Starting phenix.real_space_refine on Sun Sep 13 00:57:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbq_7847/09_2026/6dbq_7847_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbq_7847/09_2026/6dbq_7847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dbq_7847/09_2026/6dbq_7847_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbq_7847/09_2026/6dbq_7847_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dbq_7847/09_2026/6dbq_7847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbq_7847/09_2026/6dbq_7847.map" } resolution = 4.22 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= 0.009 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 11837 2.51 5 N 3565 2.21 5 O 4214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19956 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4999 Classifications: {'peptide': 621} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 596} 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: 4972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4972 Classifications: {'peptide': 616} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 590} 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 2680 SG CYS A 749 57.331 83.908 33.106 1.00 74.96 S ATOM 10357 SG CYS C 749 61.990 61.912 113.881 1.00 62.00 S Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" P DA E 39 " occ=0.80 ... (19 atoms not shown) pdb=" C4 DA E 39 " occ=0.80 residue: pdb=" P DA E 40 " occ=0.71 ... (19 atoms not shown) pdb=" C4 DA E 40 " occ=0.71 residue: pdb=" P DA E 41 " occ=0.70 ... (19 atoms not shown) pdb=" C4 DA E 41 " occ=0.70 residue: pdb=" P DA E 42 " occ=0.48 ... (19 atoms not shown) pdb=" C4 DA E 42 " occ=0.48 residue: pdb=" P DC E 44 " occ=0.47 ... (17 atoms not shown) pdb=" C6 DC E 44 " occ=0.47 residue: pdb=" P DG F 7 " occ=0.62 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.62 residue: pdb=" P DG F 8 " occ=0.72 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.72 residue: pdb=" P DT F 9 " occ=0.66 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.66 residue: pdb=" P DT F 10 " occ=0.76 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.76 residue: pdb=" P DT F 11 " occ=0.70 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.70 residue: pdb=" P DT F 12 " occ=0.74 ... (18 atoms not shown) pdb=" C6 DT F 12 " occ=0.74 residue: pdb=" P DT F 13 " occ=0.76 ... (18 atoms not shown) pdb=" C6 DT F 13 " occ=0.76 ... (remaining 16 not shown) Time building chain proxies: 4.28, per 1000 atoms: 0.21 Number of scatterers: 19956 At special positions: 0 Unit cell: (154.75, 149.798, 134.942, 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 4214 8.00 N 3565 7.00 C 11837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 698.4 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 C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 18 sheets defined 37.5% alpha, 23.0% beta 86 base pairs and 171 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.510A pdb=" N SER A 417 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 442 removed outlier: 5.784A pdb=" N ASP A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 461 removed outlier: 3.511A pdb=" N VAL A 449 " --> pdb=" O ASP A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.605A pdb=" N ALA A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 497 through 511 Processing helix chain 'A' and resid 518 through 527 Processing helix chain 'A' and resid 577 through 601 removed outlier: 4.901A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.603A pdb=" N CYS A 607 " --> pdb=" O ASP A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 687 through 704 Proline residue: A 696 - end of helix Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.680A pdb=" N ALA A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 819 through 835 Processing helix chain 'A' and resid 844 through 863 removed outlier: 3.919A pdb=" N ARG A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 894 through 912 Processing helix chain 'A' and resid 912 through 917 removed outlier: 4.024A pdb=" N ARG A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 946 removed outlier: 3.759A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TYR A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.560A pdb=" N HIS A 959 " --> pdb=" O THR A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.603A pdb=" N GLU A 984 " --> pdb=" O SER A 980 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1017 Processing helix chain 'A' and resid 1018 through 1025 Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 419 through 442 removed outlier: 6.074A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 461 removed outlier: 4.021A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 526 removed outlier: 3.757A pdb=" N LEU C 522 " --> pdb=" O PRO C 518 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN C 524 " --> pdb=" O HIS C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 529 No H-bonds generated for 'chain 'C' and resid 527 through 529' Processing helix chain 'C' and resid 577 through 600 removed outlier: 5.022A pdb=" N GLU C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 705 Proline residue: C 696 - end of helix removed outlier: 3.744A 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 757 through 762 removed outlier: 3.579A pdb=" N GLN C 761 " --> pdb=" O ALA C 757 " (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 815 through 835 removed outlier: 4.226A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 890 Processing helix chain 'C' and resid 894 through 912 Processing helix chain 'C' and resid 912 through 917 removed outlier: 3.701A pdb=" N ARG C 916 " --> pdb=" O LYS C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 930 removed outlier: 4.048A pdb=" N LEU C 928 " --> pdb=" O CYS C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 964 through 972 Processing helix chain 'C' and resid 980 through 985 removed outlier: 3.578A pdb=" N GLU C 984 " --> pdb=" O SER C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 997 removed outlier: 4.004A pdb=" N PHE C 990 " --> pdb=" O GLY C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 4.665A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 removed outlier: 3.513A pdb=" N GLN C1022 " --> pdb=" O SER C1018 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C1027 " --> pdb=" O LYS C1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 168 through 172 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: 6.659A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 612 " --> pdb=" O SER A 650 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N PHE A 644 " --> pdb=" O PRO A 676 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 575 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.659A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 612 " --> pdb=" O SER A 650 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 651 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR A 661 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.275A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU B 55 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE B 345 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.364A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS B 89 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 129 through 130 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 160 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 536 through 539 removed outlier: 6.589A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR C 727 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLU C 617 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 639 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 536 through 539 removed outlier: 6.589A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR C 727 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLU C 617 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 639 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N MET C 647 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLN C 664 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE C 649 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 23 removed outlier: 4.498A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE D 318 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 61 through 62 removed outlier: 6.774A pdb=" N SER D 61 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N CYS D 124 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 96 through 97 removed outlier: 3.517A pdb=" N GLU D 101 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 138 through 147 removed outlier: 6.830A pdb=" N GLY D 139 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY D 158 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 147 removed outlier: 6.830A pdb=" N GLY D 139 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY D 158 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLY D 157 " --> pdb=" O GLN D 181 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLN D 181 " --> pdb=" O GLY D 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AB9, first strand: chain 'D' and resid 263 through 265 715 hydrogen bonds defined for protein. 1995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 212 hydrogen bonds 408 hydrogen bond angles 0 basepair planarities 86 basepair parallelities 171 stacking parallelities Total time for adding SS restraints: 5.47 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4309 1.33 - 1.45: 5718 1.45 - 1.57: 10198 1.57 - 1.70: 441 1.70 - 1.82: 168 Bond restraints: 20834 Sorted by residual: bond pdb=" C1' DC G 35 " pdb=" N1 DC G 35 " ideal model delta sigma weight residual 1.468 1.554 -0.086 1.40e-02 5.10e+03 3.82e+01 bond pdb=" CG GLN D 83 " pdb=" CD GLN D 83 " ideal model delta sigma weight residual 1.516 1.380 0.136 2.50e-02 1.60e+03 2.95e+01 bond pdb=" CG HIS C 817 " pdb=" CD2 HIS C 817 " ideal model delta sigma weight residual 1.354 1.409 -0.055 1.10e-02 8.26e+03 2.53e+01 bond pdb=" CG ASN B 10 " pdb=" OD1 ASN B 10 " ideal model delta sigma weight residual 1.231 1.321 -0.090 1.90e-02 2.77e+03 2.25e+01 bond pdb=" C1' DT H 36 " pdb=" N1 DT H 36 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.89e+01 ... (remaining 20829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.08: 29080 10.08 - 20.16: 15 20.16 - 30.25: 2 30.25 - 40.33: 2 40.33 - 50.41: 2 Bond angle restraints: 29101 Sorted by residual: angle pdb=" CB ASN C 432 " pdb=" CG ASN C 432 " pdb=" ND2 ASN C 432 " ideal model delta sigma weight residual 116.40 66.60 49.80 1.50e+00 4.44e-01 1.10e+03 angle pdb=" CB ASN C 432 " pdb=" CG ASN C 432 " pdb=" OD1 ASN C 432 " ideal model delta sigma weight residual 120.80 171.21 -50.41 2.00e+00 2.50e-01 6.35e+02 angle pdb=" CG GLN A 423 " pdb=" CD GLN A 423 " pdb=" NE2 GLN A 423 " ideal model delta sigma weight residual 116.40 79.13 37.27 1.50e+00 4.44e-01 6.17e+02 angle pdb=" CG GLN A 423 " pdb=" CD GLN A 423 " pdb=" OE1 GLN A 423 " ideal model delta sigma weight residual 120.80 157.58 -36.78 2.00e+00 2.50e-01 3.38e+02 angle pdb=" OD1 ASN C 432 " pdb=" CG ASN C 432 " pdb=" ND2 ASN C 432 " ideal model delta sigma weight residual 122.60 106.78 15.82 1.00e+00 1.00e+00 2.50e+02 ... (remaining 29096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 10739 35.53 - 71.05: 1202 71.05 - 106.58: 30 106.58 - 142.10: 2 142.10 - 177.63: 5 Dihedral angle restraints: 11978 sinusoidal: 6380 harmonic: 5598 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 180.00 153.37 26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" N HIS B 344 " pdb=" C HIS B 344 " pdb=" CA HIS B 344 " pdb=" CB HIS B 344 " ideal model delta harmonic sigma weight residual 122.80 109.89 12.91 0 2.50e+00 1.60e-01 2.67e+01 dihedral pdb=" CA PRO D 98 " pdb=" C PRO D 98 " pdb=" N ASN D 99 " pdb=" CA ASN D 99 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 11975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2571 0.060 - 0.120: 546 0.120 - 0.180: 63 0.180 - 0.240: 5 0.240 - 0.300: 2 Chirality restraints: 3187 Sorted by residual: chirality pdb=" CA HIS C 817 " pdb=" N HIS C 817 " pdb=" C HIS C 817 " pdb=" CB HIS C 817 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA GLN D 83 " pdb=" N GLN D 83 " pdb=" C GLN D 83 " pdb=" CB GLN D 83 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA HIS B 344 " pdb=" N HIS B 344 " pdb=" C HIS B 344 " pdb=" CB HIS B 344 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3184 not shown) Planarity restraints: 2984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 817 " 0.149 2.00e-02 2.50e+03 1.49e-01 3.33e+02 pdb=" CG HIS C 817 " -0.313 2.00e-02 2.50e+03 pdb=" ND1 HIS C 817 " 0.088 2.00e-02 2.50e+03 pdb=" CD2 HIS C 817 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS C 817 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS C 817 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 344 " 0.085 2.00e-02 2.50e+03 1.12e-01 1.88e+02 pdb=" CG HIS B 344 " -0.237 2.00e-02 2.50e+03 pdb=" ND1 HIS B 344 " 0.073 2.00e-02 2.50e+03 pdb=" CD2 HIS B 344 " 0.080 2.00e-02 2.50e+03 pdb=" CE1 HIS B 344 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 344 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 10 " 0.058 2.00e-02 2.50e+03 1.18e-01 1.40e+02 pdb=" CG ASN B 10 " -0.204 2.00e-02 2.50e+03 pdb=" OD1 ASN B 10 " 0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN B 10 " 0.069 2.00e-02 2.50e+03 ... (remaining 2981 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 118 2.34 - 2.98: 10527 2.98 - 3.62: 32798 3.62 - 4.26: 48285 4.26 - 4.90: 72855 Nonbonded interactions: 164583 Sorted by model distance: nonbonded pdb=" NH1 ARG D 123 " pdb=" OE2 GLU D 125 " model vdw 1.700 3.120 nonbonded pdb=" OD1 ASN B 99 " pdb=" OE2 GLU B 101 " model vdw 1.806 3.040 nonbonded pdb=" NZ LYS C 435 " pdb=" OE2 GLU C 439 " model vdw 1.807 3.120 nonbonded pdb=" OE2 GLU A 789 " pdb=" NH1 ARG A 797 " model vdw 1.837 3.120 nonbonded pdb=" OG1 THR B 97 " pdb=" OE2 GLU B 101 " model vdw 1.856 3.040 ... (remaining 164578 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' and (resid 408 through 628 or resid 635 through 1103)) selection = (chain 'C' and (resid 408 through 1028 or resid 1101 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: 0.520 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: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.610 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.007 0.283 20839 Z= 0.466 Angle : 1.103 50.410 29101 Z= 0.754 Chirality : 0.048 0.300 3187 Planarity : 0.007 0.149 2984 Dihedral : 23.407 177.626 8376 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 27.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.37 % Favored : 89.53 % Rotamer: Outliers : 0.12 % Allowed : 27.39 % Favored : 72.50 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.15), residues: 1929 helix: -2.72 (0.14), residues: 660 sheet: -1.82 (0.26), residues: 323 loop : -3.19 (0.17), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 123 TYR 0.036 0.003 TYR D 29 PHE 0.023 0.003 PHE B 62 TRP 0.040 0.003 TRP A 538 HIS 0.151 0.005 HIS C 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.46 (20834) covalent geometry : angle 1.10298 / 0.75 (29101) hydrogen bonds : bond 0.14497 / 10.64 ( 889) hydrogen bonds : angle 6.73345 / 4.62 ( 2403) metal coordination : bond 0.16540 / 11.83 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 376 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ARG cc_start: 0.6533 (mtt-85) cc_final: 0.6297 (mpt180) REVERT: A 705 MET cc_start: 0.7386 (mmm) cc_final: 0.6832 (mtp) REVERT: B 23 ASP cc_start: 0.7779 (t0) cc_final: 0.7318 (t0) REVERT: B 39 ARG cc_start: 0.8394 (tpt-90) cc_final: 0.7937 (ttp-170) REVERT: B 270 GLU cc_start: 0.8274 (mp0) cc_final: 0.8041 (mm-30) REVERT: B 285 MET cc_start: 0.8313 (mmm) cc_final: 0.8058 (mpp) REVERT: C 466 GLN cc_start: 0.8628 (mt0) cc_final: 0.7634 (mp10) REVERT: C 617 GLU cc_start: 0.9009 (pt0) cc_final: 0.8715 (pt0) REVERT: C 691 THR cc_start: 0.9251 (p) cc_final: 0.9014 (p) REVERT: C 898 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7480 (ttm-80) REVERT: C 909 LEU cc_start: 0.9069 (mt) cc_final: 0.8698 (mt) REVERT: C 945 MET cc_start: 0.8637 (mtp) cc_final: 0.8422 (mmm) REVERT: C 1028 HIS cc_start: 0.8657 (t70) cc_final: 0.8171 (t-170) REVERT: D 1 MET cc_start: 0.6785 (pmt) cc_final: 0.6287 (pmt) REVERT: D 51 LYS cc_start: 0.8564 (mttt) cc_final: 0.8193 (mmmt) REVERT: D 86 LYS cc_start: 0.8133 (tptp) cc_final: 0.7902 (tptp) outliers start: 2 outliers final: 0 residues processed: 378 average time/residue: 0.1793 time to fit residues: 99.3719 Evaluate side-chains 198 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 30.0000 chunk 212 optimal weight: 50.0000 chunk 77 optimal weight: 30.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 HIS A 517 GLN A 687 HIS A 775 ASN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN A 936 GLN A 964 HIS A1028 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS B 344 HIS C 432 ASN C 433 GLN C 761 GLN ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 ASN ** C 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1028 HIS D 33 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.089594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.063730 restraints weight = 85749.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.065254 restraints weight = 48246.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066196 restraints weight = 33557.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066762 restraints weight = 27020.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067110 restraints weight = 23787.123| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 12 (18 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.515 20839 Z= 0.392 Angle : 0.949 10.440 29101 Z= 0.521 Chirality : 0.054 0.362 3187 Planarity : 0.008 0.093 2984 Dihedral : 26.459 178.848 4566 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.61 % Favored : 91.34 % Rotamer: Outliers : 0.18 % Allowed : 5.95 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.16), residues: 1929 helix: -1.89 (0.16), residues: 667 sheet: -1.63 (0.27), residues: 307 loop : -2.83 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 675 TYR 0.034 0.003 TYR C 578 PHE 0.023 0.003 PHE C 806 TRP 0.067 0.004 TRP A 560 HIS 0.018 0.003 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.37 (20834) covalent geometry : angle 0.94918 / 0.52 (29101) hydrogen bonds : bond 0.06794 / 4.63 ( 889) hydrogen bonds : angle 5.74410 / 3.96 ( 2403) metal coordination : bond 0.23070 / 12.82 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 264 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ARG cc_start: 0.6950 (mtt-85) cc_final: 0.6384 (mpt180) REVERT: A 486 CYS cc_start: 0.8450 (t) cc_final: 0.8125 (t) REVERT: A 869 MET cc_start: 0.8208 (ppp) cc_final: 0.7953 (ppp) REVERT: A 914 VAL cc_start: 0.9279 (m) cc_final: 0.8977 (p) REVERT: C 898 ARG cc_start: 0.7583 (ttm170) cc_final: 0.7366 (ttm-80) REVERT: C 951 ASP cc_start: 0.8812 (p0) cc_final: 0.8527 (p0) REVERT: C 987 ASN cc_start: 0.8175 (t0) cc_final: 0.7972 (t0) REVERT: C 1007 GLU cc_start: 0.8580 (tt0) cc_final: 0.8233 (mt-10) REVERT: D 24 LEU cc_start: 0.8379 (pt) cc_final: 0.8099 (tp) REVERT: D 27 ASP cc_start: 0.7737 (t0) cc_final: 0.7528 (t70) REVERT: D 51 LYS cc_start: 0.8638 (mttt) cc_final: 0.8220 (mmmt) REVERT: D 187 LEU cc_start: 0.8772 (tt) cc_final: 0.8524 (tt) REVERT: D 289 TYR cc_start: 0.8135 (t80) cc_final: 0.7689 (t80) outliers start: 3 outliers final: 1 residues processed: 267 average time/residue: 0.1711 time to fit residues: 68.0286 Evaluate side-chains 165 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 171 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 188 optimal weight: 30.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS C 761 GLN C 997 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.091611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.064167 restraints weight = 85905.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065880 restraints weight = 45055.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.066939 restraints weight = 30373.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.067582 restraints weight = 23983.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.067868 restraints weight = 20995.192| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 20839 Z= 0.194 Angle : 0.774 8.459 29101 Z= 0.431 Chirality : 0.050 0.342 3187 Planarity : 0.006 0.083 2984 Dihedral : 26.361 177.317 4566 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.96 % Favored : 93.99 % Rotamer: Outliers : 0.12 % Allowed : 3.89 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.17), residues: 1929 helix: -0.91 (0.18), residues: 661 sheet: -1.61 (0.25), residues: 343 loop : -2.50 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 870 TYR 0.026 0.002 TYR C 500 PHE 0.018 0.002 PHE A 826 TRP 0.030 0.002 TRP A1014 HIS 0.012 0.002 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (20834) covalent geometry : angle 0.77375 / 0.43 (29101) hydrogen bonds : bond 0.05540 / 3.88 ( 889) hydrogen bonds : angle 5.08327 / 3.51 ( 2403) metal coordination : bond 0.00898 / 0.54 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ARG cc_start: 0.6861 (mtt-85) cc_final: 0.6153 (mpt180) REVERT: A 486 CYS cc_start: 0.8440 (t) cc_final: 0.8201 (t) REVERT: A 499 GLN cc_start: 0.8385 (mt0) cc_final: 0.7877 (mt0) REVERT: A 629 HIS cc_start: 0.5373 (t70) cc_final: 0.4950 (t70) REVERT: A 733 MET cc_start: 0.8954 (tpp) cc_final: 0.8703 (tpp) REVERT: A 825 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8469 (mm-30) REVERT: A 908 TYR cc_start: 0.8852 (t80) cc_final: 0.8624 (t80) REVERT: A 914 VAL cc_start: 0.9192 (m) cc_final: 0.8834 (p) REVERT: A 936 GLN cc_start: 0.8407 (tp-100) cc_final: 0.8150 (tp-100) REVERT: A 1017 THR cc_start: 0.7624 (t) cc_final: 0.7415 (t) REVERT: B 39 ARG cc_start: 0.7904 (tpt-90) cc_final: 0.7638 (ttp-170) REVERT: C 528 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7289 (tm-30) REVERT: C 594 MET cc_start: 0.9309 (mmm) cc_final: 0.9004 (mmm) REVERT: C 691 THR cc_start: 0.8549 (p) cc_final: 0.8276 (p) REVERT: C 711 ILE cc_start: 0.8540 (mm) cc_final: 0.8330 (mm) REVERT: C 735 ARG cc_start: 0.8769 (mtp-110) cc_final: 0.8536 (mtp-110) REVERT: C 898 ARG cc_start: 0.7313 (ttm170) cc_final: 0.6996 (ttm110) REVERT: C 951 ASP cc_start: 0.8787 (p0) cc_final: 0.8490 (p0) REVERT: C 1007 GLU cc_start: 0.8569 (tt0) cc_final: 0.8203 (mt-10) REVERT: D 51 LYS cc_start: 0.8660 (mttt) cc_final: 0.8195 (mmmt) REVERT: D 100 ASN cc_start: 0.7948 (p0) cc_final: 0.7729 (p0) outliers start: 2 outliers final: 1 residues processed: 249 average time/residue: 0.1602 time to fit residues: 60.7603 Evaluate side-chains 172 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 130 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 175 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN A 936 GLN B 33 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN C 501 HIS C 817 HIS D 170 GLN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.092549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.064933 restraints weight = 86737.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066634 restraints weight = 45566.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.067672 restraints weight = 30734.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.068307 restraints weight = 24448.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068622 restraints weight = 21447.106| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20839 Z= 0.166 Angle : 0.732 8.512 29101 Z= 0.409 Chirality : 0.048 0.344 3187 Planarity : 0.005 0.064 2984 Dihedral : 26.215 177.716 4566 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.36 % Rotamer: Outliers : 0.12 % Allowed : 4.71 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.17), residues: 1929 helix: -0.41 (0.19), residues: 658 sheet: -1.30 (0.26), residues: 337 loop : -2.31 (0.18), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 721 TYR 0.029 0.002 TYR C 500 PHE 0.018 0.002 PHE C 494 TRP 0.022 0.002 TRP C 549 HIS 0.008 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (20834) covalent geometry : angle 0.73240 / 0.41 (29101) hydrogen bonds : bond 0.05096 / 3.55 ( 889) hydrogen bonds : angle 4.77501 / 3.30 ( 2403) metal coordination : bond 0.00912 / 0.55 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 0.680 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 477 ARG cc_start: 0.6751 (mtt-85) cc_final: 0.6088 (mpt180) REVERT: A 486 CYS cc_start: 0.8439 (t) cc_final: 0.8157 (t) REVERT: A 499 GLN cc_start: 0.8467 (mt0) cc_final: 0.7959 (mt0) REVERT: A 629 HIS cc_start: 0.5072 (t70) cc_final: 0.4764 (t70) REVERT: A 737 MET cc_start: 0.7659 (mtm) cc_final: 0.7195 (mtt) REVERT: A 825 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8321 (mm-30) REVERT: A 914 VAL cc_start: 0.9182 (m) cc_final: 0.8807 (p) REVERT: A 936 GLN cc_start: 0.8374 (tp40) cc_final: 0.8135 (tp-100) REVERT: B 23 ASP cc_start: 0.6530 (t0) cc_final: 0.6287 (t0) REVERT: B 33 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7739 (pp30) REVERT: B 39 ARG cc_start: 0.7920 (tpt-90) cc_final: 0.7437 (ttp-170) REVERT: C 528 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7180 (tm-30) REVERT: C 735 ARG cc_start: 0.8793 (mtp-110) cc_final: 0.8375 (mtp-110) REVERT: C 898 ARG cc_start: 0.7419 (ttm170) cc_final: 0.7034 (ttm110) REVERT: C 951 ASP cc_start: 0.8763 (p0) cc_final: 0.8460 (p0) REVERT: C 1004 PHE cc_start: 0.8323 (m-80) cc_final: 0.8051 (m-10) REVERT: C 1007 GLU cc_start: 0.8426 (tt0) cc_final: 0.8104 (mt-10) REVERT: C 1017 THR cc_start: 0.9307 (m) cc_final: 0.8989 (p) REVERT: D 51 LYS cc_start: 0.8692 (mttt) cc_final: 0.8221 (mmmt) REVERT: D 56 LYS cc_start: 0.8312 (tptt) cc_final: 0.7991 (tptt) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.1489 time to fit residues: 54.7996 Evaluate side-chains 176 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 136 optimal weight: 5.9990 chunk 205 optimal weight: 50.0000 chunk 186 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS C 501 HIS C 517 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 535 GLN C 666 GLN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1028 HIS ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.090120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.063036 restraints weight = 86445.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.064510 restraints weight = 50852.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.065213 restraints weight = 33990.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.065713 restraints weight = 26318.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.065703 restraints weight = 23905.719| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20839 Z= 0.274 Angle : 0.794 8.170 29101 Z= 0.440 Chirality : 0.050 0.348 3187 Planarity : 0.005 0.061 2984 Dihedral : 26.242 178.564 4566 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.05 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.17), residues: 1929 helix: -0.41 (0.18), residues: 654 sheet: -1.34 (0.26), residues: 329 loop : -2.18 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 577 TYR 0.026 0.002 TYR C 500 PHE 0.022 0.002 PHE C 663 TRP 0.022 0.003 TRP C 782 HIS 0.014 0.002 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.27 (20834) covalent geometry : angle 0.79406 / 0.44 (29101) hydrogen bonds : bond 0.05608 / 3.84 ( 889) hydrogen bonds : angle 4.98235 / 3.45 ( 2403) metal coordination : bond 0.01332 / 0.81 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ARG cc_start: 0.6830 (mtt-85) cc_final: 0.6161 (mpt180) REVERT: A 486 CYS cc_start: 0.8534 (t) cc_final: 0.8217 (t) REVERT: A 499 GLN cc_start: 0.8340 (mt0) cc_final: 0.7887 (mt0) REVERT: A 594 MET cc_start: 0.8994 (mmt) cc_final: 0.8684 (mmt) REVERT: A 629 HIS cc_start: 0.5025 (t70) cc_final: 0.4774 (t70) REVERT: A 704 MET cc_start: 0.8652 (ptm) cc_final: 0.8089 (ptm) REVERT: A 737 MET cc_start: 0.7631 (mtm) cc_final: 0.6894 (mtm) REVERT: A 825 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8282 (mm-30) REVERT: A 936 GLN cc_start: 0.8414 (tp40) cc_final: 0.8146 (tp-100) REVERT: B 23 ASP cc_start: 0.6821 (t0) cc_final: 0.6055 (t0) REVERT: C 466 GLN cc_start: 0.8826 (mt0) cc_final: 0.8265 (mp10) REVERT: C 594 MET cc_start: 0.9346 (mmm) cc_final: 0.9089 (mmm) REVERT: C 898 ARG cc_start: 0.7701 (ttm170) cc_final: 0.6955 (ttm110) REVERT: C 951 ASP cc_start: 0.8679 (p0) cc_final: 0.8385 (p0) REVERT: C 1007 GLU cc_start: 0.8486 (tt0) cc_final: 0.8229 (mt-10) REVERT: C 1017 THR cc_start: 0.9432 (m) cc_final: 0.9065 (p) REVERT: D 51 LYS cc_start: 0.8695 (mttt) cc_final: 0.8126 (mmmt) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1419 time to fit residues: 48.8639 Evaluate side-chains 159 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 174 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 205 optimal weight: 40.0000 chunk 83 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 193 optimal weight: 50.0000 chunk 12 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 202 optimal weight: 40.0000 chunk 213 optimal weight: 40.0000 chunk 18 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.089635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.062153 restraints weight = 84935.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.063790 restraints weight = 45063.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.064793 restraints weight = 30536.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.065380 restraints weight = 24256.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065751 restraints weight = 21390.546| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20839 Z= 0.260 Angle : 0.782 8.058 29101 Z= 0.434 Chirality : 0.049 0.348 3187 Planarity : 0.005 0.060 2984 Dihedral : 26.267 177.667 4566 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.15 % Favored : 92.79 % Rotamer: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.18), residues: 1929 helix: -0.33 (0.19), residues: 654 sheet: -1.34 (0.27), residues: 328 loop : -2.10 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 39 TYR 0.029 0.002 TYR C 500 PHE 0.026 0.002 PHE C 724 TRP 0.015 0.002 TRP D 307 HIS 0.010 0.002 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.26 (20834) covalent geometry : angle 0.78249 / 0.43 (29101) hydrogen bonds : bond 0.05430 / 3.73 ( 889) hydrogen bonds : angle 4.98907 / 3.47 ( 2403) metal coordination : bond 0.01134 / 0.67 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ARG cc_start: 0.6775 (mtt-85) cc_final: 0.6281 (ttt180) REVERT: A 486 CYS cc_start: 0.8612 (t) cc_final: 0.8279 (t) REVERT: A 499 GLN cc_start: 0.8444 (mt0) cc_final: 0.7920 (mt0) REVERT: A 594 MET cc_start: 0.8990 (mmt) cc_final: 0.8778 (mmt) REVERT: A 704 MET cc_start: 0.8631 (ptm) cc_final: 0.8092 (ptm) REVERT: A 737 MET cc_start: 0.7825 (mtm) cc_final: 0.6958 (mtm) REVERT: A 807 MET cc_start: 0.7627 (ttt) cc_final: 0.7421 (ttt) REVERT: A 825 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8372 (mm-30) REVERT: A 922 ARG cc_start: 0.8378 (ttp80) cc_final: 0.7875 (ttp80) REVERT: B 23 ASP cc_start: 0.6637 (t0) cc_final: 0.5929 (t0) REVERT: B 162 MET cc_start: 0.8495 (mpp) cc_final: 0.8200 (mpp) REVERT: C 466 GLN cc_start: 0.8803 (mt0) cc_final: 0.8288 (mp10) REVERT: C 504 TYR cc_start: 0.8359 (t80) cc_final: 0.8094 (t80) REVERT: C 594 MET cc_start: 0.9392 (mmm) cc_final: 0.9069 (mmm) REVERT: C 711 ILE cc_start: 0.8644 (mm) cc_final: 0.8442 (mm) REVERT: C 898 ARG cc_start: 0.7766 (ttm170) cc_final: 0.7021 (ttm110) REVERT: C 945 MET cc_start: 0.8220 (mtp) cc_final: 0.7947 (tmm) REVERT: C 951 ASP cc_start: 0.8613 (p0) cc_final: 0.8248 (p0) REVERT: C 1007 GLU cc_start: 0.8490 (tt0) cc_final: 0.8224 (mt-10) REVERT: C 1017 THR cc_start: 0.9397 (m) cc_final: 0.9023 (p) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.1467 time to fit residues: 47.9147 Evaluate side-chains 154 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 14 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 198 optimal weight: 50.0000 chunk 150 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN A 831 GLN A 910 GLN ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.090483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.063684 restraints weight = 84142.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.065507 restraints weight = 47873.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.065922 restraints weight = 30186.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066318 restraints weight = 25414.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.066381 restraints weight = 22719.924| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20839 Z= 0.212 Angle : 0.749 8.861 29101 Z= 0.417 Chirality : 0.048 0.344 3187 Planarity : 0.005 0.059 2984 Dihedral : 26.223 177.012 4566 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.53 % Favored : 93.42 % Rotamer: Outliers : 0.06 % Allowed : 1.88 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.18), residues: 1929 helix: -0.15 (0.19), residues: 654 sheet: -1.40 (0.27), residues: 336 loop : -1.99 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 39 TYR 0.031 0.002 TYR C 500 PHE 0.029 0.002 PHE B 62 TRP 0.023 0.002 TRP A 782 HIS 0.009 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (20834) covalent geometry : angle 0.74855 / 0.42 (29101) hydrogen bonds : bond 0.05189 / 3.58 ( 889) hydrogen bonds : angle 4.87059 / 3.39 ( 2403) metal coordination : bond 0.00995 / 0.60 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ARG cc_start: 0.6546 (mtt-85) cc_final: 0.6134 (ttt180) REVERT: A 486 CYS cc_start: 0.8655 (t) cc_final: 0.8401 (t) REVERT: A 499 GLN cc_start: 0.8238 (mt0) cc_final: 0.7802 (mt0) REVERT: A 594 MET cc_start: 0.9000 (mmt) cc_final: 0.8791 (mmt) REVERT: A 704 MET cc_start: 0.8687 (ptm) cc_final: 0.8168 (ptm) REVERT: A 733 MET cc_start: 0.8993 (tpp) cc_final: 0.8683 (tpp) REVERT: A 737 MET cc_start: 0.7619 (mtm) cc_final: 0.6751 (mtm) REVERT: A 807 MET cc_start: 0.7620 (ttt) cc_final: 0.7318 (ttt) REVERT: A 825 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8322 (mm-30) REVERT: A 922 ARG cc_start: 0.8419 (ttp80) cc_final: 0.7956 (ttp80) REVERT: A 1000 GLN cc_start: 0.8378 (tp40) cc_final: 0.7700 (tp-100) REVERT: B 23 ASP cc_start: 0.6638 (t0) cc_final: 0.5861 (t0) REVERT: B 39 ARG cc_start: 0.8028 (tpt-90) cc_final: 0.7445 (ttp-170) REVERT: C 466 GLN cc_start: 0.8855 (mt0) cc_final: 0.8295 (mp10) REVERT: C 504 TYR cc_start: 0.8454 (t80) cc_final: 0.8168 (t80) REVERT: C 594 MET cc_start: 0.9394 (mmm) cc_final: 0.9089 (mmm) REVERT: C 711 ILE cc_start: 0.8589 (mm) cc_final: 0.8379 (mm) REVERT: C 898 ARG cc_start: 0.7677 (ttm170) cc_final: 0.6908 (ttm110) REVERT: C 945 MET cc_start: 0.8241 (mtp) cc_final: 0.7946 (tmm) REVERT: C 951 ASP cc_start: 0.8658 (p0) cc_final: 0.8296 (p0) REVERT: C 1007 GLU cc_start: 0.8496 (tt0) cc_final: 0.8197 (mt-10) REVERT: C 1017 THR cc_start: 0.9421 (m) cc_final: 0.9133 (p) outliers start: 1 outliers final: 1 residues processed: 211 average time/residue: 0.1414 time to fit residues: 47.5593 Evaluate side-chains 155 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 213 optimal weight: 40.0000 chunk 151 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 140 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.091427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.063844 restraints weight = 84541.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.065510 restraints weight = 44769.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066524 restraints weight = 30230.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067123 restraints weight = 23983.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.067415 restraints weight = 21048.323| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20839 Z= 0.164 Angle : 0.720 8.967 29101 Z= 0.400 Chirality : 0.047 0.338 3187 Planarity : 0.005 0.056 2984 Dihedral : 26.123 177.120 4566 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.17 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.18), residues: 1929 helix: 0.01 (0.19), residues: 657 sheet: -1.23 (0.27), residues: 336 loop : -1.86 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 39 TYR 0.019 0.002 TYR C 500 PHE 0.030 0.002 PHE B 62 TRP 0.021 0.002 TRP C 782 HIS 0.008 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (20834) covalent geometry : angle 0.71991 / 0.40 (29101) hydrogen bonds : bond 0.04893 / 3.44 ( 889) hydrogen bonds : angle 4.69332 / 3.27 ( 2403) metal coordination : bond 0.00656 / 0.40 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ARG cc_start: 0.6344 (mtt-85) cc_final: 0.5970 (ttt180) REVERT: A 486 CYS cc_start: 0.8597 (t) cc_final: 0.8332 (t) REVERT: A 499 GLN cc_start: 0.8098 (mt0) cc_final: 0.7694 (mt0) REVERT: A 677 LEU cc_start: 0.8826 (tp) cc_final: 0.8391 (tt) REVERT: A 678 CYS cc_start: 0.8236 (m) cc_final: 0.7601 (m) REVERT: A 704 MET cc_start: 0.8684 (ptm) cc_final: 0.8151 (ptm) REVERT: A 737 MET cc_start: 0.7570 (mtm) cc_final: 0.6724 (mtm) REVERT: A 825 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8185 (mm-30) REVERT: A 869 MET cc_start: 0.7593 (ppp) cc_final: 0.6825 (ppp) REVERT: A 922 ARG cc_start: 0.8477 (ttp80) cc_final: 0.7971 (ttp80) REVERT: A 1000 GLN cc_start: 0.8261 (tp40) cc_final: 0.7655 (tp-100) REVERT: B 23 ASP cc_start: 0.6452 (t0) cc_final: 0.5649 (t0) REVERT: B 39 ARG cc_start: 0.8067 (tpt-90) cc_final: 0.7471 (ttp-170) REVERT: B 256 LEU cc_start: 0.8414 (tp) cc_final: 0.7983 (tt) REVERT: C 466 GLN cc_start: 0.8753 (mt0) cc_final: 0.8250 (mp10) REVERT: C 504 TYR cc_start: 0.8512 (t80) cc_final: 0.8039 (t80) REVERT: C 594 MET cc_start: 0.9365 (mmm) cc_final: 0.9053 (mmm) REVERT: C 711 ILE cc_start: 0.8579 (mm) cc_final: 0.8305 (mm) REVERT: C 898 ARG cc_start: 0.7610 (ttm170) cc_final: 0.7008 (ttm110) REVERT: C 951 ASP cc_start: 0.8681 (p0) cc_final: 0.8366 (p0) REVERT: C 1007 GLU cc_start: 0.8486 (tt0) cc_final: 0.8146 (mt-10) REVERT: C 1017 THR cc_start: 0.9309 (m) cc_final: 0.9020 (p) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1348 time to fit residues: 46.9031 Evaluate side-chains 160 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 72 optimal weight: 7.9990 chunk 69 optimal weight: 0.0570 chunk 44 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 15 optimal weight: 0.0270 chunk 197 optimal weight: 50.0000 chunk 174 optimal weight: 6.9990 overall best weight: 1.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.092086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064596 restraints weight = 83319.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066270 restraints weight = 44491.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.067306 restraints weight = 30179.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067939 restraints weight = 23932.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068236 restraints weight = 20944.115| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20839 Z= 0.149 Angle : 0.709 9.010 29101 Z= 0.394 Chirality : 0.047 0.327 3187 Planarity : 0.005 0.088 2984 Dihedral : 26.055 177.720 4566 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.18), residues: 1929 helix: 0.24 (0.20), residues: 655 sheet: -1.08 (0.28), residues: 336 loop : -1.84 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 870 TYR 0.025 0.002 TYR C 500 PHE 0.029 0.002 PHE B 62 TRP 0.016 0.002 TRP C 782 HIS 0.017 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (20834) covalent geometry : angle 0.70943 / 0.39 (29101) hydrogen bonds : bond 0.04744 / 3.39 ( 889) hydrogen bonds : angle 4.60975 / 3.21 ( 2403) metal coordination : bond 0.00523 / 0.32 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ARG cc_start: 0.6388 (mtt-85) cc_final: 0.5931 (ttt180) REVERT: A 486 CYS cc_start: 0.8606 (t) cc_final: 0.8332 (t) REVERT: A 499 GLN cc_start: 0.8078 (mt0) cc_final: 0.7642 (mt0) REVERT: A 677 LEU cc_start: 0.8738 (tp) cc_final: 0.8292 (tt) REVERT: A 678 CYS cc_start: 0.8236 (m) cc_final: 0.7667 (m) REVERT: A 704 MET cc_start: 0.8714 (ptm) cc_final: 0.8150 (ptm) REVERT: A 733 MET cc_start: 0.9066 (tpp) cc_final: 0.8836 (tpp) REVERT: A 737 MET cc_start: 0.7595 (mtm) cc_final: 0.6593 (mtm) REVERT: A 807 MET cc_start: 0.7322 (ttt) cc_final: 0.7081 (ttt) REVERT: A 825 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8341 (mm-30) REVERT: A 922 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7973 (ttp80) REVERT: A 1000 GLN cc_start: 0.8279 (tp40) cc_final: 0.7595 (tp-100) REVERT: B 39 ARG cc_start: 0.8016 (tpt-90) cc_final: 0.7390 (ttp-170) REVERT: B 256 LEU cc_start: 0.8362 (tp) cc_final: 0.7992 (tt) REVERT: C 466 GLN cc_start: 0.8749 (mt0) cc_final: 0.8254 (mp10) REVERT: C 504 TYR cc_start: 0.8485 (t80) cc_final: 0.8062 (t80) REVERT: C 594 MET cc_start: 0.9342 (mmm) cc_final: 0.9114 (mmm) REVERT: C 711 ILE cc_start: 0.8538 (mm) cc_final: 0.8184 (mm) REVERT: C 898 ARG cc_start: 0.7595 (ttm170) cc_final: 0.6793 (ttm110) REVERT: C 950 TYR cc_start: 0.7204 (m-10) cc_final: 0.6926 (m-80) REVERT: C 951 ASP cc_start: 0.8667 (p0) cc_final: 0.8084 (p0) REVERT: C 1007 GLU cc_start: 0.8514 (tt0) cc_final: 0.8134 (mt-10) REVERT: C 1017 THR cc_start: 0.9290 (m) cc_final: 0.9008 (p) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1387 time to fit residues: 47.8570 Evaluate side-chains 161 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 126 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.090818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.064220 restraints weight = 83513.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.065783 restraints weight = 48268.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066506 restraints weight = 30917.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.066972 restraints weight = 24623.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.067033 restraints weight = 22523.735| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20839 Z= 0.202 Angle : 0.744 10.021 29101 Z= 0.408 Chirality : 0.047 0.331 3187 Planarity : 0.005 0.088 2984 Dihedral : 26.046 177.717 4566 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 1929 helix: 0.18 (0.19), residues: 659 sheet: -1.14 (0.28), residues: 331 loop : -1.79 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 860 TYR 0.025 0.002 TYR C 500 PHE 0.029 0.002 PHE B 62 TRP 0.015 0.002 TRP C 782 HIS 0.015 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (20834) covalent geometry : angle 0.74364 / 0.41 (29101) hydrogen bonds : bond 0.04932 / 3.48 ( 889) hydrogen bonds : angle 4.71331 / 3.29 ( 2403) metal coordination : bond 0.00805 / 0.49 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ARG cc_start: 0.6339 (mtt-85) cc_final: 0.5927 (ttt180) REVERT: A 486 CYS cc_start: 0.8524 (t) cc_final: 0.8263 (t) REVERT: A 499 GLN cc_start: 0.8072 (mt0) cc_final: 0.7656 (mt0) REVERT: A 677 LEU cc_start: 0.8932 (tp) cc_final: 0.8510 (tt) REVERT: A 678 CYS cc_start: 0.8228 (m) cc_final: 0.7632 (m) REVERT: A 704 MET cc_start: 0.8584 (ptm) cc_final: 0.8028 (ptm) REVERT: A 733 MET cc_start: 0.9014 (tpp) cc_final: 0.8770 (tpp) REVERT: A 737 MET cc_start: 0.7557 (mtm) cc_final: 0.6622 (mtm) REVERT: A 807 MET cc_start: 0.7435 (ttt) cc_final: 0.7185 (ttt) REVERT: A 825 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8318 (mm-30) REVERT: A 922 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8144 (ttp80) REVERT: A 1000 GLN cc_start: 0.8390 (tp40) cc_final: 0.7792 (tp-100) REVERT: B 39 ARG cc_start: 0.8055 (tpt-90) cc_final: 0.7396 (ttp-170) REVERT: B 256 LEU cc_start: 0.8363 (tp) cc_final: 0.8006 (tt) REVERT: C 466 GLN cc_start: 0.8815 (mt0) cc_final: 0.8277 (mp10) REVERT: C 504 TYR cc_start: 0.8542 (t80) cc_final: 0.8063 (t80) REVERT: C 647 MET cc_start: 0.8943 (mmm) cc_final: 0.8670 (mmm) REVERT: C 711 ILE cc_start: 0.8544 (mm) cc_final: 0.8329 (mm) REVERT: C 875 TYR cc_start: 0.8508 (t80) cc_final: 0.8300 (t80) REVERT: C 898 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7198 (ttm110) REVERT: C 951 ASP cc_start: 0.8664 (p0) cc_final: 0.8081 (p0) REVERT: C 1007 GLU cc_start: 0.8526 (tt0) cc_final: 0.8217 (mt-10) REVERT: C 1017 THR cc_start: 0.9285 (m) cc_final: 0.9019 (p) REVERT: D 100 ASN cc_start: 0.8928 (t0) cc_final: 0.8670 (t0) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1392 time to fit residues: 45.9911 Evaluate side-chains 157 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 196 optimal weight: 50.0000 chunk 174 optimal weight: 0.0970 chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 76 optimal weight: 0.0020 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 HIS ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.092931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.065176 restraints weight = 83805.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.066936 restraints weight = 44270.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068007 restraints weight = 29799.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.068637 restraints weight = 23539.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.069010 restraints weight = 20620.159| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20839 Z= 0.141 Angle : 0.719 9.117 29101 Z= 0.396 Chirality : 0.047 0.306 3187 Planarity : 0.005 0.059 2984 Dihedral : 25.958 178.806 4566 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.18), residues: 1929 helix: 0.32 (0.20), residues: 659 sheet: -0.96 (0.28), residues: 328 loop : -1.76 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 860 TYR 0.024 0.002 TYR C 500 PHE 0.029 0.002 PHE B 62 TRP 0.014 0.002 TRP C 782 HIS 0.014 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (20834) covalent geometry : angle 0.71856 / 0.40 (29101) hydrogen bonds : bond 0.04654 / 3.37 ( 889) hydrogen bonds : angle 4.57568 / 3.20 ( 2403) metal coordination : bond 0.00287 / 0.18 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3475.67 seconds wall clock time: 61 minutes 7.53 seconds (3667.53 seconds total)