 (tpt) cc_final: 0.8904 (tpt) REVERT: C 922 ARG cc_start: 0.8910 (ttp-110) cc_final: 0.8483 (ptm-80) REVERT: C 945 MET cc_start: 0.9198 (tpt) cc_final: 0.8865 (tpp) REVERT: C 967 GLU cc_start: 0.9178 (mp0) cc_final: 0.8910 (mp0) REVERT: C 1013 HIS cc_start: 0.9129 (t-90) cc_final: 0.8691 (t-90) REVERT: C 1016 TYR cc_start: 0.8899 (t80) cc_final: 0.8470 (t80) REVERT: D 285 MET cc_start: 0.8669 (mmp) cc_final: 0.8117 (tpp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1210 time to fit residues: 38.9288 Evaluate side-chains 153 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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: 5.9990 chunk 188 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 0.0470 chunk 133 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.056507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.041142 restraints weight = 98031.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.042469 restraints weight = 61814.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.043322 restraints weight = 45699.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.043928 restraints weight = 37595.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.044286 restraints weight = 33007.351| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17454 Z= 0.198 Angle : 0.716 9.492 24134 Z= 0.383 Chirality : 0.043 0.193 2640 Planarity : 0.005 0.062 2670 Dihedral : 23.239 108.634 3364 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.06 % Allowed : 1.46 % 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 aren not related in a simple way. whole: -0.99 (0.19), residues: 1774 helix: 0.24 (0.20), residues: 578 sheet: -0.20 (0.28), residues: 370 loop : -1.51 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 302 TYR 0.025 0.002 TYR B 271 PHE 0.022 0.002 PHE D 62 TRP 0.028 0.001 TRP A 782 HIS 0.008 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00414 (17446) covalent geometry : angle 0.71013 (24130) hydrogen bonds : bond 0.05006 ( 763) hydrogen bonds : angle 4.72486 ( 2137) metal coordination : bond 0.01844 ( 8) metal coordination : angle 6.98496 ( 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 198 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.544 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 503 MET cc_start: 0.9394 (ttp) cc_final: 0.9074 (ppp) REVERT: A 522 LEU cc_start: 0.9680 (mp) cc_final: 0.9212 (mp) REVERT: A 530 LEU cc_start: 0.9620 (mm) cc_final: 0.9187 (pp) REVERT: A 592 ASP cc_start: 0.9684 (m-30) cc_final: 0.9000 (m-30) REVERT: A 669 ASN cc_start: 0.8737 (m-40) cc_final: 0.8492 (t0) REVERT: A 705 MET cc_start: 0.9012 (mpp) cc_final: 0.8710 (mpp) REVERT: A 738 GLU cc_start: 0.8567 (tp30) cc_final: 0.8166 (tp30) REVERT: A 1005 GLU cc_start: 0.9205 (tt0) cc_final: 0.8744 (pt0) REVERT: B 56 LYS cc_start: 0.9198 (mmpt) cc_final: 0.8717 (tttp) REVERT: B 69 LEU cc_start: 0.9311 (tp) cc_final: 0.9086 (tp) REVERT: B 109 LEU cc_start: 0.9092 (tp) cc_final: 0.8627 (pp) REVERT: B 146 ASN cc_start: 0.9068 (p0) cc_final: 0.8355 (t0) REVERT: B 213 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7575 (tp-100) REVERT: B 274 PHE cc_start: 0.8547 (m-80) cc_final: 0.8260 (m-80) REVERT: C 496 SER cc_start: 0.8861 (m) cc_final: 0.7414 (t) REVERT: C 598 ARG cc_start: 0.9123 (ppt170) cc_final: 0.8827 (ttp80) REVERT: C 622 MET cc_start: 0.7789 (mmt) cc_final: 0.7253 (mmt) REVERT: C 700 GLU cc_start: 0.8838 (pt0) cc_final: 0.8087 (pt0) REVERT: C 733 MET cc_start: 0.9562 (tpp) cc_final: 0.9290 (tpp) REVERT: C 737 MET cc_start: 0.9669 (tpp) cc_final: 0.9157 (tpp) REVERT: C 794 LEU cc_start: 0.9458 (tp) cc_final: 0.9225 (mt) REVERT: C 905 MET cc_start: 0.9366 (tpt) cc_final: 0.8928 (tpt) REVERT: C 922 ARG cc_start: 0.8918 (ttp-110) cc_final: 0.8511 (tmm-80) REVERT: C 945 MET cc_start: 0.9198 (tpt) cc_final: 0.8847 (tpp) REVERT: C 967 GLU cc_start: 0.9185 (mp0) cc_final: 0.8934 (mp0) REVERT: C 1010 LEU cc_start: 0.9668 (tp) cc_final: 0.9449 (tp) REVERT: C 1013 HIS cc_start: 0.9269 (t-90) cc_final: 0.8278 (t-90) REVERT: C 1016 TYR cc_start: 0.8899 (t80) cc_final: 0.8505 (t80) REVERT: D 285 MET cc_start: 0.8760 (mmp) cc_final: 0.8341 (tpp) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.1197 time to fit residues: 36.9828 Evaluate side-chains 158 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 1.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 687 HIS ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 GLN B 99 ASN C 501 HIS C 517 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.057555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042182 restraints weight = 96661.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.043527 restraints weight = 60975.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.044455 restraints weight = 44949.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.045060 restraints weight = 36791.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.045400 restraints weight = 32225.728| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17454 Z= 0.162 Angle : 0.703 9.150 24134 Z= 0.373 Chirality : 0.043 0.188 2640 Planarity : 0.004 0.060 2670 Dihedral : 23.184 110.773 3364 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.06 % Allowed : 0.89 % Favored : 99.05 % 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 aren not related in a simple way. whole: -0.96 (0.19), residues: 1774 helix: 0.31 (0.21), residues: 574 sheet: -0.14 (0.28), residues: 370 loop : -1.55 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 735 TYR 0.025 0.002 TYR B 271 PHE 0.013 0.001 PHE D 62 TRP 0.011 0.001 TRP A1014 HIS 0.006 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00345 (17446) covalent geometry : angle 0.70047 (24130) hydrogen bonds : bond 0.04613 ( 763) hydrogen bonds : angle 4.61948 ( 2137) metal coordination : bond 0.00985 ( 8) metal coordination : angle 4.42131 ( 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 200 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.646 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 503 MET cc_start: 0.9379 (ttp) cc_final: 0.9075 (ppp) REVERT: A 522 LEU cc_start: 0.9641 (mp) cc_final: 0.9350 (mp) REVERT: A 530 LEU cc_start: 0.9599 (mm) cc_final: 0.9185 (pp) REVERT: A 592 ASP cc_start: 0.9643 (m-30) cc_final: 0.8932 (m-30) REVERT: A 669 ASN cc_start: 0.8615 (m-40) cc_final: 0.8158 (t0) REVERT: A 705 MET cc_start: 0.9066 (mpp) cc_final: 0.8626 (mpp) REVERT: A 731 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8634 (mm-30) REVERT: A 738 GLU cc_start: 0.8589 (tp30) cc_final: 0.7175 (tp30) REVERT: A 794 LEU cc_start: 0.9348 (mt) cc_final: 0.8935 (mt) REVERT: A 1005 GLU cc_start: 0.9180 (tt0) cc_final: 0.8784 (pt0) REVERT: B 56 LYS cc_start: 0.9211 (mmpt) cc_final: 0.8745 (tttp) REVERT: B 69 LEU cc_start: 0.9292 (tp) cc_final: 0.9083 (tp) REVERT: B 109 LEU cc_start: 0.9071 (tp) cc_final: 0.8639 (pp) REVERT: B 142 LEU cc_start: 0.9372 (tp) cc_final: 0.9148 (tp) REVERT: B 146 ASN cc_start: 0.8856 (p0) cc_final: 0.8282 (t0) REVERT: B 213 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7579 (tp-100) REVERT: C 496 SER cc_start: 0.8752 (m) cc_final: 0.7231 (t) REVERT: C 594 MET cc_start: 0.9240 (mmm) cc_final: 0.8891 (mpp) REVERT: C 598 ARG cc_start: 0.9107 (ppt170) cc_final: 0.8778 (ttp80) REVERT: C 622 MET cc_start: 0.7730 (mmt) cc_final: 0.7227 (mmt) REVERT: C 700 GLU cc_start: 0.8826 (pt0) cc_final: 0.8052 (pt0) REVERT: C 733 MET cc_start: 0.9514 (tpp) cc_final: 0.9241 (tpp) REVERT: C 737 MET cc_start: 0.9687 (tpp) cc_final: 0.9234 (tpp) REVERT: C 794 LEU cc_start: 0.9421 (tp) cc_final: 0.9184 (mt) REVERT: C 905 MET cc_start: 0.9333 (tpt) cc_final: 0.8881 (tpt) REVERT: C 922 ARG cc_start: 0.8914 (ttp-110) cc_final: 0.8495 (tmm-80) REVERT: C 967 GLU cc_start: 0.9149 (mp0) cc_final: 0.8893 (mp0) REVERT: C 1013 HIS cc_start: 0.9181 (t-90) cc_final: 0.8159 (t-90) REVERT: C 1016 TYR cc_start: 0.8886 (t80) cc_final: 0.8539 (t80) REVERT: D 33 GLN cc_start: 0.8646 (pt0) cc_final: 0.8365 (pm20) REVERT: D 100 ASN cc_start: 0.8681 (t0) cc_final: 0.8479 (t0) REVERT: D 285 MET cc_start: 0.8739 (mmp) cc_final: 0.8355 (tpp) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.1179 time to fit residues: 37.6004 Evaluate side-chains 153 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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: 1.9990 chunk 58 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 187 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.055893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.040596 restraints weight = 98209.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.041870 restraints weight = 61421.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.042746 restraints weight = 45287.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.043284 restraints weight = 37235.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.043681 restraints weight = 32878.442| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17454 Z= 0.245 Angle : 0.754 10.572 24134 Z= 0.400 Chirality : 0.044 0.209 2640 Planarity : 0.005 0.070 2670 Dihedral : 23.289 107.744 3364 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.06 % Allowed : 0.38 % 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 aren not related in a simple way. whole: -1.12 (0.19), residues: 1774 helix: 0.17 (0.21), residues: 574 sheet: -0.37 (0.27), residues: 372 loop : -1.55 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 490 TYR 0.022 0.002 TYR B 271 PHE 0.016 0.002 PHE B 80 TRP 0.008 0.002 TRP A 978 HIS 0.010 0.002 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00509 (17446) covalent geometry : angle 0.74562 (24130) hydrogen bonds : bond 0.05358 ( 763) hydrogen bonds : angle 4.77945 ( 2137) metal coordination : bond 0.02136 ( 8) metal coordination : angle 8.79509 ( 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 189 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.531 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: A 522 LEU cc_start: 0.9606 (mp) cc_final: 0.9240 (mp) REVERT: A 530 LEU cc_start: 0.9572 (mm) cc_final: 0.9285 (pp) REVERT: A 669 ASN cc_start: 0.8677 (m-40) cc_final: 0.8323 (t0) REVERT: A 700 GLU cc_start: 0.8703 (pp20) cc_final: 0.8500 (pp20) REVERT: A 705 MET cc_start: 0.9212 (mpp) cc_final: 0.8791 (mpp) REVERT: A 738 GLU cc_start: 0.8704 (tp30) cc_final: 0.7596 (tp30) REVERT: A 794 LEU cc_start: 0.9415 (mt) cc_final: 0.9112 (mt) REVERT: A 807 MET cc_start: 0.8081 (ppp) cc_final: 0.7668 (ppp) REVERT: B 56 LYS cc_start: 0.9174 (mmpt) cc_final: 0.8730 (tttp) REVERT: B 69 LEU cc_start: 0.9322 (tp) cc_final: 0.9111 (tp) REVERT: B 109 LEU cc_start: 0.8988 (tp) cc_final: 0.8550 (pp) REVERT: C 496 SER cc_start: 0.8846 (m) cc_final: 0.7589 (t) REVERT: C 499 GLN cc_start: 0.9351 (mt0) cc_final: 0.9149 (mt0) REVERT: C 594 MET cc_start: 0.9282 (mmm) cc_final: 0.8932 (mpp) REVERT: C 598 ARG cc_start: 0.9197 (ppt170) cc_final: 0.8848 (ttp80) REVERT: C 700 GLU cc_start: 0.8898 (pt0) cc_final: 0.8192 (pt0) REVERT: C 733 MET cc_start: 0.9590 (tpp) cc_final: 0.9324 (tpp) REVERT: C 737 MET cc_start: 0.9678 (tpp) cc_final: 0.9188 (tpp) REVERT: C 794 LEU cc_start: 0.9469 (tp) cc_final: 0.9261 (mt) REVERT: C 905 MET cc_start: 0.9420 (tpt) cc_final: 0.8773 (tpt) REVERT: C 967 GLU cc_start: 0.9178 (mp0) cc_final: 0.8949 (mp0) REVERT: C 1013 HIS cc_start: 0.9321 (t-90) cc_final: 0.8390 (t-90) REVERT: C 1016 TYR cc_start: 0.8961 (t80) cc_final: 0.8547 (t80) REVERT: D 285 MET cc_start: 0.8990 (mmp) cc_final: 0.8425 (tpt) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.1256 time to fit residues: 36.8604 Evaluate side-chains 142 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 10.0000 chunk 66 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS C 501 HIS C 517 GLN C 858 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.057208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.041905 restraints weight = 96877.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.043229 restraints weight = 61312.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.044131 restraints weight = 45285.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.044696 restraints weight = 37217.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.045105 restraints weight = 32763.494| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17454 Z= 0.163 Angle : 0.711 8.503 24134 Z= 0.377 Chirality : 0.043 0.198 2640 Planarity : 0.004 0.060 2670 Dihedral : 23.223 111.018 3364 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % 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 aren not related in a simple way. whole: -1.03 (0.19), residues: 1774 helix: 0.34 (0.21), residues: 568 sheet: -0.41 (0.26), residues: 398 loop : -1.54 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 701 TYR 0.020 0.002 TYR B 271 PHE 0.014 0.001 PHE D 62 TRP 0.013 0.001 TRP A1014 HIS 0.014 0.001 HIS C 687 Details of bonding type rmsd covalent geometry : bond 0.00348 (17446) covalent geometry : angle 0.70870 (24130) hydrogen bonds : bond 0.04659 ( 763) hydrogen bonds : angle 4.64184 ( 2137) metal coordination : bond 0.01138 ( 8) metal coordination : angle 4.94739 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2303.90 seconds wall clock time: 41 minutes 2.74 seconds (2462.74 seconds total)