Starting phenix.real_space_refine on Sun Oct 12 01:23:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbq_7847/10_2025/6dbq_7847_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbq_7847/10_2025/6dbq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6dbq_7847/10_2025/6dbq_7847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbq_7847/10_2025/6dbq_7847.map" model { file = "/net/cci-nas-00/data/ceres_data/6dbq_7847/10_2025/6dbq_7847_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbq_7847/10_2025/6dbq_7847_neut.cif" } 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-2.0-5842/lib/python3.9/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: 5.10, per 1000 atoms: 0.26 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: 2.10 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 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: 3.43 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: 6.67 Time building geometry restraints manager: 2.90 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=" 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=" CB ILE D 234 " pdb=" CG1 ILE D 234 " ideal model delta sigma weight residual 1.530 1.444 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CB GLN A 423 " pdb=" CG GLN A 423 " ideal model delta sigma weight residual 1.520 1.398 0.122 3.00e-02 1.11e+03 1.66e+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: 2690 0.060 - 0.120: 449 0.120 - 0.180: 41 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 29.700 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.006 0.283 20839 Z= 0.270 Angle : 1.053 50.410 29101 Z= 0.618 Chirality : 0.044 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 aren 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 covalent geometry : bond 0.00532 (20834) covalent geometry : angle 1.05335 (29101) hydrogen bonds : bond 0.14497 ( 889) hydrogen bonds : angle 6.73345 ( 2403) metal coordination : bond 0.16540 ( 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 : 0.727 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: 0.6833 (mtp) REVERT: B 23 ASP cc_start: 0.7779 (t0) cc_final: 0.7317 (t0) REVERT: B 39 ARG cc_start: 0.8394 (tpt-90) cc_final: 0.7873 (ttp-170) REVERT: B 270 GLU cc_start: 0.8275 (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: 0.7483 (ttm-80) REVERT: C 909 LEU cc_start: 0.9069 (mt) cc_final: 0.8699 (mt) REVERT: C 945 MET cc_start: 0.8637 (mtp) cc_final: 0.8424 (mmm) REVERT: C 1028 HIS cc_start: 0.8657 (t70) cc_final: 0.8170 (t-170) REVERT: D 1 MET cc_start: 0.6785 (pmt) cc_final: 0.6292 (pmt) REVERT: D 51 LYS cc_start: 0.8564 (mttt) cc_final: 0.8196 (mmmt) REVERT: D 86 LYS cc_start: 0.8133 (tptp) cc_final: 0.7901 (tptp) outliers start: 2 outliers final: 0 residues processed: 378 average time/residue: 0.1901 time to fit residues: 103.8799 Evaluate side-chains 199 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 501 HIS C 761 GLN C 817 HIS C 937 GLN C 956 ASN ** C 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 997 ASN C1012 HIS C1028 HIS D 33 GLN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.090447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.064256 restraints weight = 84968.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.065902 restraints weight = 45466.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.066933 restraints weight = 30739.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.067536 restraints weight = 24264.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.067912 restraints weight = 21249.480| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 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 = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.473 20839 Z= 0.342 Angle : 0.841 9.281 29101 Z= 0.461 Chirality : 0.047 0.191 3187 Planarity : 0.007 0.075 2984 Dihedral : 26.352 176.793 4566 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.04 % Favored : 91.91 % Rotamer: Outliers : 0.24 % Allowed : 5.24 % Favored : 94.52 % 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 aren not related in a simple way. whole: -3.28 (0.17), residues: 1929 helix: -1.63 (0.17), residues: 658 sheet: -1.74 (0.26), residues: 333 loop : -2.74 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 675 TYR 0.030 0.003 TYR C 578 PHE 0.027 0.003 PHE C 724 TRP 0.060 0.004 TRP A 560 HIS 0.016 0.002 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00688 (20834) covalent geometry : angle 0.84106 (29101) hydrogen bonds : bond 0.05984 ( 889) hydrogen bonds : angle 5.44627 ( 2403) metal coordination : bond 0.21187 ( 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 272 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 268 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ARG cc_start: 0.6896 (mtt-85) cc_final: 0.6243 (mpt180) REVERT: A 486 CYS cc_start: 0.8357 (t) cc_final: 0.7988 (t) REVERT: A 499 GLN cc_start: 0.8617 (mt0) cc_final: 0.8284 (mt0) REVERT: A 872 ASN cc_start: 0.7589 (p0) cc_final: 0.7379 (p0) REVERT: A 914 VAL cc_start: 0.9273 (m) cc_final: 0.8950 (p) REVERT: A 936 GLN cc_start: 0.8574 (tp40) cc_final: 0.8282 (tp-100) REVERT: B 39 ARG cc_start: 0.7894 (tpt-90) cc_final: 0.7645 (ttp-170) REVERT: B 100 ASN cc_start: 0.8837 (m-40) cc_final: 0.8604 (m110) REVERT: C 504 TYR cc_start: 0.8445 (t80) cc_final: 0.8129 (t80) REVERT: C 740 LEU cc_start: 0.9278 (mt) cc_final: 0.9070 (mp) REVERT: C 898 ARG cc_start: 0.7482 (ttm170) cc_final: 0.7137 (ttm110) REVERT: C 909 LEU cc_start: 0.9023 (mt) cc_final: 0.8797 (mt) REVERT: C 951 ASP cc_start: 0.8778 (p0) cc_final: 0.8512 (p0) REVERT: C 1004 PHE cc_start: 0.8356 (m-80) cc_final: 0.8119 (m-80) REVERT: C 1007 GLU cc_start: 0.8607 (tt0) cc_final: 0.8254 (mt-10) REVERT: D 27 ASP cc_start: 0.7618 (t0) cc_final: 0.7417 (t70) REVERT: D 51 LYS cc_start: 0.8643 (mttt) cc_final: 0.8194 (mmmt) REVERT: D 187 LEU cc_start: 0.8761 (tt) cc_final: 0.8510 (tt) REVERT: D 289 TYR cc_start: 0.8127 (t80) cc_final: 0.7684 (t80) REVERT: D 306 GLN cc_start: 0.8721 (pm20) cc_final: 0.8436 (tp40) outliers start: 4 outliers final: 1 residues processed: 272 average time/residue: 0.1703 time to fit residues: 69.1478 Evaluate side-chains 174 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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: 9.9990 chunk 43 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 0.0020 chunk 145 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 102 optimal weight: 0.2980 chunk 168 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 overall best weight: 2.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN B 33 GLN C 501 HIS ** C 761 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.092367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.065027 restraints weight = 85094.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066732 restraints weight = 44489.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.067822 restraints weight = 29775.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068434 restraints weight = 23555.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068796 restraints weight = 20601.842| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 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 = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20839 Z= 0.169 Angle : 0.695 7.963 29101 Z= 0.386 Chirality : 0.043 0.179 3187 Planarity : 0.005 0.065 2984 Dihedral : 26.152 175.769 4566 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.34 % Favored : 94.61 % Rotamer: Outliers : 0.18 % Allowed : 3.89 % Favored : 95.94 % 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 aren not related in a simple way. whole: -2.34 (0.17), residues: 1929 helix: -0.52 (0.18), residues: 652 sheet: -1.41 (0.26), residues: 327 loop : -2.38 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 992 TYR 0.021 0.002 TYR D 268 PHE 0.018 0.002 PHE D 274 TRP 0.013 0.002 TRP A 538 HIS 0.011 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00365 (20834) covalent geometry : angle 0.69542 (29101) hydrogen bonds : bond 0.04791 ( 889) hydrogen bonds : angle 4.77444 ( 2403) metal coordination : bond 0.01519 ( 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 263 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 260 time to evaluate : 0.528 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: 0.6727 (mtt-85) cc_final: 0.6086 (mpt180) REVERT: A 499 GLN cc_start: 0.8461 (mt0) cc_final: 0.8036 (mt0) REVERT: A 629 HIS cc_start: 0.5299 (t70) cc_final: 0.4846 (t70) REVERT: A 737 MET cc_start: 0.7766 (mtm) cc_final: 0.7268 (mtp) REVERT: A 807 MET cc_start: 0.7650 (ttt) cc_final: 0.7150 (ttt) REVERT: A 825 GLU cc_start: 0.8633 (tp30) cc_final: 0.8372 (tp30) REVERT: A 906 ASP cc_start: 0.8613 (t0) cc_final: 0.8363 (t0) REVERT: A 908 TYR cc_start: 0.8842 (t80) cc_final: 0.8639 (t80) REVERT: A 909 LEU cc_start: 0.8845 (tp) cc_final: 0.8617 (pp) REVERT: A 914 VAL cc_start: 0.9170 (m) cc_final: 0.8815 (p) REVERT: B 23 ASP cc_start: 0.6915 (t0) cc_final: 0.6709 (t0) REVERT: B 33 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7730 (pp30) REVERT: B 39 ARG cc_start: 0.7915 (tpt-90) cc_final: 0.7364 (ttp-170) REVERT: C 691 THR cc_start: 0.8628 (p) cc_final: 0.8125 (p) REVERT: C 735 ARG cc_start: 0.8798 (mtp-110) cc_final: 0.8335 (mtp-110) REVERT: C 740 LEU cc_start: 0.9287 (mt) cc_final: 0.9042 (mp) REVERT: C 898 ARG cc_start: 0.7346 (ttm170) cc_final: 0.7024 (ttm110) REVERT: C 951 ASP cc_start: 0.8779 (p0) cc_final: 0.8492 (p0) REVERT: C 1004 PHE cc_start: 0.8052 (m-80) cc_final: 0.7841 (m-10) REVERT: C 1007 GLU cc_start: 0.8395 (tt0) cc_final: 0.8110 (mt-10) REVERT: C 1017 THR cc_start: 0.9264 (m) cc_final: 0.8939 (p) REVERT: D 51 LYS cc_start: 0.8703 (mttt) cc_final: 0.8216 (mmmt) REVERT: D 64 ASN cc_start: 0.9194 (m-40) cc_final: 0.8993 (t0) REVERT: D 100 ASN cc_start: 0.7988 (p0) cc_final: 0.7700 (p0) outliers start: 3 outliers final: 1 residues processed: 263 average time/residue: 0.1575 time to fit residues: 63.4771 Evaluate side-chains 171 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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: 9.9990 chunk 133 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.092118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.065225 restraints weight = 85107.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067210 restraints weight = 47317.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.067684 restraints weight = 32024.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.068226 restraints weight = 23413.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.068265 restraints weight = 21545.543| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 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 = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20839 Z= 0.190 Angle : 0.689 7.580 29101 Z= 0.383 Chirality : 0.042 0.254 3187 Planarity : 0.005 0.061 2984 Dihedral : 26.033 178.728 4566 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.12 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % 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 aren not related in a simple way. whole: -1.94 (0.18), residues: 1929 helix: -0.15 (0.19), residues: 650 sheet: -1.33 (0.26), residues: 334 loop : -2.11 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 795 TYR 0.029 0.002 TYR C 500 PHE 0.024 0.002 PHE B 62 TRP 0.015 0.002 TRP C 549 HIS 0.010 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00413 (20834) covalent geometry : angle 0.68909 (29101) hydrogen bonds : bond 0.04708 ( 889) hydrogen bonds : angle 4.65631 ( 2403) metal coordination : bond 0.00854 ( 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 234 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.708 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: 0.6539 (mtt-85) cc_final: 0.5864 (mpt180) REVERT: A 499 GLN cc_start: 0.8405 (mt0) cc_final: 0.7979 (mt0) REVERT: A 578 TYR cc_start: 0.8130 (t80) cc_final: 0.7926 (t80) REVERT: A 617 GLU cc_start: 0.8338 (tt0) cc_final: 0.7665 (tt0) REVERT: A 729 TYR cc_start: 0.9458 (m-80) cc_final: 0.9181 (m-10) REVERT: A 737 MET cc_start: 0.7769 (mtm) cc_final: 0.7199 (mtp) REVERT: A 807 MET cc_start: 0.7768 (ttt) cc_final: 0.7097 (ttt) REVERT: A 825 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8327 (mm-30) REVERT: A 936 GLN cc_start: 0.8282 (tp40) cc_final: 0.8061 (tp40) REVERT: B 23 ASP cc_start: 0.6553 (t0) cc_final: 0.6335 (t0) REVERT: B 39 ARG cc_start: 0.7743 (tpt-90) cc_final: 0.7309 (ttp-170) REVERT: C 466 GLN cc_start: 0.8667 (mt0) cc_final: 0.8288 (mp10) REVERT: C 594 MET cc_start: 0.9313 (mmm) cc_final: 0.9029 (mmm) REVERT: C 711 ILE cc_start: 0.8726 (mm) cc_final: 0.8511 (mm) REVERT: C 898 ARG cc_start: 0.7532 (ttm170) cc_final: 0.6806 (ttm110) REVERT: C 945 MET cc_start: 0.8416 (mtt) cc_final: 0.8004 (tmm) REVERT: C 951 ASP cc_start: 0.8752 (p0) cc_final: 0.8211 (p0) REVERT: C 1007 GLU cc_start: 0.8471 (tt0) cc_final: 0.8102 (mt-10) REVERT: C 1017 THR cc_start: 0.9243 (m) cc_final: 0.8984 (p) REVERT: D 24 LEU cc_start: 0.8471 (tp) cc_final: 0.8235 (tp) REVERT: D 51 LYS cc_start: 0.8688 (mttt) cc_final: 0.8172 (mmmt) REVERT: D 108 MET cc_start: 0.8708 (mmm) cc_final: 0.8174 (mmm) REVERT: D 109 LEU cc_start: 0.9111 (mp) cc_final: 0.8877 (mp) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.1441 time to fit residues: 53.2117 Evaluate side-chains 174 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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: 3.9990 chunk 205 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 167 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN A 831 GLN ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 535 GLN C 666 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.091319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.063812 restraints weight = 84950.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.065530 restraints weight = 44788.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066559 restraints weight = 30051.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067177 restraints weight = 23813.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.067560 restraints weight = 20881.062| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 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 = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20839 Z= 0.203 Angle : 0.690 7.692 29101 Z= 0.385 Chirality : 0.042 0.191 3187 Planarity : 0.005 0.058 2984 Dihedral : 25.988 178.965 4566 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.06 % Allowed : 2.47 % Favored : 97.47 % 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 aren not related in a simple way. whole: -1.76 (0.18), residues: 1929 helix: -0.09 (0.19), residues: 656 sheet: -1.20 (0.27), residues: 336 loop : -1.95 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 860 TYR 0.024 0.002 TYR C 500 PHE 0.020 0.002 PHE B 62 TRP 0.020 0.002 TRP A 782 HIS 0.010 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00437 (20834) covalent geometry : angle 0.69019 (29101) hydrogen bonds : bond 0.04647 ( 889) hydrogen bonds : angle 4.68546 ( 2403) metal coordination : bond 0.00791 ( 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 217 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.610 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: 0.6598 (mtt-85) cc_final: 0.6092 (ttt180) REVERT: A 486 CYS cc_start: 0.8614 (t) cc_final: 0.8354 (t) REVERT: A 594 MET cc_start: 0.8820 (mmt) cc_final: 0.8589 (mmt) REVERT: A 617 GLU cc_start: 0.8237 (tt0) cc_final: 0.7770 (tt0) REVERT: A 667 LYS cc_start: 0.9251 (ptpt) cc_final: 0.8941 (ptmm) REVERT: A 700 GLU cc_start: 0.8574 (pm20) cc_final: 0.8363 (pp20) REVERT: A 704 MET cc_start: 0.8598 (ptm) cc_final: 0.8209 (ptm) REVERT: A 729 TYR cc_start: 0.9433 (m-80) cc_final: 0.9126 (m-10) REVERT: A 733 MET cc_start: 0.9034 (tpp) cc_final: 0.8631 (tpp) REVERT: A 737 MET cc_start: 0.7812 (mtm) cc_final: 0.7311 (ttm) REVERT: A 825 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8310 (mm-30) REVERT: A 864 LYS cc_start: 0.8431 (mptt) cc_final: 0.8212 (mmtt) REVERT: A 906 ASP cc_start: 0.8578 (t0) cc_final: 0.8299 (t0) REVERT: A 909 LEU cc_start: 0.8894 (tp) cc_final: 0.8684 (pp) REVERT: B 23 ASP cc_start: 0.6485 (t0) cc_final: 0.5670 (t0) REVERT: B 39 ARG cc_start: 0.7824 (tpt-90) cc_final: 0.7265 (ttp-170) REVERT: B 253 HIS cc_start: 0.8455 (p-80) cc_final: 0.8115 (p90) REVERT: B 256 LEU cc_start: 0.8440 (tp) cc_final: 0.7939 (tt) REVERT: C 466 GLN cc_start: 0.8746 (mt0) cc_final: 0.8248 (mp10) REVERT: C 711 ILE cc_start: 0.8572 (mm) cc_final: 0.8365 (mm) REVERT: C 898 ARG cc_start: 0.7703 (ttm170) cc_final: 0.6981 (ttm110) REVERT: C 945 MET cc_start: 0.8397 (mtt) cc_final: 0.8071 (tmm) REVERT: C 951 ASP cc_start: 0.8720 (p0) cc_final: 0.8167 (p0) REVERT: C 1007 GLU cc_start: 0.8525 (tt0) cc_final: 0.8129 (mt-10) REVERT: C 1017 THR cc_start: 0.9296 (m) cc_final: 0.8988 (p) REVERT: D 108 MET cc_start: 0.8884 (mmm) cc_final: 0.8474 (mmm) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.1472 time to fit residues: 50.0631 Evaluate side-chains 163 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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: 9.9990 chunk 24 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 HIS A 831 GLN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 GLN ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS C 517 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.089409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.062098 restraints weight = 85132.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.064026 restraints weight = 46746.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.064469 restraints weight = 28046.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.064708 restraints weight = 23733.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064791 restraints weight = 22505.787| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 20839 Z= 0.303 Angle : 0.766 14.899 29101 Z= 0.424 Chirality : 0.044 0.206 3187 Planarity : 0.006 0.081 2984 Dihedral : 26.015 177.591 4566 Min Nonbonded Distance : 1.604 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.36 % Favored : 92.59 % Rotamer: Outliers : 0.06 % Allowed : 2.47 % Favored : 97.47 % 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 aren not related in a simple way. whole: -1.84 (0.18), residues: 1929 helix: -0.21 (0.19), residues: 655 sheet: -1.32 (0.27), residues: 334 loop : -1.91 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 870 TYR 0.028 0.003 TYR C1020 PHE 0.022 0.003 PHE A 938 TRP 0.021 0.002 TRP A 782 HIS 0.014 0.002 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00643 (20834) covalent geometry : angle 0.76635 (29101) hydrogen bonds : bond 0.05398 ( 889) hydrogen bonds : angle 4.97055 ( 2403) metal coordination : bond 0.01286 ( 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 195 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.620 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: 0.6510 (mtt-85) cc_final: 0.5929 (ttt180) REVERT: A 499 GLN cc_start: 0.8278 (mt0) cc_final: 0.7910 (mt0) REVERT: A 617 GLU cc_start: 0.8150 (tt0) cc_final: 0.7775 (tt0) REVERT: A 704 MET cc_start: 0.8516 (ptm) cc_final: 0.8147 (ptm) REVERT: A 733 MET cc_start: 0.9086 (tpp) cc_final: 0.8848 (tpp) REVERT: A 825 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8339 (mm-30) REVERT: B 23 ASP cc_start: 0.6809 (t0) cc_final: 0.5954 (t0) REVERT: B 39 ARG cc_start: 0.8039 (tpt-90) cc_final: 0.7573 (ttp-170) REVERT: C 466 GLN cc_start: 0.8831 (mt0) cc_final: 0.8309 (mp10) REVERT: C 594 MET cc_start: 0.9339 (mmm) cc_final: 0.9100 (mmm) REVERT: C 898 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7235 (ttm110) REVERT: C 945 MET cc_start: 0.8363 (mtt) cc_final: 0.8102 (tmm) REVERT: C 951 ASP cc_start: 0.8663 (p0) cc_final: 0.8341 (p0) REVERT: C 958 LEU cc_start: 0.9707 (tp) cc_final: 0.9394 (tp) REVERT: C 1007 GLU cc_start: 0.8572 (tt0) cc_final: 0.8219 (mt-10) REVERT: C 1017 THR cc_start: 0.9409 (m) cc_final: 0.9063 (p) REVERT: D 108 MET cc_start: 0.8729 (mmm) cc_final: 0.8364 (mmm) outliers start: 1 outliers final: 1 residues processed: 195 average time/residue: 0.1429 time to fit residues: 44.2509 Evaluate side-chains 144 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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: 5.9990 chunk 164 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 110 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 198 optimal weight: 30.0000 chunk 150 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 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 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.090399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.062826 restraints weight = 84026.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.064512 restraints weight = 44366.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.065514 restraints weight = 29898.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.066084 restraints weight = 23678.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.066368 restraints weight = 20852.055| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4871 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= 0.205 Angle : 0.691 7.726 29101 Z= 0.385 Chirality : 0.042 0.193 3187 Planarity : 0.005 0.057 2984 Dihedral : 25.940 177.500 4566 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.75 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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 aren not related in a simple way. whole: -1.64 (0.18), residues: 1929 helix: -0.01 (0.19), residues: 663 sheet: -1.23 (0.27), residues: 334 loop : -1.82 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 860 TYR 0.022 0.002 TYR C 500 PHE 0.032 0.002 PHE A 993 TRP 0.014 0.002 TRP A 782 HIS 0.009 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00443 (20834) covalent geometry : angle 0.69069 (29101) hydrogen bonds : bond 0.04696 ( 889) hydrogen bonds : angle 4.75314 ( 2403) metal coordination : bond 0.00816 ( 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 204 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.737 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: 0.6419 (mtt-85) cc_final: 0.5879 (ttt180) REVERT: A 499 GLN cc_start: 0.8053 (mt0) cc_final: 0.7702 (mt0) REVERT: A 617 GLU cc_start: 0.8278 (tt0) cc_final: 0.8057 (tt0) REVERT: A 704 MET cc_start: 0.8472 (ptm) cc_final: 0.8105 (ptm) REVERT: A 737 MET cc_start: 0.7688 (mtm) cc_final: 0.7230 (mtm) REVERT: A 807 MET cc_start: 0.8031 (ttt) cc_final: 0.7044 (ttt) REVERT: A 825 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8435 (mm-30) REVERT: A 869 MET cc_start: 0.7500 (ppp) cc_final: 0.6944 (ppp) REVERT: A 871 MET cc_start: 0.8591 (mpp) cc_final: 0.8373 (mpp) REVERT: B 23 ASP cc_start: 0.6529 (t0) cc_final: 0.5773 (t0) REVERT: B 39 ARG cc_start: 0.8079 (tpt-90) cc_final: 0.7427 (ttp-170) REVERT: B 256 LEU cc_start: 0.8314 (tp) cc_final: 0.7935 (tt) REVERT: C 466 GLN cc_start: 0.8747 (mt0) cc_final: 0.8262 (mp10) REVERT: C 504 TYR cc_start: 0.8420 (t80) cc_final: 0.8211 (t80) REVERT: C 594 MET cc_start: 0.9365 (mmm) cc_final: 0.9056 (mmm) REVERT: C 711 ILE cc_start: 0.8644 (mm) cc_final: 0.8393 (mm) REVERT: C 738 GLU cc_start: 0.8528 (tp30) cc_final: 0.8271 (tp30) REVERT: C 898 ARG cc_start: 0.7916 (ttm170) cc_final: 0.7287 (ttm110) REVERT: C 945 MET cc_start: 0.8306 (mtt) cc_final: 0.8027 (tmm) REVERT: C 951 ASP cc_start: 0.8637 (p0) cc_final: 0.8289 (p0) REVERT: C 958 LEU cc_start: 0.9676 (tp) cc_final: 0.9383 (tp) REVERT: C 1007 GLU cc_start: 0.8535 (tt0) cc_final: 0.8168 (mt-10) REVERT: C 1017 THR cc_start: 0.9322 (m) cc_final: 0.8956 (p) REVERT: D 108 MET cc_start: 0.8756 (mmm) cc_final: 0.8273 (mmm) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1574 time to fit residues: 49.6402 Evaluate side-chains 149 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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: 10.0000 chunk 151 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS A 874 ASN ** A1013 HIS ** 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 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** 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 = 0.3745 r_free = 0.3745 target = 0.090935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.063775 restraints weight = 84504.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065554 restraints weight = 46507.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066138 restraints weight = 29632.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.066527 restraints weight = 23761.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066576 restraints weight = 21919.050| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5066 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= 0.193 Angle : 0.695 8.885 29101 Z= 0.384 Chirality : 0.042 0.194 3187 Planarity : 0.005 0.056 2984 Dihedral : 25.842 177.074 4566 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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 aren not related in a simple way. whole: -1.45 (0.18), residues: 1929 helix: 0.20 (0.20), residues: 656 sheet: -1.05 (0.28), residues: 330 loop : -1.78 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 870 TYR 0.024 0.002 TYR C1020 PHE 0.034 0.002 PHE B 62 TRP 0.012 0.001 TRP C 915 HIS 0.009 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00420 (20834) covalent geometry : angle 0.69474 (29101) hydrogen bonds : bond 0.04616 ( 889) hydrogen bonds : angle 4.65883 ( 2403) metal coordination : bond 0.00733 ( 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 202 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ARG cc_start: 0.6347 (mtt-85) cc_final: 0.5779 (ttt180) REVERT: A 499 GLN cc_start: 0.8008 (mt0) cc_final: 0.7651 (mt0) REVERT: A 704 MET cc_start: 0.8450 (ptm) cc_final: 0.8089 (ptm) REVERT: A 737 MET cc_start: 0.7526 (mtm) cc_final: 0.7213 (mtm) REVERT: A 807 MET cc_start: 0.7714 (ttt) cc_final: 0.7144 (ttt) REVERT: A 825 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8218 (mm-30) REVERT: B 39 ARG cc_start: 0.8040 (tpt-90) cc_final: 0.7387 (ttp-170) REVERT: C 504 TYR cc_start: 0.8505 (t80) cc_final: 0.8213 (t80) REVERT: C 590 GLU cc_start: 0.9089 (tt0) cc_final: 0.8313 (tm-30) REVERT: C 594 MET cc_start: 0.9356 (mmm) cc_final: 0.9021 (mmm) REVERT: C 898 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7233 (ttm110) REVERT: C 951 ASP cc_start: 0.8724 (p0) cc_final: 0.8210 (p0) REVERT: C 958 LEU cc_start: 0.9668 (tp) cc_final: 0.9390 (tp) REVERT: C 996 MET cc_start: 0.9291 (mmm) cc_final: 0.9028 (mpp) REVERT: C 1007 GLU cc_start: 0.8560 (tt0) cc_final: 0.8165 (mt-10) REVERT: C 1017 THR cc_start: 0.9331 (m) cc_final: 0.9101 (p) REVERT: D 108 MET cc_start: 0.8760 (mmm) cc_final: 0.8250 (mmm) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1432 time to fit residues: 46.1329 Evaluate side-chains 146 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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: 0.9980 chunk 69 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 108 optimal weight: 0.0070 chunk 135 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 197 optimal weight: 20.0000 chunk 174 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 817 HIS ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN C 822 ASN C1012 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.093187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.066226 restraints weight = 82632.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.067895 restraints weight = 45264.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068750 restraints weight = 29724.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.068956 restraints weight = 22102.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069086 restraints weight = 22072.513| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5290 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= 0.144 Angle : 0.680 9.102 29101 Z= 0.373 Chirality : 0.042 0.168 3187 Planarity : 0.005 0.060 2984 Dihedral : 25.716 177.052 4566 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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 aren not related in a simple way. whole: -1.27 (0.19), residues: 1929 helix: 0.33 (0.20), residues: 656 sheet: -0.68 (0.28), residues: 324 loop : -1.78 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 994 TYR 0.039 0.002 TYR C 933 PHE 0.030 0.002 PHE B 62 TRP 0.012 0.001 TRP A 978 HIS 0.007 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00314 (20834) covalent geometry : angle 0.68005 (29101) hydrogen bonds : bond 0.04342 ( 889) hydrogen bonds : angle 4.49858 ( 2403) metal coordination : bond 0.00340 ( 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 221 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.674 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: 0.6177 (mtt-85) cc_final: 0.5597 (ttt180) REVERT: A 486 CYS cc_start: 0.8361 (t) cc_final: 0.8118 (t) REVERT: A 499 GLN cc_start: 0.7895 (mt0) cc_final: 0.7582 (mt0) REVERT: A 617 GLU cc_start: 0.7881 (tt0) cc_final: 0.7515 (mt-10) REVERT: A 704 MET cc_start: 0.8363 (ptm) cc_final: 0.8020 (ptm) REVERT: A 729 TYR cc_start: 0.9121 (m-10) cc_final: 0.8795 (m-80) REVERT: A 737 MET cc_start: 0.7485 (mtm) cc_final: 0.7106 (mtm) REVERT: A 807 MET cc_start: 0.7179 (ttt) cc_final: 0.6816 (ttt) REVERT: A 825 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8173 (mm-30) REVERT: A 905 MET cc_start: 0.8466 (tpt) cc_final: 0.8229 (tpt) REVERT: A 906 ASP cc_start: 0.8582 (t0) cc_final: 0.8206 (t0) REVERT: B 1 MET cc_start: 0.6340 (mmp) cc_final: 0.6019 (pmm) REVERT: B 39 ARG cc_start: 0.7938 (tpt-90) cc_final: 0.7043 (ttp-170) REVERT: C 504 TYR cc_start: 0.8414 (t80) cc_final: 0.7978 (t80) REVERT: C 590 GLU cc_start: 0.8872 (tt0) cc_final: 0.8337 (tm-30) REVERT: C 594 MET cc_start: 0.9322 (mmm) cc_final: 0.9013 (mmt) REVERT: C 711 ILE cc_start: 0.8572 (mm) cc_final: 0.8192 (mm) REVERT: C 898 ARG cc_start: 0.7744 (ttm170) cc_final: 0.7057 (ttm110) REVERT: C 938 PHE cc_start: 0.8821 (t80) cc_final: 0.8619 (t80) REVERT: C 945 MET cc_start: 0.8341 (mtt) cc_final: 0.8077 (tmm) REVERT: C 951 ASP cc_start: 0.8774 (p0) cc_final: 0.8302 (p0) REVERT: C 996 MET cc_start: 0.9251 (mmm) cc_final: 0.9007 (mpp) REVERT: C 1007 GLU cc_start: 0.8538 (tt0) cc_final: 0.8092 (mt-10) REVERT: C 1017 THR cc_start: 0.9234 (m) cc_final: 0.8990 (p) REVERT: D 108 MET cc_start: 0.8770 (mmm) cc_final: 0.8234 (mmm) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1428 time to fit residues: 49.2493 Evaluate side-chains 168 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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: 5.9990 chunk 96 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 534 HIS ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.090826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.063598 restraints weight = 84896.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065651 restraints weight = 47154.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066031 restraints weight = 30321.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066519 restraints weight = 23910.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066570 restraints weight = 21805.675| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20839 Z= 0.217 Angle : 0.708 8.965 29101 Z= 0.389 Chirality : 0.042 0.173 3187 Planarity : 0.005 0.065 2984 Dihedral : 25.652 175.989 4566 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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 aren not related in a simple way. whole: -1.30 (0.19), residues: 1929 helix: 0.27 (0.20), residues: 652 sheet: -0.89 (0.28), residues: 332 loop : -1.67 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 459 TYR 0.026 0.002 TYR C 500 PHE 0.032 0.002 PHE B 62 TRP 0.012 0.002 TRP A 782 HIS 0.008 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00469 (20834) covalent geometry : angle 0.70816 (29101) hydrogen bonds : bond 0.04632 ( 889) hydrogen bonds : angle 4.64660 ( 2403) metal coordination : bond 0.00777 ( 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 200 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ARG cc_start: 0.6269 (mtt-85) cc_final: 0.5641 (ttt180) REVERT: A 486 CYS cc_start: 0.8423 (t) cc_final: 0.8217 (t) REVERT: A 617 GLU cc_start: 0.8125 (tt0) cc_final: 0.7615 (mt-10) REVERT: A 704 MET cc_start: 0.8398 (ptm) cc_final: 0.8074 (ptm) REVERT: A 737 MET cc_start: 0.7643 (mtm) cc_final: 0.7133 (mtm) REVERT: A 807 MET cc_start: 0.7592 (ttt) cc_final: 0.7012 (ttt) REVERT: A 825 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8303 (mm-30) REVERT: B 39 ARG cc_start: 0.8044 (tpt-90) cc_final: 0.7181 (ttp-170) REVERT: B 256 LEU cc_start: 0.8499 (tp) cc_final: 0.8199 (mm) REVERT: C 504 TYR cc_start: 0.8566 (t80) cc_final: 0.8194 (t80) REVERT: C 590 GLU cc_start: 0.8935 (tt0) cc_final: 0.8290 (tm-30) REVERT: C 711 ILE cc_start: 0.8610 (mm) cc_final: 0.8259 (mm) REVERT: C 898 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7300 (ttm110) REVERT: C 951 ASP cc_start: 0.8785 (p0) cc_final: 0.8298 (p0) REVERT: C 996 MET cc_start: 0.9261 (mmm) cc_final: 0.9054 (mpp) REVERT: C 1007 GLU cc_start: 0.8533 (tt0) cc_final: 0.8122 (mt-10) REVERT: C 1017 THR cc_start: 0.9322 (m) cc_final: 0.9095 (p) REVERT: D 108 MET cc_start: 0.8875 (mmm) cc_final: 0.8327 (mmm) REVERT: D 109 LEU cc_start: 0.9016 (mp) cc_final: 0.8809 (mp) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1455 time to fit residues: 46.4629 Evaluate side-chains 150 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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: 5.9990 chunk 47 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** C 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.089379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.061851 restraints weight = 84961.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.063497 restraints weight = 45040.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.064497 restraints weight = 30525.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.065089 restraints weight = 24311.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.065385 restraints weight = 21397.002| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20839 Z= 0.272 Angle : 0.760 8.912 29101 Z= 0.419 Chirality : 0.044 0.190 3187 Planarity : 0.006 0.059 2984 Dihedral : 25.711 175.804 4566 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.84 % Favored : 93.11 % 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 aren not related in a simple way. whole: -1.47 (0.18), residues: 1929 helix: -0.02 (0.19), residues: 654 sheet: -0.91 (0.28), residues: 322 loop : -1.67 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 575 TYR 0.033 0.002 TYR C1020 PHE 0.033 0.002 PHE B 62 TRP 0.017 0.002 TRP A 782 HIS 0.010 0.002 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00582 (20834) covalent geometry : angle 0.75972 (29101) hydrogen bonds : bond 0.05149 ( 889) hydrogen bonds : angle 4.92699 ( 2403) metal coordination : bond 0.00971 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3468.30 seconds wall clock time: 60 minutes 57.49 seconds (3657.49 seconds total)