Starting phenix.real_space_refine on Sun Aug 24 12:12:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbt_7849/08_2025/6dbt_7849_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbt_7849/08_2025/6dbt_7849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dbt_7849/08_2025/6dbt_7849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbt_7849/08_2025/6dbt_7849.map" model { file = "/net/cci-nas-00/data/ceres_data/6dbt_7849/08_2025/6dbt_7849_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbt_7849/08_2025/6dbt_7849_neut.cif" } resolution = 4.3 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= 0.006 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 222 5.49 5 S 112 5.16 5 C 11800 2.51 5 N 3553 2.21 5 O 4203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19896 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4955 Classifications: {'peptide': 614} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 588} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 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: 4956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4956 Classifications: {'peptide': 614} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 589} 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: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1023 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1027 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "G" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1245 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "H" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1256 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} 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 2636 SG CYS A 749 106.665 99.076 96.537 1.00123.70 S ATOM 2657 SG CYS A 752 108.556 101.879 97.372 1.00227.41 S ATOM 10306 SG CYS C 749 47.965 32.858 95.607 1.00 60.43 S Residues with excluded nonbonded symmetry interactions: 26 residue: pdb=" P DA E 39 " occ=0.90 ... (19 atoms not shown) pdb=" C4 DA E 39 " occ=0.90 residue: pdb=" P DA E 40 " occ=0.91 ... (19 atoms not shown) pdb=" C4 DA E 40 " occ=0.91 residue: pdb=" P DA E 41 " occ=0.97 ... (19 atoms not shown) pdb=" C4 DA E 41 " occ=0.97 residue: pdb=" P DA E 42 " occ=0.92 ... (19 atoms not shown) pdb=" C4 DA E 42 " occ=0.92 residue: pdb=" P DC E 44 " occ=0.84 ... (17 atoms not shown) pdb=" C6 DC E 44 " occ=0.84 residue: pdb=" P DG F 7 " occ=0.73 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.73 residue: pdb=" P DG F 8 " occ=0.76 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.76 residue: pdb=" P DT F 9 " occ=0.82 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.82 residue: pdb=" P DT F 10 " occ=0.91 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.91 residue: pdb=" P DT F 11 " occ=0.87 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.87 residue: pdb=" P DT F 12 " occ=0.82 ... (18 atoms not shown) pdb=" C6 DT F 12 " occ=0.82 residue: pdb=" P DT F 13 " occ=0.93 ... (18 atoms not shown) pdb=" C6 DT F 13 " occ=0.93 ... (remaining 14 not shown) Time building chain proxies: 4.65, per 1000 atoms: 0.23 Number of scatterers: 19896 At special positions: 0 Unit cell: (156.88, 132.5, 150.52, 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 112 16.00 P 222 15.00 O 4203 8.00 N 3553 7.00 C 11800 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: 1.46 Conformation dependent library (CDL) restraints added in 589.3 milliseconds Enol-peptide restraints added in 715.3 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 749 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 752 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " Number of angles added : 2 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 19 sheets defined 37.7% alpha, 19.8% beta 96 base pairs and 174 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 419 through 442 removed outlier: 5.508A pdb=" N ASP A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 460 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 518 through 528 removed outlier: 3.977A pdb=" N GLU A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 600 removed outlier: 5.304A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 705 removed outlier: 3.717A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix removed outlier: 3.570A pdb=" N MET A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 757 through 762 removed outlier: 3.826A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 799 Processing helix chain 'A' and resid 819 through 835 Processing helix chain 'A' and resid 846 through 863 Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 895 through 912 removed outlier: 3.608A pdb=" N GLU A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 4.101A pdb=" N ARG A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 947 removed outlier: 3.530A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TYR A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.753A pdb=" N HIS A 964 " --> pdb=" O LYS A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 973 Processing helix chain 'A' and resid 975 through 979 removed outlier: 3.517A pdb=" N TRP A 978 " --> pdb=" O ILE A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.511A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 997 " --> pdb=" O PHE A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1017 removed outlier: 4.559A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1025 removed outlier: 3.626A pdb=" N PHE A1024 " --> pdb=" O TYR A1020 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.797A pdb=" N LEU B 14 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 15 " --> pdb=" O GLY B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 15' Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 419 through 441 removed outlier: 5.274A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 461 Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.565A pdb=" N ALA C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.626A pdb=" N SER C 511 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 527 Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 589 through 601 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.641A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix removed outlier: 3.535A pdb=" N MET C 705 " --> pdb=" O ARG C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 738 Processing helix chain 'C' and resid 755 through 762 removed outlier: 3.879A pdb=" N ASN C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 819 through 835 removed outlier: 3.867A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 removed outlier: 3.692A pdb=" N ARG C 848 " --> pdb=" O SER C 844 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG C 849 " --> pdb=" O ARG C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 892 Processing helix chain 'C' and resid 895 through 917 removed outlier: 4.027A pdb=" N GLU C 899 " --> pdb=" O GLU C 895 " (cutoff:3.500A) Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 927 through 945 removed outlier: 4.638A pdb=" N SER C 932 " --> pdb=" O LEU C 928 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR C 933 " --> pdb=" O CYS C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 949 Processing helix chain 'C' and resid 955 through 964 removed outlier: 3.775A pdb=" N HIS C 959 " --> pdb=" O THR C 955 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 960 " --> pdb=" O ASN C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 972 Processing helix chain 'C' and resid 975 through 979 removed outlier: 3.625A pdb=" N TRP C 978 " --> pdb=" O ILE C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.510A pdb=" N GLU C 984 " --> pdb=" O SER C 980 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY C 986 " --> pdb=" O GLY C 982 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 991 " --> pdb=" O ASN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1017 removed outlier: 4.498A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1024 Processing helix chain 'D' and resid 308 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.559A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.843A 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: 6.559A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 651 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR A 661 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 5.934A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 22 removed outlier: 4.107A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.756A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B 106 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB1, first strand: chain 'C' and resid 537 through 539 removed outlier: 6.684A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 612 " --> pdb=" O SER C 650 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 648 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS C 616 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE C 646 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER C 618 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N PHE C 644 " --> pdb=" O SER C 618 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP C 620 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE C 642 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N MET C 622 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL C 640 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE C 651 " --> pdb=" O THR C 661 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR C 661 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 554 through 555 removed outlier: 6.928A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL C 640 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N MET C 622 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE C 642 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP C 620 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N PHE C 644 " --> pdb=" O SER C 618 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER C 618 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE C 646 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS C 616 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 648 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 612 " --> pdb=" O SER C 650 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLY C 726 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU C 617 " --> pdb=" O GLY C 726 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 5 removed outlier: 5.650A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 22 removed outlier: 4.506A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 75 through 80 Processing sheet with id=AB6, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AB7, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB9, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AC1, first strand: chain 'D' and resid 263 through 265 672 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 240 hydrogen bonds 480 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 174 stacking parallelities Total time for adding SS restraints: 4.80 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5273 1.34 - 1.46: 5875 1.46 - 1.58: 9015 1.58 - 1.71: 440 1.71 - 1.83: 168 Bond restraints: 20771 Sorted by residual: bond pdb=" C LYS A 912 " pdb=" N PRO A 913 " ideal model delta sigma weight residual 1.337 1.361 -0.024 9.80e-03 1.04e+04 5.97e+00 bond pdb=" C LYS A 840 " pdb=" N PRO A 841 " ideal model delta sigma weight residual 1.334 1.350 -0.017 8.40e-03 1.42e+04 3.99e+00 bond pdb=" CA PRO B 70 " pdb=" C PRO B 70 " ideal model delta sigma weight residual 1.514 1.504 0.010 5.50e-03 3.31e+04 3.64e+00 bond pdb=" C HIS C 482 " pdb=" N PRO C 483 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.65e+00 bond pdb=" C PRO D 17 " pdb=" N GLY D 18 " ideal model delta sigma weight residual 1.332 1.340 -0.008 5.00e-03 4.00e+04 2.49e+00 ... (remaining 20766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 28640 2.67 - 5.33: 340 5.33 - 8.00: 25 8.00 - 10.66: 2 10.66 - 13.33: 4 Bond angle restraints: 29011 Sorted by residual: angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 127.00 140.33 -13.33 2.40e+00 1.74e-01 3.08e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CA PRO D 340 " ideal model delta sigma weight residual 127.00 140.21 -13.21 2.40e+00 1.74e-01 3.03e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CD PRO D 340 " ideal model delta sigma weight residual 120.60 109.10 11.50 2.20e+00 2.07e-01 2.73e+01 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CD PRO B 340 " ideal model delta sigma weight residual 120.60 109.57 11.03 2.20e+00 2.07e-01 2.51e+01 angle pdb=" C TYR C1016 " pdb=" N THR C1017 " pdb=" CA THR C1017 " ideal model delta sigma weight residual 123.17 116.22 6.95 1.49e+00 4.50e-01 2.18e+01 ... (remaining 29006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 10593 35.28 - 70.55: 1310 70.55 - 105.83: 34 105.83 - 141.10: 0 141.10 - 176.38: 5 Dihedral angle restraints: 11942 sinusoidal: 6368 harmonic: 5574 Sorted by residual: dihedral pdb=" CA SER A 511 " pdb=" C SER A 511 " pdb=" N GLY A 512 " pdb=" CA GLY A 512 " ideal model delta harmonic sigma weight residual 180.00 142.81 37.19 0 5.00e+00 4.00e-02 5.53e+01 dihedral pdb=" CA SER C 511 " pdb=" C SER C 511 " pdb=" N GLY C 512 " pdb=" CA GLY C 512 " ideal model delta harmonic sigma weight residual 180.00 148.91 31.09 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA SER B 147 " pdb=" C SER B 147 " pdb=" N ARG B 148 " pdb=" CA ARG B 148 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 11939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2016 0.035 - 0.070: 839 0.070 - 0.105: 234 0.105 - 0.140: 79 0.140 - 0.175: 10 Chirality restraints: 3178 Sorted by residual: chirality pdb=" CA ILE B 77 " pdb=" N ILE B 77 " pdb=" C ILE B 77 " pdb=" CB ILE B 77 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA ASP A 624 " pdb=" N ASP A 624 " pdb=" C ASP A 624 " pdb=" CB ASP A 624 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" C3' DA G 18 " pdb=" C4' DA G 18 " pdb=" O3' DA G 18 " pdb=" C2' DA G 18 " both_signs ideal model delta sigma weight residual False -2.66 -2.50 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 3175 not shown) Planarity restraints: 2969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 197 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO D 198 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 198 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 198 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 338 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO B 339 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG E 34 " -0.028 2.00e-02 2.50e+03 1.22e-02 4.48e+00 pdb=" N9 DG E 34 " 0.028 2.00e-02 2.50e+03 pdb=" C8 DG E 34 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG E 34 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG E 34 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DG E 34 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG E 34 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG E 34 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG E 34 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG E 34 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG E 34 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG E 34 " 0.002 2.00e-02 2.50e+03 ... (remaining 2966 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 152 2.47 - 3.08: 13626 3.08 - 3.68: 33277 3.68 - 4.29: 44787 4.29 - 4.90: 67298 Nonbonded interactions: 159140 Sorted by model distance: nonbonded pdb=" NZ LYS C 638 " pdb=" OD2 ASP C 683 " model vdw 1.860 3.120 nonbonded pdb=" OE2 GLU A 463 " pdb=" NZ LYS C 447 " model vdw 1.900 3.120 nonbonded pdb=" NE2 HIS D 222 " pdb=" OE2 GLU D 280 " model vdw 1.961 3.120 nonbonded pdb=" NZ LYS A 804 " pdb=" OE1 GLU B 101 " model vdw 1.976 3.120 nonbonded pdb=" NH1 ARG C 575 " pdb=" O PHE C 576 " model vdw 1.999 3.120 ... (remaining 159135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 408 through 459 or (resid 460 and (name N or name CA or na \ me C or name CB )) or resid 461 through 1103)) } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.330 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.598 20778 Z= 0.321 Angle : 0.845 35.800 29013 Z= 0.468 Chirality : 0.043 0.175 3178 Planarity : 0.005 0.060 2969 Dihedral : 24.264 176.378 8354 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.18 % Favored : 90.62 % Rotamer: Outliers : 0.12 % Allowed : 37.59 % Favored : 62.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.16 (0.15), residues: 1918 helix: -2.41 (0.16), residues: 631 sheet: -1.82 (0.27), residues: 312 loop : -3.40 (0.16), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 284 TYR 0.021 0.003 TYR C 500 PHE 0.024 0.003 PHE D 274 TRP 0.030 0.003 TRP A1014 HIS 0.016 0.002 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00527 (20771) covalent geometry : angle 0.81804 (29011) hydrogen bonds : bond 0.13853 ( 896) hydrogen bonds : angle 7.30431 ( 2346) metal coordination : bond 0.35998 ( 7) metal coordination : angle 25.52318 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 277 time to evaluate : 0.411 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 622 MET cc_start: 0.9315 (ttm) cc_final: 0.8982 (mtm) REVERT: A 671 GLU cc_start: 0.9464 (pm20) cc_final: 0.8972 (pt0) REVERT: A 869 MET cc_start: 0.8612 (ttt) cc_final: 0.8196 (tpp) REVERT: A 947 LYS cc_start: 0.8763 (tttt) cc_final: 0.8458 (tppt) REVERT: B 43 THR cc_start: 0.9574 (m) cc_final: 0.9348 (p) REVERT: C 427 LEU cc_start: 0.9237 (mt) cc_final: 0.8982 (mm) REVERT: C 617 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8546 (mm-30) REVERT: C 737 MET cc_start: 0.8588 (mmt) cc_final: 0.8174 (mmt) REVERT: D 52 LYS cc_start: 0.8525 (ptpt) cc_final: 0.7959 (ptpt) REVERT: D 91 LEU cc_start: 0.7785 (mt) cc_final: 0.7480 (mt) REVERT: D 129 LEU cc_start: 0.9399 (mt) cc_final: 0.8986 (tp) outliers start: 2 outliers final: 0 residues processed: 278 average time/residue: 0.1872 time to fit residues: 73.3629 Evaluate side-chains 150 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS A 669 ASN A 687 HIS ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS B 83 GLN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN C 772 HIS C 817 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 GLN C 983 ASN D 79 HIS ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.070131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.050751 restraints weight = 111455.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051984 restraints weight = 60917.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.052741 restraints weight = 41162.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.053192 restraints weight = 32397.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.053457 restraints weight = 28209.199| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20778 Z= 0.194 Angle : 0.757 11.115 29013 Z= 0.416 Chirality : 0.044 0.177 3178 Planarity : 0.006 0.053 2969 Dihedral : 26.247 175.039 4556 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.35 % Favored : 92.60 % Rotamer: Outliers : 0.12 % Allowed : 3.31 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.85 (0.17), residues: 1918 helix: -1.00 (0.18), residues: 646 sheet: -1.65 (0.28), residues: 319 loop : -2.64 (0.17), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 999 TYR 0.023 0.002 TYR D 268 PHE 0.028 0.002 PHE A 993 TRP 0.030 0.003 TRP C 915 HIS 0.019 0.002 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00426 (20771) covalent geometry : angle 0.75446 (29011) hydrogen bonds : bond 0.04998 ( 896) hydrogen bonds : angle 5.32831 ( 2346) metal coordination : bond 0.03226 ( 7) metal coordination : angle 7.91107 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 0.462 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 471 GLU cc_start: 0.9256 (tp30) cc_final: 0.8923 (tp30) REVERT: A 557 LEU cc_start: 0.8983 (mp) cc_final: 0.8531 (mp) REVERT: A 671 GLU cc_start: 0.8761 (pm20) cc_final: 0.8551 (pt0) REVERT: A 902 LEU cc_start: 0.9318 (mt) cc_final: 0.9081 (mt) REVERT: A 905 MET cc_start: 0.8867 (tpp) cc_final: 0.8622 (tpp) REVERT: B 43 THR cc_start: 0.9305 (m) cc_final: 0.9044 (p) REVERT: B 56 LYS cc_start: 0.8805 (tptm) cc_final: 0.8384 (tptp) REVERT: B 162 MET cc_start: 0.7952 (mtm) cc_final: 0.7208 (mtp) REVERT: B 232 ARG cc_start: 0.8260 (mpt90) cc_final: 0.8043 (ptp-170) REVERT: B 271 TYR cc_start: 0.8186 (m-80) cc_final: 0.7950 (m-10) REVERT: C 436 THR cc_start: 0.9180 (p) cc_final: 0.8826 (p) REVERT: C 524 ASN cc_start: 0.9025 (t0) cc_final: 0.8739 (t0) REVERT: C 606 MET cc_start: 0.6267 (tpt) cc_final: 0.6006 (tpt) REVERT: C 652 ARG cc_start: 0.7563 (tpt90) cc_final: 0.6869 (tpt90) REVERT: C 704 MET cc_start: 0.8385 (tpp) cc_final: 0.7793 (tpp) REVERT: C 748 ILE cc_start: 0.8589 (pt) cc_final: 0.8371 (tp) REVERT: C 905 MET cc_start: 0.8971 (tpp) cc_final: 0.8610 (tpp) REVERT: D 52 LYS cc_start: 0.8688 (ptpt) cc_final: 0.8315 (ptpt) REVERT: D 146 ASN cc_start: 0.8806 (m-40) cc_final: 0.8498 (p0) outliers start: 2 outliers final: 0 residues processed: 267 average time/residue: 0.1642 time to fit residues: 62.9380 Evaluate side-chains 144 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 19 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 196 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 146 ASN ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.067287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.047838 restraints weight = 113970.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049045 restraints weight = 63044.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049805 restraints weight = 42977.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.050283 restraints weight = 33894.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.050533 restraints weight = 29436.212| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20778 Z= 0.219 Angle : 0.726 9.649 29013 Z= 0.398 Chirality : 0.042 0.172 3178 Planarity : 0.005 0.073 2969 Dihedral : 25.986 173.880 4556 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.14 % Favored : 92.81 % Rotamer: Outliers : 0.18 % Allowed : 4.55 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.31 (0.18), residues: 1918 helix: -0.52 (0.19), residues: 641 sheet: -1.59 (0.28), residues: 343 loop : -2.25 (0.18), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 850 TYR 0.017 0.002 TYR C 500 PHE 0.019 0.002 PHE A 993 TRP 0.032 0.003 TRP C 915 HIS 0.010 0.002 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00477 (20771) covalent geometry : angle 0.72565 (29011) hydrogen bonds : bond 0.04752 ( 896) hydrogen bonds : angle 5.16708 ( 2346) metal coordination : bond 0.02234 ( 7) metal coordination : angle 2.81577 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 200 time to evaluate : 0.676 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 453 LEU cc_start: 0.9426 (mm) cc_final: 0.9204 (mm) REVERT: A 471 GLU cc_start: 0.9233 (tp30) cc_final: 0.8884 (tp30) REVERT: A 474 MET cc_start: 0.8914 (tpp) cc_final: 0.8345 (tpp) REVERT: A 869 MET cc_start: 0.8378 (tmm) cc_final: 0.8108 (tmm) REVERT: A 882 ARG cc_start: 0.9115 (tmm160) cc_final: 0.8699 (ttp80) REVERT: A 902 LEU cc_start: 0.9337 (mt) cc_final: 0.9060 (mt) REVERT: A 947 LYS cc_start: 0.9149 (tttm) cc_final: 0.8596 (tppt) REVERT: B 244 SER cc_start: 0.8839 (t) cc_final: 0.8608 (m) REVERT: C 436 THR cc_start: 0.8921 (p) cc_final: 0.8167 (p) REVERT: C 524 ASN cc_start: 0.9068 (t0) cc_final: 0.8769 (t0) REVERT: C 880 MET cc_start: 0.8693 (ppp) cc_final: 0.8186 (ppp) REVERT: C 905 MET cc_start: 0.9065 (tpp) cc_final: 0.8616 (tpp) REVERT: D 52 LYS cc_start: 0.8566 (ptpt) cc_final: 0.8234 (ptpt) REVERT: D 129 LEU cc_start: 0.9155 (mm) cc_final: 0.8765 (tt) outliers start: 3 outliers final: 2 residues processed: 203 average time/residue: 0.1669 time to fit residues: 49.2195 Evaluate side-chains 133 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 185 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 HIS ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.065889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.046649 restraints weight = 114669.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.047778 restraints weight = 64880.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.048511 restraints weight = 45005.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.048948 restraints weight = 35663.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.049174 restraints weight = 31238.158| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 81 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 20778 Z= 0.241 Angle : 0.742 17.991 29013 Z= 0.399 Chirality : 0.043 0.163 3178 Planarity : 0.005 0.054 2969 Dihedral : 25.812 173.243 4556 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.25 % Favored : 92.70 % Rotamer: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.14 (0.18), residues: 1918 helix: -0.40 (0.19), residues: 650 sheet: -1.45 (0.29), residues: 338 loop : -2.16 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 897 TYR 0.024 0.002 TYR A 578 PHE 0.019 0.002 PHE C 437 TRP 0.031 0.002 TRP C 915 HIS 0.008 0.002 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00516 (20771) covalent geometry : angle 0.73254 (29011) hydrogen bonds : bond 0.04627 ( 896) hydrogen bonds : angle 5.09981 ( 2346) metal coordination : bond 0.04226 ( 7) metal coordination : angle 14.04242 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.668 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 471 GLU cc_start: 0.9191 (tp30) cc_final: 0.8779 (tp30) REVERT: A 474 MET cc_start: 0.8878 (tpp) cc_final: 0.8369 (tpp) REVERT: A 622 MET cc_start: 0.8299 (tmm) cc_final: 0.7715 (tmm) REVERT: A 869 MET cc_start: 0.8127 (tmm) cc_final: 0.7758 (tmm) REVERT: A 902 LEU cc_start: 0.9354 (mt) cc_final: 0.9053 (mt) REVERT: A 1010 LEU cc_start: 0.9562 (tp) cc_final: 0.9356 (tp) REVERT: B 271 TYR cc_start: 0.8328 (m-80) cc_final: 0.8092 (m-10) REVERT: C 524 ASN cc_start: 0.9040 (t0) cc_final: 0.8747 (t0) REVERT: C 825 GLU cc_start: 0.8774 (tp30) cc_final: 0.8542 (tp30) REVERT: C 880 MET cc_start: 0.8693 (ppp) cc_final: 0.8161 (ppp) REVERT: C 905 MET cc_start: 0.9056 (tpp) cc_final: 0.8843 (tpp) REVERT: D 52 LYS cc_start: 0.8512 (ptpt) cc_final: 0.8267 (ptpt) REVERT: D 65 ASN cc_start: 0.7868 (p0) cc_final: 0.7612 (p0) REVERT: D 129 LEU cc_start: 0.9207 (mm) cc_final: 0.8856 (tp) REVERT: D 150 LYS cc_start: 0.8441 (ptpp) cc_final: 0.8215 (ptpp) outliers start: 1 outliers final: 1 residues processed: 173 average time/residue: 0.1605 time to fit residues: 40.7855 Evaluate side-chains 123 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 17 optimal weight: 0.9980 chunk 87 optimal weight: 0.0010 chunk 186 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.067218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.047984 restraints weight = 111501.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049135 restraints weight = 62533.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.049866 restraints weight = 43075.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.050305 restraints weight = 34219.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.050539 restraints weight = 29866.680| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 81 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20778 Z= 0.159 Angle : 0.680 10.706 29013 Z= 0.372 Chirality : 0.041 0.180 3178 Planarity : 0.004 0.051 2969 Dihedral : 25.654 172.574 4556 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.79 (0.18), residues: 1918 helix: -0.05 (0.20), residues: 646 sheet: -1.19 (0.30), residues: 322 loop : -2.01 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 477 TYR 0.018 0.002 TYR A 578 PHE 0.028 0.001 PHE A 993 TRP 0.026 0.001 TRP C 915 HIS 0.007 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00343 (20771) covalent geometry : angle 0.67781 (29011) hydrogen bonds : bond 0.03924 ( 896) hydrogen bonds : angle 4.86432 ( 2346) metal coordination : bond 0.01124 ( 7) metal coordination : angle 6.35388 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.532 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 471 GLU cc_start: 0.9178 (tp30) cc_final: 0.8745 (tp30) REVERT: A 474 MET cc_start: 0.8864 (tpp) cc_final: 0.7943 (tpp) REVERT: A 680 MET cc_start: 0.8124 (mpp) cc_final: 0.7918 (mpp) REVERT: A 869 MET cc_start: 0.8257 (tmm) cc_final: 0.7983 (tmm) REVERT: A 882 ARG cc_start: 0.9133 (tmm160) cc_final: 0.8788 (ttp80) REVERT: A 902 LEU cc_start: 0.9322 (mt) cc_final: 0.8999 (mt) REVERT: B 155 LEU cc_start: 0.9163 (tt) cc_final: 0.8856 (mt) REVERT: C 503 MET cc_start: 0.8991 (tmm) cc_final: 0.8711 (tmm) REVERT: C 524 ASN cc_start: 0.9048 (t0) cc_final: 0.8754 (t0) REVERT: C 825 GLU cc_start: 0.8761 (tp30) cc_final: 0.8527 (tp30) REVERT: C 863 MET cc_start: 0.8779 (mmm) cc_final: 0.8430 (mmt) REVERT: C 880 MET cc_start: 0.8667 (ppp) cc_final: 0.8132 (ppp) REVERT: C 905 MET cc_start: 0.9039 (tpp) cc_final: 0.8790 (tpp) REVERT: D 52 LYS cc_start: 0.8482 (ptpt) cc_final: 0.8251 (ptpt) REVERT: D 65 ASN cc_start: 0.7851 (p0) cc_final: 0.7543 (p0) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1552 time to fit residues: 41.4588 Evaluate side-chains 130 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 17 optimal weight: 0.6980 chunk 79 optimal weight: 0.0270 chunk 122 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 213 optimal weight: 10.0000 chunk 74 optimal weight: 0.0170 chunk 70 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.068355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.049330 restraints weight = 110322.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.050536 restraints weight = 61049.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.051297 restraints weight = 41540.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.051734 restraints weight = 32728.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.052040 restraints weight = 28506.050| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20778 Z= 0.144 Angle : 0.671 12.568 29013 Z= 0.365 Chirality : 0.041 0.175 3178 Planarity : 0.004 0.049 2969 Dihedral : 25.448 172.191 4556 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.06 % Allowed : 2.07 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.47 (0.19), residues: 1918 helix: 0.18 (0.20), residues: 646 sheet: -0.98 (0.29), residues: 331 loop : -1.81 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 73 TYR 0.018 0.001 TYR A 578 PHE 0.034 0.001 PHE A 993 TRP 0.029 0.001 TRP C 915 HIS 0.008 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00304 (20771) covalent geometry : angle 0.67029 (29011) hydrogen bonds : bond 0.03629 ( 896) hydrogen bonds : angle 4.65571 ( 2346) metal coordination : bond 0.00494 ( 7) metal coordination : angle 4.50262 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ASP cc_start: 0.9122 (t70) cc_final: 0.8866 (t0) REVERT: A 471 GLU cc_start: 0.9198 (tp30) cc_final: 0.8929 (tm-30) REVERT: A 474 MET cc_start: 0.8973 (tpp) cc_final: 0.8301 (tpp) REVERT: A 622 MET cc_start: 0.8375 (tmm) cc_final: 0.7911 (tmm) REVERT: A 680 MET cc_start: 0.8248 (mpp) cc_final: 0.7695 (mpp) REVERT: A 869 MET cc_start: 0.8297 (tmm) cc_final: 0.8042 (tmm) REVERT: A 882 ARG cc_start: 0.9095 (tmm160) cc_final: 0.8814 (ttp80) REVERT: A 902 LEU cc_start: 0.9261 (mt) cc_final: 0.8937 (mt) REVERT: A 1010 LEU cc_start: 0.9511 (tp) cc_final: 0.9301 (tp) REVERT: B 271 TYR cc_start: 0.7947 (m-10) cc_final: 0.7613 (m-10) REVERT: C 503 MET cc_start: 0.9068 (tmm) cc_final: 0.8716 (tmm) REVERT: C 524 ASN cc_start: 0.9066 (t0) cc_final: 0.8750 (t0) REVERT: C 825 GLU cc_start: 0.8671 (tp30) cc_final: 0.8425 (tp30) REVERT: C 863 MET cc_start: 0.8689 (mmm) cc_final: 0.8420 (mmt) REVERT: C 880 MET cc_start: 0.8657 (ppp) cc_final: 0.8129 (ppp) REVERT: C 905 MET cc_start: 0.9026 (tpp) cc_final: 0.8755 (tpp) REVERT: D 52 LYS cc_start: 0.8486 (ptpt) cc_final: 0.8218 (ptpt) REVERT: D 65 ASN cc_start: 0.7874 (p0) cc_final: 0.7539 (p0) REVERT: D 310 GLU cc_start: 0.8220 (tm-30) cc_final: 0.8010 (tp30) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.1498 time to fit residues: 43.3494 Evaluate side-chains 135 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 23 optimal weight: 6.9990 chunk 133 optimal weight: 0.0050 chunk 64 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 30.0000 chunk 149 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 174 optimal weight: 0.0970 overall best weight: 2.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.067252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.048198 restraints weight = 114520.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.049438 restraints weight = 62240.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.050206 restraints weight = 41900.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050632 restraints weight = 32814.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.050945 restraints weight = 28500.240| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20778 Z= 0.162 Angle : 0.671 12.376 29013 Z= 0.366 Chirality : 0.040 0.173 3178 Planarity : 0.004 0.049 2969 Dihedral : 25.358 172.128 4556 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.36 (0.19), residues: 1918 helix: 0.29 (0.20), residues: 646 sheet: -0.87 (0.29), residues: 328 loop : -1.78 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 39 TYR 0.016 0.001 TYR C 500 PHE 0.020 0.001 PHE A 993 TRP 0.024 0.001 TRP C 915 HIS 0.006 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00352 (20771) covalent geometry : angle 0.67016 (29011) hydrogen bonds : bond 0.03690 ( 896) hydrogen bonds : angle 4.66346 ( 2346) metal coordination : bond 0.00743 ( 7) metal coordination : angle 5.03243 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.559 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 468 ASP cc_start: 0.9147 (t70) cc_final: 0.8892 (t0) REVERT: A 471 GLU cc_start: 0.9224 (tp30) cc_final: 0.8908 (tm-30) REVERT: A 474 MET cc_start: 0.9010 (tpp) cc_final: 0.8361 (tpp) REVERT: A 592 ASP cc_start: 0.9446 (m-30) cc_final: 0.9045 (t0) REVERT: A 622 MET cc_start: 0.8507 (tmm) cc_final: 0.7987 (tmm) REVERT: A 680 MET cc_start: 0.8267 (mpp) cc_final: 0.7728 (mpp) REVERT: A 807 MET cc_start: 0.8694 (tpp) cc_final: 0.8372 (ttm) REVERT: A 869 MET cc_start: 0.8266 (tmm) cc_final: 0.8014 (tmm) REVERT: A 882 ARG cc_start: 0.9130 (tmm160) cc_final: 0.8852 (ttp80) REVERT: A 902 LEU cc_start: 0.9287 (mt) cc_final: 0.8963 (mt) REVERT: C 503 MET cc_start: 0.9146 (tmm) cc_final: 0.8763 (tmm) REVERT: C 524 ASN cc_start: 0.9142 (t0) cc_final: 0.8830 (t0) REVERT: C 825 GLU cc_start: 0.8731 (tp30) cc_final: 0.8476 (tp30) REVERT: C 880 MET cc_start: 0.8655 (ppp) cc_final: 0.8123 (ppp) REVERT: C 905 MET cc_start: 0.9013 (tpp) cc_final: 0.8757 (tpp) REVERT: D 65 ASN cc_start: 0.8021 (p0) cc_final: 0.7673 (p0) REVERT: D 129 LEU cc_start: 0.9173 (mm) cc_final: 0.8883 (tt) REVERT: D 310 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8006 (tp30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1616 time to fit residues: 44.3326 Evaluate side-chains 126 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 176 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 ASN A 997 ASN C 983 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.065534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.046168 restraints weight = 114548.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.047276 restraints weight = 64910.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.047916 restraints weight = 45203.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.048403 restraints weight = 36375.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048656 restraints weight = 31688.151| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 20778 Z= 0.263 Angle : 0.759 12.953 29013 Z= 0.407 Chirality : 0.043 0.267 3178 Planarity : 0.005 0.051 2969 Dihedral : 25.458 172.899 4556 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.56 (0.18), residues: 1918 helix: 0.01 (0.20), residues: 652 sheet: -0.87 (0.29), residues: 326 loop : -1.86 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 459 TYR 0.023 0.002 TYR C 500 PHE 0.019 0.002 PHE A 993 TRP 0.021 0.002 TRP C 915 HIS 0.011 0.002 HIS C 959 Details of bonding type rmsd covalent geometry : bond 0.00565 (20771) covalent geometry : angle 0.75625 (29011) hydrogen bonds : bond 0.04803 ( 896) hydrogen bonds : angle 4.91028 ( 2346) metal coordination : bond 0.01941 ( 7) metal coordination : angle 8.15857 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ASP cc_start: 0.9199 (t70) cc_final: 0.8970 (t0) REVERT: A 471 GLU cc_start: 0.9217 (tp30) cc_final: 0.8766 (tp30) REVERT: A 474 MET cc_start: 0.8984 (tpp) cc_final: 0.7695 (tpp) REVERT: A 592 ASP cc_start: 0.9443 (m-30) cc_final: 0.9062 (t0) REVERT: A 680 MET cc_start: 0.8394 (mpp) cc_final: 0.7820 (mpp) REVERT: A 807 MET cc_start: 0.8710 (tpp) cc_final: 0.8324 (ttm) REVERT: A 869 MET cc_start: 0.8162 (tmm) cc_final: 0.7842 (tmm) REVERT: A 882 ARG cc_start: 0.9078 (tmm160) cc_final: 0.8858 (ttp80) REVERT: A 902 LEU cc_start: 0.9353 (mt) cc_final: 0.9022 (mt) REVERT: C 503 MET cc_start: 0.9118 (tmm) cc_final: 0.8719 (tmm) REVERT: C 680 MET cc_start: 0.8513 (mmm) cc_final: 0.8203 (mmm) REVERT: C 737 MET cc_start: 0.8950 (tpt) cc_final: 0.8590 (tpp) REVERT: C 825 GLU cc_start: 0.8880 (tp30) cc_final: 0.8619 (tp30) REVERT: C 880 MET cc_start: 0.8725 (ppp) cc_final: 0.8200 (ppp) REVERT: C 905 MET cc_start: 0.9123 (tpp) cc_final: 0.8882 (tpp) REVERT: C 945 MET cc_start: 0.8668 (tpt) cc_final: 0.8450 (tpp) REVERT: D 65 ASN cc_start: 0.8085 (p0) cc_final: 0.7698 (p0) REVERT: D 129 LEU cc_start: 0.9174 (mm) cc_final: 0.8897 (tt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1359 time to fit residues: 33.5489 Evaluate side-chains 120 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 5 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 97 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.067544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.047796 restraints weight = 109514.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049020 restraints weight = 60655.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049760 restraints weight = 41641.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.050260 restraints weight = 33135.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.050552 restraints weight = 28755.840| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20778 Z= 0.157 Angle : 0.684 12.301 29013 Z= 0.369 Chirality : 0.041 0.160 3178 Planarity : 0.004 0.051 2969 Dihedral : 25.375 171.389 4556 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.22 (0.19), residues: 1918 helix: 0.39 (0.21), residues: 647 sheet: -0.63 (0.30), residues: 312 loop : -1.73 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 459 TYR 0.018 0.002 TYR A 747 PHE 0.033 0.001 PHE A 993 TRP 0.027 0.001 TRP C 915 HIS 0.006 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00343 (20771) covalent geometry : angle 0.68334 (29011) hydrogen bonds : bond 0.03625 ( 896) hydrogen bonds : angle 4.60224 ( 2346) metal coordination : bond 0.00672 ( 7) metal coordination : angle 4.44695 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ASP cc_start: 0.9158 (t70) cc_final: 0.8869 (t0) REVERT: A 471 GLU cc_start: 0.9188 (tp30) cc_final: 0.8788 (tm-30) REVERT: A 474 MET cc_start: 0.8980 (tpp) cc_final: 0.8226 (tpp) REVERT: A 592 ASP cc_start: 0.9416 (m-30) cc_final: 0.9068 (t0) REVERT: A 622 MET cc_start: 0.8494 (tmm) cc_final: 0.8036 (tmm) REVERT: A 680 MET cc_start: 0.8316 (mpp) cc_final: 0.7714 (mpp) REVERT: A 807 MET cc_start: 0.8725 (tpp) cc_final: 0.8351 (ttm) REVERT: A 869 MET cc_start: 0.8221 (tmm) cc_final: 0.7887 (tmm) REVERT: A 882 ARG cc_start: 0.9083 (tmm160) cc_final: 0.8862 (ttp80) REVERT: A 902 LEU cc_start: 0.9301 (mt) cc_final: 0.8969 (mt) REVERT: B 271 TYR cc_start: 0.8249 (m-80) cc_final: 0.7998 (m-10) REVERT: C 825 GLU cc_start: 0.8697 (tp30) cc_final: 0.8427 (tp30) REVERT: C 863 MET cc_start: 0.8720 (mmm) cc_final: 0.8344 (mmt) REVERT: C 880 MET cc_start: 0.8672 (ppp) cc_final: 0.8199 (ppp) REVERT: D 14 LEU cc_start: 0.9141 (mt) cc_final: 0.8862 (mp) REVERT: D 65 ASN cc_start: 0.8042 (p0) cc_final: 0.7641 (p0) REVERT: D 129 LEU cc_start: 0.9135 (mm) cc_final: 0.8873 (tt) REVERT: D 233 LEU cc_start: 0.8972 (tp) cc_final: 0.8765 (tp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1346 time to fit residues: 35.6871 Evaluate side-chains 124 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 47 optimal weight: 0.0040 chunk 108 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN D 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.067236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.048192 restraints weight = 113948.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049432 restraints weight = 62161.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.050197 restraints weight = 42202.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.050673 restraints weight = 33163.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050909 restraints weight = 28716.281| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20778 Z= 0.145 Angle : 0.679 12.886 29013 Z= 0.364 Chirality : 0.040 0.155 3178 Planarity : 0.004 0.078 2969 Dihedral : 25.265 172.133 4556 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.15 (0.19), residues: 1918 helix: 0.46 (0.20), residues: 646 sheet: -0.69 (0.29), residues: 326 loop : -1.67 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 73 TYR 0.020 0.001 TYR D 268 PHE 0.032 0.001 PHE A 993 TRP 0.025 0.001 TRP C 915 HIS 0.006 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00315 (20771) covalent geometry : angle 0.67862 (29011) hydrogen bonds : bond 0.03578 ( 896) hydrogen bonds : angle 4.52364 ( 2346) metal coordination : bond 0.00508 ( 7) metal coordination : angle 4.06384 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.576 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 468 ASP cc_start: 0.9123 (t70) cc_final: 0.8854 (t0) REVERT: A 471 GLU cc_start: 0.9217 (tp30) cc_final: 0.8755 (tm-30) REVERT: A 474 MET cc_start: 0.9050 (tpp) cc_final: 0.8244 (tpp) REVERT: A 592 ASP cc_start: 0.9429 (m-30) cc_final: 0.9063 (t0) REVERT: A 680 MET cc_start: 0.8270 (mpp) cc_final: 0.7656 (mpp) REVERT: A 807 MET cc_start: 0.8650 (tpp) cc_final: 0.8351 (ttm) REVERT: A 869 MET cc_start: 0.8210 (tmm) cc_final: 0.7958 (tmm) REVERT: A 902 LEU cc_start: 0.9329 (mt) cc_final: 0.8985 (mt) REVERT: B 271 TYR cc_start: 0.8245 (m-80) cc_final: 0.8012 (m-10) REVERT: C 825 GLU cc_start: 0.8728 (tp30) cc_final: 0.8425 (tp30) REVERT: C 863 MET cc_start: 0.8692 (mmm) cc_final: 0.8305 (mmt) REVERT: C 880 MET cc_start: 0.8688 (ppp) cc_final: 0.8177 (ppp) REVERT: C 945 MET cc_start: 0.8684 (tpt) cc_final: 0.8466 (tpp) REVERT: D 14 LEU cc_start: 0.9163 (mt) cc_final: 0.8803 (mt) REVERT: D 65 ASN cc_start: 0.8100 (p0) cc_final: 0.7717 (p0) REVERT: D 129 LEU cc_start: 0.9158 (mm) cc_final: 0.8890 (tt) REVERT: D 233 LEU cc_start: 0.8992 (tp) cc_final: 0.8764 (tp) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1517 time to fit residues: 38.3874 Evaluate side-chains 127 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 185 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 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 = 0.3532 r_free = 0.3532 target = 0.066954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.047770 restraints weight = 112577.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048969 restraints weight = 62843.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049736 restraints weight = 43116.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.050193 restraints weight = 33930.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.050432 restraints weight = 29589.512| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20778 Z= 0.179 Angle : 0.688 13.038 29013 Z= 0.370 Chirality : 0.040 0.154 3178 Planarity : 0.004 0.068 2969 Dihedral : 25.245 172.846 4556 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.11 (0.19), residues: 1918 helix: 0.48 (0.20), residues: 653 sheet: -0.65 (0.29), residues: 326 loop : -1.66 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 897 TYR 0.018 0.001 TYR C 500 PHE 0.029 0.001 PHE A 993 TRP 0.024 0.002 TRP C 915 HIS 0.006 0.001 HIS C 959 Details of bonding type rmsd covalent geometry : bond 0.00390 (20771) covalent geometry : angle 0.68704 (29011) hydrogen bonds : bond 0.03839 ( 896) hydrogen bonds : angle 4.53248 ( 2346) metal coordination : bond 0.00802 ( 7) metal coordination : angle 5.06341 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3092.28 seconds wall clock time: 54 minutes 16.42 seconds (3256.42 seconds total)