Starting phenix.real_space_refine on Sun Sep 13 01:01:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbt_7849/09_2026/6dbt_7849_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbt_7849/09_2026/6dbt_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_7849/09_2026/6dbt_7849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbt_7849/09_2026/6dbt_7849.map" model { file = "/net/cci-nas-00/data/ceres_data/6dbt_7849/09_2026/6dbt_7849_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbt_7849/09_2026/6dbt_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.71, per 1000 atoms: 0.19 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: 2.18 Conformation dependent library (CDL) restraints added in 865.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 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: 2.63 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: 5.39 Time building geometry restraints manager: 2.89 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=" C1' DC G 35 " pdb=" N1 DC G 35 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.23e+01 bond pdb=" C1' DT F 33 " pdb=" N1 DT F 33 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.87e+01 bond pdb=" C3' DA E 36 " pdb=" C2' DA E 36 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.59e+01 bond pdb=" C3' DT F 33 " pdb=" C2' DT F 33 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.53e+01 bond pdb=" C1' DC G 43 " pdb=" N1 DC G 43 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.49e+01 ... (remaining 20766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 28587 2.67 - 5.33: 393 5.33 - 8.00: 25 8.00 - 10.66: 2 10.66 - 13.33: 4 Bond angle restraints: 29011 Sorted by residual: angle pdb=" O4' DG E 33 " pdb=" C4' DG E 33 " pdb=" C3' DG E 33 " ideal model delta sigma weight residual 106.00 101.74 4.26 6.00e-01 2.78e+00 5.04e+01 angle pdb=" O4' DA E 35 " pdb=" C4' DA E 35 " pdb=" C3' DA E 35 " ideal model delta sigma weight residual 106.00 102.01 3.99 6.00e-01 2.78e+00 4.42e+01 angle pdb=" O4' DG F 42 " pdb=" C1' DG F 42 " pdb=" N9 DG F 42 " ideal model delta sigma weight residual 108.00 112.40 -4.40 7.00e-01 2.04e+00 3.94e+01 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 127.00 140.33 -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 ... (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 - 0.046: 2221 0.046 - 0.092: 757 0.092 - 0.138: 178 0.138 - 0.184: 21 0.184 - 0.230: 1 Chirality restraints: 3178 Sorted by residual: 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 -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C3' DA E 18 " pdb=" C4' DA E 18 " pdb=" O3' DA E 18 " pdb=" C2' DA E 18 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.18 2.00e-01 2.50e+01 7.66e-01 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 ... (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: 1.600 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: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.180 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.598 20778 Z= 0.500 Angle : 0.907 35.800 29013 Z= 0.634 Chirality : 0.048 0.230 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 are 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/Z covalent geometry : bond 0.00621 / 0.46 (20771) covalent geometry : angle 0.88183 / 0.63 (29011) hydrogen bonds : bond 0.13853 / 9.00 ( 896) hydrogen bonds : angle 7.30431 / 5.15 ( 2346) metal coordination : bond 0.35998 / 21.79 ( 7) metal coordination : angle 25.52318 / 12.11 ( 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 : 0.707 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 622 MET cc_start: 0.9315 (ttm) cc_final: 0.8981 (mtm) REVERT: A 671 GLU cc_start: 0.9464 (pm20) cc_final: 0.8921 (pt0) REVERT: A 947 LYS cc_start: 0.8763 (tttt) cc_final: 0.8459 (tppt) REVERT: A 988 LYS cc_start: 0.8751 (pttm) cc_final: 0.8467 (mtmm) REVERT: B 43 THR cc_start: 0.9574 (m) cc_final: 0.9350 (p) REVERT: C 427 LEU cc_start: 0.9237 (mt) cc_final: 0.8986 (mm) REVERT: C 617 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8548 (mm-30) REVERT: C 737 MET cc_start: 0.8588 (mmt) cc_final: 0.8176 (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: 0.8987 (tp) outliers start: 2 outliers final: 0 residues processed: 278 average time/residue: 0.1984 time to fit residues: 79.0498 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 : 0.684 ------------------------------------------------------------------------------- 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: 20.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0970 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: 20.0000 chunk 212 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 overall best weight: 2.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS A 669 ASN A 687 HIS ** 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 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 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.070309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.050883 restraints weight = 111219.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.052105 restraints weight = 60848.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.052877 restraints weight = 41183.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053330 restraints weight = 32257.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.053603 restraints weight = 28057.317| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 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 = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 81 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 17 (23 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20778 Z= 0.191 Angle : 0.818 11.681 29013 Z= 0.449 Chirality : 0.051 0.359 3178 Planarity : 0.006 0.069 2969 Dihedral : 26.402 175.631 4556 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.66 % Favored : 92.28 % Rotamer: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.81 % 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 are not related in a simple way. whole: -2.97 (0.17), residues: 1918 helix: -1.16 (0.18), residues: 644 sheet: -1.65 (0.28), residues: 318 loop : -2.69 (0.17), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 999 TYR 0.032 0.002 TYR D 268 PHE 0.024 0.002 PHE A 993 TRP 0.026 0.002 TRP C 915 HIS 0.017 0.002 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (20771) covalent geometry : angle 0.81498 / 0.45 (29011) hydrogen bonds : bond 0.05532 / 3.67 ( 896) hydrogen bonds : angle 5.44105 / 3.88 ( 2346) metal coordination : bond 0.02610 / 1.66 ( 7) metal coordination : angle 8.47746 / 3.97 ( 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 270 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 268 time to evaluate : 0.736 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 471 GLU cc_start: 0.9244 (tp30) cc_final: 0.8935 (tp30) REVERT: A 557 LEU cc_start: 0.8996 (mp) cc_final: 0.8039 (mt) REVERT: A 902 LEU cc_start: 0.9315 (mt) cc_final: 0.9081 (mt) REVERT: A 905 MET cc_start: 0.8879 (tpp) cc_final: 0.8634 (tpp) REVERT: B 43 THR cc_start: 0.9308 (m) cc_final: 0.9056 (p) REVERT: B 56 LYS cc_start: 0.8794 (tptm) cc_final: 0.8368 (tptp) REVERT: B 232 ARG cc_start: 0.8343 (mpt90) cc_final: 0.8001 (ptp-170) REVERT: B 271 TYR cc_start: 0.8222 (m-80) cc_final: 0.7984 (m-10) REVERT: C 436 THR cc_start: 0.9174 (p) cc_final: 0.8818 (p) REVERT: C 524 ASN cc_start: 0.9032 (t0) cc_final: 0.8748 (t0) REVERT: C 606 MET cc_start: 0.6176 (tpt) cc_final: 0.5953 (tpt) REVERT: C 704 MET cc_start: 0.8306 (tpp) cc_final: 0.7707 (tpp) REVERT: C 733 MET cc_start: 0.8992 (tpp) cc_final: 0.8629 (tpp) REVERT: C 748 ILE cc_start: 0.8620 (pt) cc_final: 0.8396 (tp) REVERT: C 870 ARG cc_start: 0.7100 (ptt90) cc_final: 0.6865 (ptp-170) REVERT: C 880 MET cc_start: 0.8674 (ppp) cc_final: 0.8330 (ppp) REVERT: C 905 MET cc_start: 0.8936 (tpp) cc_final: 0.8570 (tpp) REVERT: D 52 LYS cc_start: 0.8700 (ptpt) cc_final: 0.8338 (ptpt) REVERT: D 146 ASN cc_start: 0.8802 (m-40) cc_final: 0.8484 (p0) outliers start: 2 outliers final: 0 residues processed: 269 average time/residue: 0.1893 time to fit residues: 73.7330 Evaluate side-chains 149 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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: 6.9990 chunk 129 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 196 optimal weight: 50.0000 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.067971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.048502 restraints weight = 112689.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049700 restraints weight = 62362.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.050446 restraints weight = 42631.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050901 restraints weight = 33738.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.051161 restraints weight = 29357.479| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 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 = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 81 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20778 Z= 0.203 Angle : 0.758 18.528 29013 Z= 0.416 Chirality : 0.048 0.367 3178 Planarity : 0.005 0.052 2969 Dihedral : 26.276 174.197 4556 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.99 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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 are not related in a simple way. whole: -2.44 (0.18), residues: 1918 helix: -0.66 (0.19), residues: 642 sheet: -1.47 (0.29), residues: 319 loop : -2.37 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 725 TYR 0.018 0.002 TYR C 500 PHE 0.012 0.002 PHE A 990 TRP 0.033 0.002 TRP A1014 HIS 0.010 0.002 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (20771) covalent geometry : angle 0.74764 / 0.42 (29011) hydrogen bonds : bond 0.05104 / 3.36 ( 896) hydrogen bonds : angle 5.22362 / 3.72 ( 2346) metal coordination : bond 0.01436 / 0.89 ( 7) metal coordination : angle 14.83517 / 5.60 ( 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 199 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.682 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 453 LEU cc_start: 0.9436 (mm) cc_final: 0.9226 (mm) REVERT: A 471 GLU cc_start: 0.9278 (tp30) cc_final: 0.8940 (tp30) REVERT: A 882 ARG cc_start: 0.9126 (tmm160) cc_final: 0.8752 (ttp80) REVERT: A 902 LEU cc_start: 0.9308 (mt) cc_final: 0.9046 (mt) REVERT: B 162 MET cc_start: 0.8232 (mtm) cc_final: 0.7628 (mtp) REVERT: B 232 ARG cc_start: 0.8310 (mpt90) cc_final: 0.8101 (ptp-170) REVERT: B 244 SER cc_start: 0.8891 (t) cc_final: 0.8381 (p) REVERT: C 436 THR cc_start: 0.8867 (p) cc_final: 0.8130 (p) REVERT: C 524 ASN cc_start: 0.9094 (t0) cc_final: 0.8792 (t0) REVERT: C 880 MET cc_start: 0.8639 (ppp) cc_final: 0.8156 (ppp) REVERT: C 905 MET cc_start: 0.9025 (tpp) cc_final: 0.8586 (tpp) REVERT: D 52 LYS cc_start: 0.8618 (ptpt) cc_final: 0.8267 (ptpt) REVERT: D 129 LEU cc_start: 0.9169 (mm) cc_final: 0.8787 (tt) REVERT: D 146 ASN cc_start: 0.8941 (m-40) cc_final: 0.8716 (p0) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1843 time to fit residues: 53.7372 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 : 0.671 ------------------------------------------------------------------------------- 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: 0.3980 chunk 91 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 207 optimal weight: 50.0000 chunk 25 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 83 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 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 = 0.3562 r_free = 0.3562 target = 0.068435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.049003 restraints weight = 111950.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.050190 restraints weight = 62266.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.050939 restraints weight = 42757.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.051386 restraints weight = 33855.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.051604 restraints weight = 29610.504| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 81 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 81 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20778 Z= 0.164 Angle : 0.722 11.197 29013 Z= 0.398 Chirality : 0.047 0.401 3178 Planarity : 0.005 0.084 2969 Dihedral : 26.094 174.277 4556 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.78 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 are not related in a simple way. whole: -2.12 (0.18), residues: 1918 helix: -0.36 (0.19), residues: 641 sheet: -1.34 (0.29), residues: 332 loop : -2.19 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 992 TYR 0.017 0.001 TYR A 747 PHE 0.015 0.001 PHE A 494 TRP 0.033 0.002 TRP C 782 HIS 0.009 0.001 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (20771) covalent geometry : angle 0.71926 / 0.40 (29011) hydrogen bonds : bond 0.04544 / 2.99 ( 896) hydrogen bonds : angle 4.97964 / 3.55 ( 2346) metal coordination : bond 0.01084 / 0.76 ( 7) metal coordination : angle 6.93695 / 3.14 ( 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 192 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.586 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: 0.9230 (t70) cc_final: 0.9023 (t0) REVERT: A 471 GLU cc_start: 0.9259 (tp30) cc_final: 0.8835 (tp30) REVERT: A 474 MET cc_start: 0.8899 (tpp) cc_final: 0.8529 (tpp) REVERT: A 882 ARG cc_start: 0.9105 (tmm160) cc_final: 0.8717 (ttp80) REVERT: B 244 SER cc_start: 0.8855 (t) cc_final: 0.8631 (m) REVERT: B 271 TYR cc_start: 0.8288 (m-80) cc_final: 0.8037 (m-10) REVERT: C 503 MET cc_start: 0.9078 (tmm) cc_final: 0.8716 (tmm) REVERT: C 524 ASN cc_start: 0.9052 (t0) cc_final: 0.8728 (t0) REVERT: C 737 MET cc_start: 0.8891 (tpp) cc_final: 0.8614 (tpt) REVERT: C 880 MET cc_start: 0.8659 (ppp) cc_final: 0.8240 (ppp) REVERT: C 905 MET cc_start: 0.9025 (tpp) cc_final: 0.8754 (tpp) REVERT: D 52 LYS cc_start: 0.8606 (ptpt) cc_final: 0.8259 (ptpt) REVERT: D 65 ASN cc_start: 0.7743 (p0) cc_final: 0.7523 (p0) REVERT: D 129 LEU cc_start: 0.9158 (mm) cc_final: 0.8762 (tt) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1827 time to fit residues: 51.2397 Evaluate side-chains 129 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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: 0.9990 chunk 87 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 173 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 200 optimal weight: 30.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 83 GLN ** 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 = 0.3563 r_free = 0.3563 target = 0.068226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049002 restraints weight = 111530.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.050192 restraints weight = 61969.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050927 restraints weight = 42411.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.051378 restraints weight = 33609.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.051608 restraints weight = 29262.936| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 81 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 81 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20778 Z= 0.157 Angle : 0.710 9.728 29013 Z= 0.392 Chirality : 0.046 0.396 3178 Planarity : 0.005 0.053 2969 Dihedral : 25.972 173.715 4556 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.73 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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 are not related in a simple way. whole: -1.93 (0.18), residues: 1918 helix: -0.20 (0.20), residues: 645 sheet: -1.28 (0.29), residues: 332 loop : -2.05 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 992 TYR 0.026 0.002 TYR C 950 PHE 0.022 0.001 PHE A 494 TRP 0.027 0.002 TRP C 915 HIS 0.008 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (20771) covalent geometry : angle 0.70791 / 0.39 (29011) hydrogen bonds : bond 0.04425 / 2.92 ( 896) hydrogen bonds : angle 4.86034 / 3.46 ( 2346) metal coordination : bond 0.00695 / 0.46 ( 7) metal coordination : angle 6.28761 / 2.79 ( 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 189 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 LEU cc_start: 0.9408 (mm) cc_final: 0.9192 (mm) REVERT: A 468 ASP cc_start: 0.9188 (t70) cc_final: 0.8987 (t0) REVERT: A 471 GLU cc_start: 0.9188 (tp30) cc_final: 0.8782 (tp30) REVERT: A 474 MET cc_start: 0.8854 (tpp) cc_final: 0.8265 (tpp) REVERT: A 680 MET cc_start: 0.8203 (mpp) cc_final: 0.7953 (mpp) REVERT: A 882 ARG cc_start: 0.9036 (tmm160) cc_final: 0.8720 (ttp80) REVERT: A 902 LEU cc_start: 0.9460 (mt) cc_final: 0.9214 (mt) REVERT: B 244 SER cc_start: 0.8783 (t) cc_final: 0.8542 (m) REVERT: B 271 TYR cc_start: 0.8163 (m-80) cc_final: 0.7925 (m-10) REVERT: C 503 MET cc_start: 0.9044 (tmm) cc_final: 0.8639 (tmm) REVERT: C 524 ASN cc_start: 0.9052 (t0) cc_final: 0.8742 (t0) REVERT: C 880 MET cc_start: 0.8591 (ppp) cc_final: 0.8068 (ppp) REVERT: C 905 MET cc_start: 0.8991 (tpp) cc_final: 0.8711 (tpp) REVERT: C 931 TYR cc_start: 0.8218 (t80) cc_final: 0.7912 (t80) REVERT: D 52 LYS cc_start: 0.8534 (ptpt) cc_final: 0.8193 (ptpt) REVERT: D 65 ASN cc_start: 0.7774 (p0) cc_final: 0.7464 (p0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1721 time to fit residues: 48.5953 Evaluate side-chains 129 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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: 0.8980 chunk 79 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 201 optimal weight: 50.0000 chunk 15 optimal weight: 7.9990 chunk 213 optimal weight: 50.0000 chunk 74 optimal weight: 0.3980 chunk 70 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3553 r_free = 0.3553 target = 0.067843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.048492 restraints weight = 110529.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.049668 restraints weight = 61948.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.050435 restraints weight = 42648.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050856 restraints weight = 33605.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.051084 restraints weight = 29498.548| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 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 = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20778 Z= 0.177 Angle : 0.710 10.527 29013 Z= 0.391 Chirality : 0.046 0.396 3178 Planarity : 0.005 0.054 2969 Dihedral : 25.926 173.437 4556 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.67 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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 are not related in a simple way. whole: -1.74 (0.18), residues: 1918 helix: -0.08 (0.20), residues: 651 sheet: -1.12 (0.29), residues: 319 loop : -1.94 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 992 TYR 0.019 0.002 TYR A 578 PHE 0.019 0.002 PHE A 494 TRP 0.025 0.002 TRP C 915 HIS 0.008 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (20771) covalent geometry : angle 0.70769 / 0.39 (29011) hydrogen bonds : bond 0.04383 / 2.92 ( 896) hydrogen bonds : angle 4.81187 / 3.42 ( 2346) metal coordination : bond 0.00949 / 0.63 ( 7) metal coordination : angle 6.51805 / 2.66 ( 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 180 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.766 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 453 LEU cc_start: 0.9420 (mm) cc_final: 0.9193 (mm) REVERT: A 468 ASP cc_start: 0.9213 (t70) cc_final: 0.9002 (t0) REVERT: A 471 GLU cc_start: 0.9247 (tp30) cc_final: 0.8828 (tp30) REVERT: A 474 MET cc_start: 0.8912 (tpp) cc_final: 0.8330 (tpp) REVERT: A 680 MET cc_start: 0.8249 (mpp) cc_final: 0.7786 (mpp) REVERT: A 882 ARG cc_start: 0.9123 (tmm160) cc_final: 0.8801 (ttp80) REVERT: A 902 LEU cc_start: 0.9475 (mt) cc_final: 0.9214 (mt) REVERT: B 244 SER cc_start: 0.8831 (t) cc_final: 0.8599 (m) REVERT: B 271 TYR cc_start: 0.8487 (m-80) cc_final: 0.8211 (m-10) REVERT: C 503 MET cc_start: 0.9152 (tmm) cc_final: 0.8943 (tmm) REVERT: C 524 ASN cc_start: 0.9150 (t0) cc_final: 0.8838 (t0) REVERT: C 737 MET cc_start: 0.8862 (tpt) cc_final: 0.8613 (tpt) REVERT: C 880 MET cc_start: 0.8604 (ppp) cc_final: 0.8101 (ppp) REVERT: C 905 MET cc_start: 0.9032 (tpp) cc_final: 0.8743 (tpp) REVERT: C 931 TYR cc_start: 0.8305 (t80) cc_final: 0.7894 (t80) REVERT: D 65 ASN cc_start: 0.7956 (p0) cc_final: 0.7626 (p0) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1659 time to fit residues: 45.2476 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 : 0.554 ------------------------------------------------------------------------------- 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: 7.9990 chunk 64 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 205 optimal weight: 40.0000 chunk 174 optimal weight: 0.0570 overall best weight: 1.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 874 ASN ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** 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 = 0.3538 r_free = 0.3538 target = 0.067381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048607 restraints weight = 114417.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.049790 restraints weight = 63656.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.050473 restraints weight = 43323.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050942 restraints weight = 34490.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.051175 restraints weight = 30038.040| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 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 = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20778 Z= 0.153 Angle : 0.692 9.645 29013 Z= 0.384 Chirality : 0.046 0.397 3178 Planarity : 0.005 0.052 2969 Dihedral : 25.820 173.135 4556 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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 are not related in a simple way. whole: -1.58 (0.18), residues: 1918 helix: 0.09 (0.20), residues: 643 sheet: -1.00 (0.29), residues: 320 loop : -1.88 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 73 TYR 0.016 0.002 TYR C 500 PHE 0.023 0.001 PHE D 62 TRP 0.027 0.001 TRP C 915 HIS 0.006 0.001 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (20771) covalent geometry : angle 0.68997 / 0.38 (29011) hydrogen bonds : bond 0.04099 / 2.70 ( 896) hydrogen bonds : angle 4.72223 / 3.35 ( 2346) metal coordination : bond 0.00753 / 0.50 ( 7) metal coordination : angle 6.22690 / 2.86 ( 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 184 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.569 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: 0.9165 (t70) cc_final: 0.8960 (t0) REVERT: A 471 GLU cc_start: 0.9196 (tp30) cc_final: 0.8767 (tp30) REVERT: A 474 MET cc_start: 0.8876 (tpp) cc_final: 0.7916 (tpp) REVERT: A 622 MET cc_start: 0.8358 (tmm) cc_final: 0.7927 (tmm) REVERT: A 680 MET cc_start: 0.8217 (mpp) cc_final: 0.7611 (mpp) REVERT: A 882 ARG cc_start: 0.9054 (tmm160) cc_final: 0.8756 (ttp80) REVERT: A 890 GLU cc_start: 0.8815 (tt0) cc_final: 0.8501 (tm-30) REVERT: A 895 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8755 (tm-30) REVERT: A 898 ARG cc_start: 0.6675 (mtt-85) cc_final: 0.6291 (mtt-85) REVERT: A 902 LEU cc_start: 0.9432 (mt) cc_final: 0.9170 (mt) REVERT: A 1010 LEU cc_start: 0.9525 (tp) cc_final: 0.9319 (tp) REVERT: B 244 SER cc_start: 0.8766 (t) cc_final: 0.8515 (m) REVERT: B 271 TYR cc_start: 0.8354 (m-80) cc_final: 0.8124 (m-10) REVERT: C 503 MET cc_start: 0.9111 (tmm) cc_final: 0.8902 (tmm) REVERT: C 524 ASN cc_start: 0.9104 (t0) cc_final: 0.8771 (t0) REVERT: C 606 MET cc_start: 0.5388 (tpt) cc_final: 0.5133 (tpt) REVERT: C 737 MET cc_start: 0.8551 (tpt) cc_final: 0.8308 (tpt) REVERT: C 871 MET cc_start: 0.8161 (mpp) cc_final: 0.7943 (mtt) REVERT: C 880 MET cc_start: 0.8603 (ppp) cc_final: 0.8057 (ppp) REVERT: C 905 MET cc_start: 0.8993 (tpp) cc_final: 0.8686 (tpp) REVERT: C 931 TYR cc_start: 0.8130 (t80) cc_final: 0.7762 (t80) REVERT: D 65 ASN cc_start: 0.7940 (p0) cc_final: 0.7574 (p0) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1693 time to fit residues: 46.9639 Evaluate side-chains 128 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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: 0.6980 chunk 60 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 187 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** 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 = 0.3550 r_free = 0.3550 target = 0.067770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.048388 restraints weight = 113328.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049552 restraints weight = 63152.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.050273 restraints weight = 43520.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.050744 restraints weight = 34714.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050931 restraints weight = 30239.216| |-----------------------------------------------------------------------------| 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: 83 | |-----------------------------------------------------------------------------| |-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: 83 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20778 Z= 0.162 Angle : 0.700 11.254 29013 Z= 0.385 Chirality : 0.045 0.393 3178 Planarity : 0.005 0.059 2969 Dihedral : 25.748 172.777 4556 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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 are not related in a simple way. whole: -1.48 (0.18), residues: 1918 helix: 0.11 (0.20), residues: 652 sheet: -0.89 (0.29), residues: 320 loop : -1.81 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 73 TYR 0.016 0.002 TYR C 500 PHE 0.028 0.002 PHE A 993 TRP 0.026 0.002 TRP C 915 HIS 0.007 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (20771) covalent geometry : angle 0.69865 / 0.38 (29011) hydrogen bonds : bond 0.04146 / 2.77 ( 896) hydrogen bonds : angle 4.68392 / 3.33 ( 2346) metal coordination : bond 0.01554 / 1.05 ( 7) metal coordination : angle 4.53849 / 1.96 ( 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 182 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.842 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 468 ASP cc_start: 0.9141 (t70) cc_final: 0.8923 (t0) REVERT: A 471 GLU cc_start: 0.9203 (tp30) cc_final: 0.8799 (tp30) REVERT: A 474 MET cc_start: 0.8915 (tpp) cc_final: 0.7653 (tpp) REVERT: A 622 MET cc_start: 0.8397 (tmm) cc_final: 0.7957 (tmm) REVERT: A 680 MET cc_start: 0.8227 (mpp) cc_final: 0.7656 (mpp) REVERT: A 882 ARG cc_start: 0.9032 (tmm160) cc_final: 0.8755 (ttp80) REVERT: A 902 LEU cc_start: 0.9440 (mt) cc_final: 0.9157 (mt) REVERT: B 244 SER cc_start: 0.8793 (t) cc_final: 0.8547 (m) REVERT: C 503 MET cc_start: 0.9104 (tmm) cc_final: 0.8871 (tmm) REVERT: C 524 ASN cc_start: 0.9080 (t0) cc_final: 0.8777 (t0) REVERT: C 737 MET cc_start: 0.8583 (tpt) cc_final: 0.8293 (tpt) REVERT: C 880 MET cc_start: 0.8603 (ppp) cc_final: 0.8048 (ppp) REVERT: C 905 MET cc_start: 0.9002 (tpp) cc_final: 0.8724 (tpp) REVERT: D 65 ASN cc_start: 0.7905 (p0) cc_final: 0.7549 (p0) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1663 time to fit residues: 45.9808 Evaluate side-chains 129 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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: 3.9990 chunk 65 optimal weight: 3.9990 chunk 171 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 97 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 464 HIS 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 = 0.3580 r_free = 0.3580 target = 0.068954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.049362 restraints weight = 109679.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.050588 restraints weight = 61084.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.051342 restraints weight = 41897.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.051806 restraints weight = 33339.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.052099 restraints weight = 29037.812| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20778 Z= 0.138 Angle : 0.698 10.385 29013 Z= 0.381 Chirality : 0.045 0.395 3178 Planarity : 0.004 0.049 2969 Dihedral : 25.655 172.516 4556 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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 are not related in a simple way. whole: -1.34 (0.19), residues: 1918 helix: 0.24 (0.20), residues: 647 sheet: -0.68 (0.30), residues: 308 loop : -1.77 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 916 TYR 0.016 0.001 TYR C 500 PHE 0.042 0.001 PHE A 993 TRP 0.028 0.002 TRP C 915 HIS 0.008 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (20771) covalent geometry : angle 0.69693 / 0.38 (29011) hydrogen bonds : bond 0.03903 / 2.60 ( 896) hydrogen bonds : angle 4.60359 / 3.27 ( 2346) metal coordination : bond 0.00755 / 0.49 ( 7) metal coordination : angle 4.16071 / 1.93 ( 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 178 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.617 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: 0.9171 (t70) cc_final: 0.8916 (t0) REVERT: A 471 GLU cc_start: 0.9253 (tp30) cc_final: 0.8973 (tm-30) REVERT: A 474 MET cc_start: 0.8994 (tpp) cc_final: 0.8335 (tpp) REVERT: A 592 ASP cc_start: 0.9455 (m-30) cc_final: 0.9035 (t0) REVERT: A 622 MET cc_start: 0.8389 (tmm) cc_final: 0.7968 (tmm) REVERT: A 680 MET cc_start: 0.8233 (mpp) cc_final: 0.7600 (mpp) REVERT: A 882 ARG cc_start: 0.9057 (tmm160) cc_final: 0.8783 (ttp80) REVERT: A 902 LEU cc_start: 0.9441 (mt) cc_final: 0.9170 (mt) REVERT: A 1010 LEU cc_start: 0.9549 (tp) cc_final: 0.9346 (tp) REVERT: B 155 LEU cc_start: 0.9176 (tt) cc_final: 0.8865 (mt) REVERT: B 244 SER cc_start: 0.8808 (t) cc_final: 0.8584 (m) REVERT: C 503 MET cc_start: 0.9186 (tmm) cc_final: 0.8933 (tmm) REVERT: C 524 ASN cc_start: 0.9184 (t0) cc_final: 0.8866 (t0) REVERT: C 606 MET cc_start: 0.5272 (tpt) cc_final: 0.4988 (tpt) REVERT: C 880 MET cc_start: 0.8629 (ppp) cc_final: 0.8140 (ppp) REVERT: C 905 MET cc_start: 0.8991 (tpp) cc_final: 0.8689 (tpp) REVERT: D 65 ASN cc_start: 0.7957 (p0) cc_final: 0.7616 (p0) REVERT: D 233 LEU cc_start: 0.9157 (tp) cc_final: 0.8903 (tp) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1611 time to fit residues: 43.5380 Evaluate side-chains 129 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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: 6.9990 chunk 108 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 156 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** 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 = 0.3514 r_free = 0.3514 target = 0.066219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.047476 restraints weight = 113111.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.048653 restraints weight = 63282.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.049346 restraints weight = 43240.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.049850 restraints weight = 34205.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.050085 restraints weight = 29453.891| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20778 Z= 0.205 Angle : 0.739 13.109 29013 Z= 0.398 Chirality : 0.045 0.381 3178 Planarity : 0.005 0.062 2969 Dihedral : 25.687 173.337 4556 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 14.62 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 are not related in a simple way. whole: -1.42 (0.19), residues: 1918 helix: 0.14 (0.20), residues: 654 sheet: -0.83 (0.30), residues: 314 loop : -1.77 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 232 TYR 0.019 0.002 TYR C 500 PHE 0.024 0.002 PHE A 993 TRP 0.020 0.002 TRP C 915 HIS 0.009 0.001 HIS C 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (20771) covalent geometry : angle 0.73677 / 0.40 (29011) hydrogen bonds : bond 0.04471 / 2.97 ( 896) hydrogen bonds : angle 4.76052 / 3.38 ( 2346) metal coordination : bond 0.01698 / 1.14 ( 7) metal coordination : angle 6.55341 / 2.54 ( 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 172 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.724 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: 0.9127 (t70) cc_final: 0.8911 (t0) REVERT: A 471 GLU cc_start: 0.9211 (tp30) cc_final: 0.8814 (tp30) REVERT: A 474 MET cc_start: 0.8975 (tpp) cc_final: 0.7854 (tpp) REVERT: A 592 ASP cc_start: 0.9448 (m-30) cc_final: 0.9104 (t0) REVERT: A 680 MET cc_start: 0.8249 (mpp) cc_final: 0.7674 (mpp) REVERT: A 882 ARG cc_start: 0.9050 (tmm160) cc_final: 0.8810 (ttp80) REVERT: A 902 LEU cc_start: 0.9469 (mt) cc_final: 0.9169 (mt) REVERT: A 947 LYS cc_start: 0.9111 (tttm) cc_final: 0.8480 (tppt) REVERT: A 1010 LEU cc_start: 0.9570 (tp) cc_final: 0.9349 (tp) REVERT: B 155 LEU cc_start: 0.9144 (tt) cc_final: 0.8876 (mt) REVERT: B 232 ARG cc_start: 0.8343 (mpt90) cc_final: 0.8101 (ptp-170) REVERT: C 503 MET cc_start: 0.9155 (tmm) cc_final: 0.8898 (tmm) REVERT: C 880 MET cc_start: 0.8639 (ppp) cc_final: 0.8182 (ppp) REVERT: D 65 ASN cc_start: 0.8021 (p0) cc_final: 0.7640 (p0) REVERT: D 129 LEU cc_start: 0.9180 (mm) cc_final: 0.8905 (tt) REVERT: D 233 LEU cc_start: 0.9142 (tp) cc_final: 0.8900 (tp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1638 time to fit residues: 43.2823 Evaluate side-chains 122 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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: 0.8980 chunk 160 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 201 optimal weight: 50.0000 chunk 17 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 195 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** D 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.067653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048631 restraints weight = 115169.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.049806 restraints weight = 64240.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.050535 restraints weight = 44078.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050987 restraints weight = 34997.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.051252 restraints weight = 30518.025| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 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 = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20778 Z= 0.140 Angle : 0.706 11.156 29013 Z= 0.382 Chirality : 0.045 0.390 3178 Planarity : 0.004 0.050 2969 Dihedral : 25.608 172.796 4556 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.06 % Allowed : 0.41 % Favored : 99.53 % 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 are not related in a simple way. whole: -1.25 (0.19), residues: 1918 helix: 0.29 (0.20), residues: 649 sheet: -0.70 (0.29), residues: 320 loop : -1.68 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 708 TYR 0.016 0.001 TYR A 747 PHE 0.025 0.001 PHE A 993 TRP 0.029 0.002 TRP A 538 HIS 0.008 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (20771) covalent geometry : angle 0.70508 / 0.38 (29011) hydrogen bonds : bond 0.03822 / 2.55 ( 896) hydrogen bonds : angle 4.61277 / 3.27 ( 2346) metal coordination : bond 0.00615 / 0.40 ( 7) metal coordination : angle 4.57816 / 2.10 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.03 seconds wall clock time: 59 minutes 58.58 seconds (3598.58 seconds total)