Starting phenix.real_space_refine on Thu Mar 5 08:35:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pa7_20281/03_2026/6pa7_20281.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pa7_20281/03_2026/6pa7_20281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pa7_20281/03_2026/6pa7_20281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pa7_20281/03_2026/6pa7_20281.map" model { file = "/net/cci-nas-00/data/ceres_data/6pa7_20281/03_2026/6pa7_20281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pa7_20281/03_2026/6pa7_20281.cif" } resolution = 2.94 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= 0.002 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: 6 Type Number sf(0) Gaussians P 332 5.49 5 S 54 5.16 5 Cl 3 4.86 5 C 12282 2.51 5 N 3862 2.21 5 O 4486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21019 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 849 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 752 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 3385 Classifications: {'DNA': 166} Link IDs: {'rna3p': 165} Chain: "J" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 3421 Classifications: {'DNA': 166} Link IDs: {'rna3p': 165} Chain: "K" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2333 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 18, 'TRANS': 269} Chain breaks: 1 Chain: "N" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1703 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Chain: "P" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2333 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 18, 'TRANS': 269} Chain breaks: 1 Chain: "S" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1703 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="CL CL A 201 " occ=0.71 Time building chain proxies: 4.47, per 1000 atoms: 0.21 Number of scatterers: 21019 At special positions: 0 Unit cell: (137.886, 115.248, 198.597, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 54 16.00 P 332 15.00 O 4486 8.00 N 3862 7.00 C 12282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 694.0 milliseconds 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 19 sheets defined 53.4% alpha, 8.6% beta 158 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 42 through 57 removed outlier: 3.794A pdb=" N VAL A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.509A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.878A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.539A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.508A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 42 through 57 removed outlier: 3.733A pdb=" N VAL E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.531A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.680A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.566A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 44 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'K' and resid 627 through 631 removed outlier: 3.554A pdb=" N ARG K 631 " --> pdb=" O ALA K 628 " (cutoff:3.500A) Processing helix chain 'K' and resid 644 through 653 Processing helix chain 'K' and resid 666 through 678 Processing helix chain 'K' and resid 686 through 690 Processing helix chain 'K' and resid 691 through 698 Processing helix chain 'K' and resid 729 through 742 removed outlier: 3.529A pdb=" N GLU K 733 " --> pdb=" O ARG K 729 " (cutoff:3.500A) Processing helix chain 'K' and resid 762 through 774 Processing helix chain 'K' and resid 783 through 785 No H-bonds generated for 'chain 'K' and resid 783 through 785' Processing helix chain 'K' and resid 860 through 868 Processing helix chain 'K' and resid 881 through 892 removed outlier: 3.712A pdb=" N ARG K 891 " --> pdb=" O ARG K 887 " (cutoff:3.500A) Processing helix chain 'K' and resid 894 through 903 Processing helix chain 'K' and resid 904 through 908 Processing helix chain 'N' and resid 565 through 573 removed outlier: 4.079A pdb=" N LEU N 569 " --> pdb=" O ALA N 565 " (cutoff:3.500A) Processing helix chain 'N' and resid 588 through 598 removed outlier: 3.556A pdb=" N HIS N 598 " --> pdb=" O GLY N 594 " (cutoff:3.500A) Processing helix chain 'N' and resid 607 through 611 removed outlier: 3.951A pdb=" N ILE N 611 " --> pdb=" O VAL N 608 " (cutoff:3.500A) Processing helix chain 'N' and resid 612 through 619 removed outlier: 3.828A pdb=" N TRP N 619 " --> pdb=" O ASN N 615 " (cutoff:3.500A) Processing helix chain 'N' and resid 647 through 663 removed outlier: 3.682A pdb=" N TYR N 661 " --> pdb=" O HIS N 657 " (cutoff:3.500A) Processing helix chain 'N' and resid 683 through 695 Processing helix chain 'N' and resid 730 through 735 removed outlier: 3.887A pdb=" N ASP N 734 " --> pdb=" O VAL N 730 " (cutoff:3.500A) Processing helix chain 'N' and resid 740 through 747 Processing helix chain 'N' and resid 755 through 760 Processing helix chain 'N' and resid 761 through 764 removed outlier: 3.513A pdb=" N LYS N 764 " --> pdb=" O ALA N 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 761 through 764' Processing helix chain 'P' and resid 627 through 631 removed outlier: 3.554A pdb=" N ARG P 631 " --> pdb=" O ALA P 628 " (cutoff:3.500A) Processing helix chain 'P' and resid 644 through 653 Processing helix chain 'P' and resid 666 through 678 Processing helix chain 'P' and resid 686 through 690 Processing helix chain 'P' and resid 691 through 698 Processing helix chain 'P' and resid 729 through 742 removed outlier: 3.530A pdb=" N GLU P 733 " --> pdb=" O ARG P 729 " (cutoff:3.500A) Processing helix chain 'P' and resid 762 through 774 Processing helix chain 'P' and resid 783 through 785 No H-bonds generated for 'chain 'P' and resid 783 through 785' Processing helix chain 'P' and resid 860 through 868 Processing helix chain 'P' and resid 881 through 892 removed outlier: 3.712A pdb=" N ARG P 891 " --> pdb=" O ARG P 887 " (cutoff:3.500A) Processing helix chain 'P' and resid 894 through 903 Processing helix chain 'P' and resid 904 through 908 Processing helix chain 'S' and resid 566 through 573 Processing helix chain 'S' and resid 588 through 597 Processing helix chain 'S' and resid 607 through 611 removed outlier: 3.765A pdb=" N ILE S 611 " --> pdb=" O VAL S 608 " (cutoff:3.500A) Processing helix chain 'S' and resid 612 through 619 Processing helix chain 'S' and resid 647 through 663 removed outlier: 3.544A pdb=" N TYR S 661 " --> pdb=" O HIS S 657 " (cutoff:3.500A) Processing helix chain 'S' and resid 683 through 695 Processing helix chain 'S' and resid 730 through 738 removed outlier: 4.166A pdb=" N MET S 738 " --> pdb=" O ASP S 734 " (cutoff:3.500A) Processing helix chain 'S' and resid 741 through 748 Processing helix chain 'S' and resid 748 through 753 Processing helix chain 'S' and resid 753 through 760 Processing helix chain 'S' and resid 762 through 767 removed outlier: 4.006A pdb=" N TYR S 766 " --> pdb=" O PRO S 762 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.055A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 5.982A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.154A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.988A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.104A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 681 through 684 removed outlier: 8.681A pdb=" N MET K 682 " --> pdb=" O ASP K 658 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR K 660 " --> pdb=" O MET K 682 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL K 684 " --> pdb=" O TYR K 660 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA K 662 " --> pdb=" O VAL K 684 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE K 634 " --> pdb=" O VAL K 657 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 788 through 789 Processing sheet with id=AB4, first strand: chain 'K' and resid 823 through 825 removed outlier: 4.067A pdb=" N VAL K 850 " --> pdb=" O ASP K 857 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 578 through 580 removed outlier: 6.792A pdb=" N ILE N 555 " --> pdb=" O GLY N 579 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG N 556 " --> pdb=" O LEU N 624 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE N 626 " --> pdb=" O ARG N 556 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU N 558 " --> pdb=" O ILE N 626 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU N 677 " --> pdb=" O GLY N 627 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN N 678 " --> pdb=" O TYR N 714 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR N 714 " --> pdb=" O ASN N 678 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 582 through 583 Processing sheet with id=AB7, first strand: chain 'P' and resid 681 through 684 removed outlier: 8.681A pdb=" N MET P 682 " --> pdb=" O ASP P 658 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR P 660 " --> pdb=" O MET P 682 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL P 684 " --> pdb=" O TYR P 660 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA P 662 " --> pdb=" O VAL P 684 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE P 634 " --> pdb=" O VAL P 657 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 788 through 789 Processing sheet with id=AB9, first strand: chain 'P' and resid 823 through 825 removed outlier: 4.067A pdb=" N VAL P 850 " --> pdb=" O ASP P 857 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 603 through 605 removed outlier: 8.394A pdb=" N LYS S 603 " --> pdb=" O GLY S 579 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR S 581 " --> pdb=" O LYS S 603 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL S 605 " --> pdb=" O TYR S 581 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA S 583 " --> pdb=" O VAL S 605 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE S 555 " --> pdb=" O GLY S 579 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N TYR S 581 " --> pdb=" O ILE S 555 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL S 557 " --> pdb=" O TYR S 581 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA S 583 " --> pdb=" O VAL S 557 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N SER S 559 " --> pdb=" O ALA S 583 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG S 556 " --> pdb=" O LEU S 624 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE S 626 " --> pdb=" O ARG S 556 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU S 558 " --> pdb=" O ILE S 626 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN S 678 " --> pdb=" O TYR S 714 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 410 hydrogen bonds 820 hydrogen bond angles 0 basepair planarities 158 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4853 1.34 - 1.46: 6523 1.46 - 1.58: 10012 1.58 - 1.70: 662 1.70 - 1.82: 92 Bond restraints: 22142 Sorted by residual: bond pdb=" C6 SAH K1001 " pdb=" N6 SAH K1001 " ideal model delta sigma weight residual 1.334 1.438 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C6 SAH P1001 " pdb=" N6 SAH P1001 " ideal model delta sigma weight residual 1.334 1.438 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C5 SAH K1001 " pdb=" C6 SAH K1001 " ideal model delta sigma weight residual 1.407 1.337 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C4 SAH K1001 " pdb=" N9 SAH K1001 " ideal model delta sigma weight residual 1.366 1.297 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C5 SAH P1001 " pdb=" C6 SAH P1001 " ideal model delta sigma weight residual 1.407 1.338 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 22137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 30081 1.84 - 3.67: 1123 3.67 - 5.51: 105 5.51 - 7.35: 23 7.35 - 9.19: 20 Bond angle restraints: 31352 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 112.43 107.98 4.45 9.20e-01 1.18e+00 2.34e+01 angle pdb=" N VAL N 755 " pdb=" CA VAL N 755 " pdb=" C VAL N 755 " ideal model delta sigma weight residual 113.53 109.29 4.24 9.80e-01 1.04e+00 1.87e+01 angle pdb=" N VAL N 753 " pdb=" CA VAL N 753 " pdb=" C VAL N 753 " ideal model delta sigma weight residual 108.88 117.38 -8.50 2.16e+00 2.14e-01 1.55e+01 angle pdb=" C LEU N 560 " pdb=" N PHE N 561 " pdb=" CA PHE N 561 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C ALA H 71 " pdb=" N GLY H 72 " pdb=" CA GLY H 72 " ideal model delta sigma weight residual 119.94 123.97 -4.03 1.11e+00 8.12e-01 1.32e+01 ... (remaining 31347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 10763 35.98 - 71.95: 1562 71.95 - 107.93: 28 107.93 - 143.91: 2 143.91 - 179.88: 3 Dihedral angle restraints: 12358 sinusoidal: 7250 harmonic: 5108 Sorted by residual: dihedral pdb=" CA VAL N 753 " pdb=" C VAL N 753 " pdb=" N PRO N 754 " pdb=" CA PRO N 754 " ideal model delta harmonic sigma weight residual -180.00 -156.00 -24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ILE B 50 " pdb=" C ILE B 50 " pdb=" N TYR B 51 " pdb=" CA TYR B 51 " ideal model delta harmonic sigma weight residual -180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LYS S 597 " pdb=" C LYS S 597 " pdb=" N HIS S 598 " pdb=" CA HIS S 598 " ideal model delta harmonic sigma weight residual -180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 12355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2504 0.046 - 0.092: 760 0.092 - 0.138: 176 0.138 - 0.184: 28 0.184 - 0.230: 9 Chirality restraints: 3477 Sorted by residual: chirality pdb=" CB ILE S 547 " pdb=" CA ILE S 547 " pdb=" CG1 ILE S 547 " pdb=" CG2 ILE S 547 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL N 735 " pdb=" CA VAL N 735 " pdb=" CG1 VAL N 735 " pdb=" CG2 VAL N 735 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2' SAH P1001 " pdb=" C1' SAH P1001 " pdb=" C3' SAH P1001 " pdb=" O2' SAH P1001 " both_signs ideal model delta sigma weight residual False -2.53 -2.73 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 3474 not shown) Planarity restraints: 2845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE N 693 " 0.014 2.00e-02 2.50e+03 1.78e-02 5.54e+00 pdb=" CG PHE N 693 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE N 693 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE N 693 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE N 693 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 693 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE N 693 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL S 570 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C VAL S 570 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL S 570 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU S 571 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE S 547 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO S 548 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO S 548 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 548 " 0.030 5.00e-02 4.00e+02 ... (remaining 2842 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5302 2.82 - 3.34: 17927 3.34 - 3.86: 40610 3.86 - 4.38: 45238 4.38 - 4.90: 67483 Nonbonded interactions: 176560 Sorted by model distance: nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.304 3.040 nonbonded pdb=" NH1 ARG K 729 " pdb=" OD1 ASP N 686 " model vdw 2.317 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.325 3.040 nonbonded pdb=" NH2 ARG C 32 " pdb=" OE1 GLU D 32 " model vdw 2.336 3.120 nonbonded pdb=" OG SER P 786 " pdb=" O VAL P 867 " model vdw 2.337 3.040 ... (remaining 176555 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 37 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 102) } ncs_group { reference = (chain 'C' and (resid 11 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'G' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 28 through 121) } ncs_group { reference = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'N' selection = chain 'S' } 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=0.71 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.630 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.005 0.104 22142 Z= 0.225 Angle : 0.802 9.185 31352 Z= 0.460 Chirality : 0.047 0.230 3477 Planarity : 0.006 0.054 2845 Dihedral : 23.621 179.882 9066 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.16), residues: 1736 helix: -1.78 (0.14), residues: 864 sheet: -1.02 (0.47), residues: 115 loop : -2.29 (0.18), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 713 TYR 0.028 0.002 TYR F 72 PHE 0.041 0.003 PHE N 693 TRP 0.026 0.002 TRP N 716 HIS 0.015 0.002 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00464 (22142) covalent geometry : angle 0.80227 (31352) hydrogen bonds : bond 0.13638 ( 1098) hydrogen bonds : angle 6.10372 ( 2815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 591 time to evaluate : 0.670 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: C 76 THR cc_start: 0.7776 (p) cc_final: 0.7483 (t) REVERT: D 57 SER cc_start: 0.8637 (m) cc_final: 0.8379 (t) REVERT: D 76 ARG cc_start: 0.7511 (mtp85) cc_final: 0.7283 (mtp85) REVERT: F 21 VAL cc_start: 0.6112 (t) cc_final: 0.5798 (t) REVERT: G 76 THR cc_start: 0.7956 (p) cc_final: 0.7554 (t) REVERT: H 64 ASN cc_start: 0.8786 (m-40) cc_final: 0.8487 (m-40) REVERT: K 698 TRP cc_start: 0.7024 (m-10) cc_final: 0.6299 (m-10) REVERT: K 735 TYR cc_start: 0.8212 (t80) cc_final: 0.7955 (t80) REVERT: K 865 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7443 (pt0) REVERT: K 882 ARG cc_start: 0.6575 (tmm-80) cc_final: 0.6273 (ptt180) REVERT: N 585 GLU cc_start: 0.3531 (tp30) cc_final: 0.2966 (mm-30) REVERT: N 617 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8029 (pp20) REVERT: N 654 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8546 (mm-30) REVERT: N 657 HIS cc_start: 0.8534 (t70) cc_final: 0.8303 (t70) REVERT: N 672 PHE cc_start: 0.8498 (t80) cc_final: 0.8245 (t80) REVERT: N 675 MET cc_start: 0.8231 (tmm) cc_final: 0.7096 (tmt) REVERT: N 676 PHE cc_start: 0.6855 (t80) cc_final: 0.6386 (t80) REVERT: N 756 ILE cc_start: 0.8131 (mm) cc_final: 0.7575 (pt) REVERT: P 623 TYR cc_start: 0.7607 (m-80) cc_final: 0.7349 (m-10) REVERT: S 568 TYR cc_start: 0.7429 (t80) cc_final: 0.7199 (t80) REVERT: S 651 LEU cc_start: 0.8237 (mt) cc_final: 0.7739 (mt) REVERT: S 660 ASN cc_start: 0.8455 (m-40) cc_final: 0.7983 (m-40) REVERT: S 680 VAL cc_start: 0.7094 (m) cc_final: 0.6713 (m) outliers start: 0 outliers final: 2 residues processed: 591 average time/residue: 0.7508 time to fit residues: 489.9330 Evaluate side-chains 288 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 286 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain K residue 692 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 24 GLN C 38 ASN C 68 ASN D 60 ASN D 79 HIS E 68 GLN E 108 ASN F 64 ASN G 38 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 692 GLN K 717 ASN K 847 HIS ** K 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 731 HIS ** P 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 718 ASN S 758 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.133417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.095069 restraints weight = 51534.564| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.69 r_work: 0.3366 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22142 Z= 0.183 Angle : 0.646 8.683 31352 Z= 0.361 Chirality : 0.039 0.294 3477 Planarity : 0.006 0.055 2845 Dihedral : 29.045 178.891 5576 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.80 % Allowed : 18.00 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.19), residues: 1736 helix: 0.46 (0.17), residues: 885 sheet: -0.69 (0.47), residues: 111 loop : -1.59 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 767 TYR 0.025 0.002 TYR S 714 PHE 0.026 0.002 PHE S 715 TRP 0.012 0.002 TRP K 698 HIS 0.011 0.001 HIS K 739 Details of bonding type rmsd covalent geometry : bond 0.00406 (22142) covalent geometry : angle 0.64635 (31352) hydrogen bonds : bond 0.04105 ( 1098) hydrogen bonds : angle 3.93643 ( 2815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 316 time to evaluate : 0.497 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: B 24 ASP cc_start: 0.7856 (m-30) cc_final: 0.7483 (p0) REVERT: B 35 ARG cc_start: 0.8977 (mtp85) cc_final: 0.8772 (mmm-85) REVERT: C 76 THR cc_start: 0.8184 (p) cc_final: 0.7921 (t) REVERT: D 76 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7815 (mtp180) REVERT: E 122 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8489 (ptmt) REVERT: E 131 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8614 (mtt180) REVERT: F 74 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8061 (mt-10) REVERT: G 36 LYS cc_start: 0.8844 (pttt) cc_final: 0.8485 (mmtt) REVERT: G 76 THR cc_start: 0.8421 (p) cc_final: 0.8026 (t) REVERT: G 92 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8054 (mt-10) REVERT: K 656 GLN cc_start: 0.9163 (mp10) cc_final: 0.8905 (mp-120) REVERT: K 865 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7493 (pt0) REVERT: K 882 ARG cc_start: 0.6936 (tmm-80) cc_final: 0.6320 (ptt180) REVERT: N 618 GLU cc_start: 0.8693 (pt0) cc_final: 0.8473 (pp20) REVERT: N 622 PHE cc_start: 0.7452 (m-80) cc_final: 0.7233 (m-10) REVERT: N 654 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8850 (mm-30) REVERT: P 643 ILE cc_start: 0.7846 (mm) cc_final: 0.7641 (mp) REVERT: P 793 TYR cc_start: 0.7466 (m-80) cc_final: 0.7199 (m-80) REVERT: S 619 TRP cc_start: 0.8332 (m-10) cc_final: 0.8116 (m-10) REVERT: S 651 LEU cc_start: 0.8353 (mt) cc_final: 0.8122 (mm) REVERT: S 660 ASN cc_start: 0.8826 (m-40) cc_final: 0.8196 (m-40) REVERT: S 722 MET cc_start: 0.6608 (ppp) cc_final: 0.6255 (ttp) outliers start: 57 outliers final: 17 residues processed: 351 average time/residue: 0.6350 time to fit residues: 250.9598 Evaluate side-chains 281 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 263 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 802 ASN Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 719 LEU Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 789 HIS Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain P residue 888 LEU Chi-restraints excluded: chain S residue 696 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 169 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 692 GLN ** K 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 757 ASN P 810 ASN P 847 HIS S 758 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.132012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.093049 restraints weight = 51527.267| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.66 r_work: 0.3326 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22142 Z= 0.172 Angle : 0.606 10.112 31352 Z= 0.340 Chirality : 0.038 0.232 3477 Planarity : 0.005 0.044 2845 Dihedral : 29.089 179.701 5571 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.00 % Allowed : 19.80 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.19), residues: 1736 helix: 1.15 (0.17), residues: 886 sheet: -0.83 (0.45), residues: 117 loop : -1.37 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 83 TYR 0.020 0.002 TYR K 735 PHE 0.022 0.002 PHE N 561 TRP 0.008 0.001 TRP N 751 HIS 0.008 0.001 HIS S 758 Details of bonding type rmsd covalent geometry : bond 0.00385 (22142) covalent geometry : angle 0.60597 (31352) hydrogen bonds : bond 0.03769 ( 1098) hydrogen bonds : angle 3.72206 ( 2815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 282 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9211 (mp) cc_final: 0.8999 (mm) REVERT: B 24 ASP cc_start: 0.7837 (m-30) cc_final: 0.7474 (p0) REVERT: C 76 THR cc_start: 0.8282 (p) cc_final: 0.8043 (t) REVERT: D 76 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7719 (mtp180) REVERT: D 102 GLU cc_start: 0.8195 (tp30) cc_final: 0.7918 (mm-30) REVERT: E 53 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8070 (ttt-90) REVERT: E 73 GLU cc_start: 0.8956 (tt0) cc_final: 0.8588 (tt0) REVERT: E 131 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8642 (mtt180) REVERT: F 74 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8213 (mt-10) REVERT: G 36 LYS cc_start: 0.8841 (pttt) cc_final: 0.8506 (mmtt) REVERT: G 76 THR cc_start: 0.8426 (p) cc_final: 0.8037 (t) REVERT: G 92 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8060 (mt-10) REVERT: H 31 LYS cc_start: 0.7872 (tppt) cc_final: 0.7642 (mmmt) REVERT: K 656 GLN cc_start: 0.9211 (mp10) cc_final: 0.8480 (mp10) REVERT: K 682 MET cc_start: 0.7570 (tmm) cc_final: 0.7007 (tmm) REVERT: K 848 PHE cc_start: 0.7351 (m-80) cc_final: 0.7094 (m-10) REVERT: K 865 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7452 (pt0) REVERT: K 882 ARG cc_start: 0.7080 (tmm-80) cc_final: 0.6485 (ptt180) REVERT: N 617 GLU cc_start: 0.8800 (mm-30) cc_final: 0.7953 (pp20) REVERT: N 622 PHE cc_start: 0.7884 (m-80) cc_final: 0.7224 (m-80) REVERT: N 654 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8852 (mm-30) REVERT: N 665 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7424 (ttmm) REVERT: S 568 TYR cc_start: 0.7950 (t80) cc_final: 0.7672 (t80) REVERT: S 660 ASN cc_start: 0.8877 (m-40) cc_final: 0.8256 (m-40) outliers start: 60 outliers final: 26 residues processed: 316 average time/residue: 0.6270 time to fit residues: 223.8216 Evaluate side-chains 285 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 256 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 802 ASN Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 551 ARG Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 665 LYS Chi-restraints excluded: chain N residue 701 ILE Chi-restraints excluded: chain N residue 719 LEU Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 810 ASN Chi-restraints excluded: chain P residue 824 ILE Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 753 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 132 optimal weight: 0.2980 chunk 56 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS E 108 ASN G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 692 GLN K 717 ASN ** K 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 758 HIS P 757 ASN P 810 ASN ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.130564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.091102 restraints weight = 51309.717| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.58 r_work: 0.3280 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22142 Z= 0.190 Angle : 0.608 10.077 31352 Z= 0.341 Chirality : 0.038 0.253 3477 Planarity : 0.004 0.043 2845 Dihedral : 29.151 179.764 5571 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.20 % Allowed : 19.87 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1736 helix: 1.40 (0.17), residues: 888 sheet: -0.82 (0.46), residues: 117 loop : -1.10 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 35 TYR 0.026 0.002 TYR S 714 PHE 0.024 0.002 PHE S 652 TRP 0.009 0.001 TRP N 619 HIS 0.010 0.001 HIS N 758 Details of bonding type rmsd covalent geometry : bond 0.00427 (22142) covalent geometry : angle 0.60788 (31352) hydrogen bonds : bond 0.03776 ( 1098) hydrogen bonds : angle 3.66217 ( 2815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 286 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 THR cc_start: 0.8326 (p) cc_final: 0.8115 (t) REVERT: C 99 ARG cc_start: 0.7986 (mmm160) cc_final: 0.7724 (mtp85) REVERT: D 76 ARG cc_start: 0.8071 (mtp85) cc_final: 0.7758 (mtp180) REVERT: D 102 GLU cc_start: 0.8195 (tp30) cc_final: 0.7956 (mm-30) REVERT: E 53 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8091 (ttt-90) REVERT: E 56 LYS cc_start: 0.8853 (mtpp) cc_final: 0.8326 (mtmt) REVERT: E 73 GLU cc_start: 0.8959 (tt0) cc_final: 0.8654 (tt0) REVERT: E 131 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8668 (mtt180) REVERT: G 36 LYS cc_start: 0.8889 (pttt) cc_final: 0.8486 (mmmm) REVERT: G 76 THR cc_start: 0.8393 (p) cc_final: 0.8095 (t) REVERT: G 92 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8043 (mt-10) REVERT: H 31 LYS cc_start: 0.7992 (tppt) cc_final: 0.7692 (mmmt) REVERT: H 39 TYR cc_start: 0.8583 (t80) cc_final: 0.8358 (t80) REVERT: K 656 GLN cc_start: 0.9232 (mp10) cc_final: 0.8514 (mp10) REVERT: K 682 MET cc_start: 0.7722 (tmm) cc_final: 0.7097 (tmm) REVERT: K 721 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6755 (ptmm) REVERT: K 779 MET cc_start: 0.8393 (tmm) cc_final: 0.8150 (tmm) REVERT: K 848 PHE cc_start: 0.7413 (m-80) cc_final: 0.7131 (m-10) REVERT: K 882 ARG cc_start: 0.7115 (tmm-80) cc_final: 0.6798 (ptt180) REVERT: N 561 PHE cc_start: 0.6804 (t80) cc_final: 0.6557 (t80) REVERT: N 617 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8030 (pp20) REVERT: N 622 PHE cc_start: 0.7979 (m-80) cc_final: 0.7362 (m-80) REVERT: N 630 PRO cc_start: 0.1955 (Cg_endo) cc_final: 0.1460 (Cg_exo) REVERT: N 654 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8801 (mm-30) REVERT: P 775 SER cc_start: 0.8522 (t) cc_final: 0.8290 (p) REVERT: P 831 ARG cc_start: 0.7304 (mmt180) cc_final: 0.7019 (pmt170) REVERT: P 852 MET cc_start: 0.8108 (ttp) cc_final: 0.7481 (mtp) REVERT: S 560 LEU cc_start: 0.8103 (mm) cc_final: 0.7552 (tm) REVERT: S 568 TYR cc_start: 0.7875 (t80) cc_final: 0.7645 (t80) REVERT: S 604 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7370 (t80) REVERT: S 656 TYR cc_start: 0.8960 (t80) cc_final: 0.8631 (t80) REVERT: S 660 ASN cc_start: 0.8890 (m-40) cc_final: 0.8193 (m-40) REVERT: S 678 ASN cc_start: 0.7041 (t0) cc_final: 0.6837 (m-40) outliers start: 63 outliers final: 28 residues processed: 318 average time/residue: 0.6332 time to fit residues: 226.4806 Evaluate side-chains 295 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 691 THR Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 721 LYS Chi-restraints excluded: chain K residue 802 ASN Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain P residue 626 VAL Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 759 VAL Chi-restraints excluded: chain P residue 824 ILE Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain S residue 604 TYR Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 753 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 21 optimal weight: 0.5980 chunk 152 optimal weight: 0.0980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 115 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 692 GLN ** N 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 696 GLN ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.131867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.093210 restraints weight = 51062.751| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.74 r_work: 0.3318 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22142 Z= 0.145 Angle : 0.591 10.641 31352 Z= 0.332 Chirality : 0.037 0.174 3477 Planarity : 0.004 0.045 2845 Dihedral : 29.046 179.649 5571 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.80 % Allowed : 21.33 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1736 helix: 1.68 (0.17), residues: 885 sheet: -0.69 (0.45), residues: 121 loop : -0.94 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 35 TYR 0.019 0.001 TYR K 735 PHE 0.023 0.001 PHE S 652 TRP 0.008 0.001 TRP K 795 HIS 0.008 0.001 HIS S 758 Details of bonding type rmsd covalent geometry : bond 0.00320 (22142) covalent geometry : angle 0.59095 (31352) hydrogen bonds : bond 0.03327 ( 1098) hydrogen bonds : angle 3.54847 ( 2815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9174 (mp) cc_final: 0.8972 (mm) REVERT: C 99 ARG cc_start: 0.7960 (mmm160) cc_final: 0.7699 (mtp85) REVERT: C 110 ASN cc_start: 0.8360 (t0) cc_final: 0.7927 (t0) REVERT: D 34 TYR cc_start: 0.9257 (m-80) cc_final: 0.8898 (m-80) REVERT: D 76 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7745 (mtp180) REVERT: D 102 GLU cc_start: 0.8115 (tp30) cc_final: 0.7894 (mm-30) REVERT: E 56 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8402 (mtmt) REVERT: E 73 GLU cc_start: 0.8934 (tt0) cc_final: 0.8687 (tt0) REVERT: G 36 LYS cc_start: 0.8874 (pttt) cc_final: 0.8492 (mmmm) REVERT: G 76 THR cc_start: 0.8379 (p) cc_final: 0.8084 (t) REVERT: G 92 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8083 (mt-10) REVERT: H 31 LYS cc_start: 0.7976 (tppt) cc_final: 0.7713 (mmmt) REVERT: K 656 GLN cc_start: 0.9298 (mp10) cc_final: 0.8636 (mp10) REVERT: K 674 MET cc_start: 0.8927 (mtt) cc_final: 0.8505 (mpp) REVERT: K 682 MET cc_start: 0.7662 (tmm) cc_final: 0.7025 (tmm) REVERT: K 779 MET cc_start: 0.8410 (tmm) cc_final: 0.8091 (tmm) REVERT: K 848 PHE cc_start: 0.7259 (m-80) cc_final: 0.6914 (m-80) REVERT: K 882 ARG cc_start: 0.7153 (tmm-80) cc_final: 0.6573 (ptt180) REVERT: K 886 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7167 (mm110) REVERT: N 585 GLU cc_start: 0.3278 (mm-30) cc_final: 0.2231 (mt-10) REVERT: N 617 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8015 (pp20) REVERT: N 622 PHE cc_start: 0.8147 (m-80) cc_final: 0.7459 (m-80) REVERT: N 630 PRO cc_start: 0.1932 (Cg_endo) cc_final: 0.1357 (Cg_exo) REVERT: N 654 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8789 (mm-30) REVERT: N 682 MET cc_start: 0.8102 (tmm) cc_final: 0.7901 (tmm) REVERT: P 831 ARG cc_start: 0.7357 (mmt180) cc_final: 0.7075 (pmt170) REVERT: S 560 LEU cc_start: 0.8118 (mm) cc_final: 0.7627 (tm) REVERT: S 604 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7342 (t80) REVERT: S 656 TYR cc_start: 0.8946 (t80) cc_final: 0.8629 (t80) REVERT: S 660 ASN cc_start: 0.8891 (m-40) cc_final: 0.7950 (m-40) REVERT: S 722 MET cc_start: 0.7302 (ptm) cc_final: 0.6881 (mtp) outliers start: 57 outliers final: 26 residues processed: 313 average time/residue: 0.6273 time to fit residues: 221.7056 Evaluate side-chains 278 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 886 GLN Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain P residue 626 VAL Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 759 VAL Chi-restraints excluded: chain P residue 789 HIS Chi-restraints excluded: chain P residue 824 ILE Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain P residue 864 MET Chi-restraints excluded: chain S residue 604 TYR Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 753 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 48 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 195 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 84 GLN F 93 GLN G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 692 GLN ** K 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 610 ASN ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.130535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.091544 restraints weight = 50928.244| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.77 r_work: 0.3282 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22142 Z= 0.172 Angle : 0.606 11.358 31352 Z= 0.338 Chirality : 0.038 0.219 3477 Planarity : 0.004 0.064 2845 Dihedral : 29.114 179.549 5571 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.27 % Allowed : 22.87 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.20), residues: 1736 helix: 1.70 (0.17), residues: 886 sheet: -0.75 (0.47), residues: 117 loop : -0.78 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG P 767 TYR 0.026 0.002 TYR S 714 PHE 0.027 0.002 PHE S 652 TRP 0.006 0.001 TRP K 795 HIS 0.009 0.001 HIS S 758 Details of bonding type rmsd covalent geometry : bond 0.00387 (22142) covalent geometry : angle 0.60568 (31352) hydrogen bonds : bond 0.03611 ( 1098) hydrogen bonds : angle 3.53389 ( 2815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 258 time to evaluate : 0.654 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 48 LEU cc_start: 0.9215 (mp) cc_final: 0.9014 (mm) REVERT: C 99 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7789 (mtp85) REVERT: C 110 ASN cc_start: 0.8374 (t0) cc_final: 0.8024 (t0) REVERT: D 34 TYR cc_start: 0.9300 (m-80) cc_final: 0.8940 (m-80) REVERT: D 59 MET cc_start: 0.9507 (mmm) cc_final: 0.9168 (tpp) REVERT: D 76 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7833 (mtp180) REVERT: D 102 GLU cc_start: 0.8101 (tp30) cc_final: 0.7895 (mp0) REVERT: E 56 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8437 (mtmt) REVERT: E 73 GLU cc_start: 0.8940 (tt0) cc_final: 0.8680 (tt0) REVERT: E 133 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8061 (mt-10) REVERT: G 36 LYS cc_start: 0.8894 (pttt) cc_final: 0.8556 (mmmm) REVERT: G 76 THR cc_start: 0.8391 (p) cc_final: 0.8104 (t) REVERT: G 92 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8059 (mt-10) REVERT: H 31 LYS cc_start: 0.7922 (tppt) cc_final: 0.7653 (mmmt) REVERT: K 656 GLN cc_start: 0.9339 (mp10) cc_final: 0.8713 (mp10) REVERT: K 682 MET cc_start: 0.7739 (tmm) cc_final: 0.7079 (tmm) REVERT: K 721 LYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6654 (ptmm) REVERT: K 779 MET cc_start: 0.8487 (tmm) cc_final: 0.8151 (tmm) REVERT: K 812 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8321 (mttm) REVERT: K 848 PHE cc_start: 0.7357 (m-80) cc_final: 0.6987 (m-80) REVERT: K 882 ARG cc_start: 0.7207 (tmm-80) cc_final: 0.6603 (ptt180) REVERT: K 886 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7326 (mm110) REVERT: N 585 GLU cc_start: 0.3222 (mm-30) cc_final: 0.2162 (mt-10) REVERT: N 617 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8595 (mm-30) REVERT: N 622 PHE cc_start: 0.8204 (m-80) cc_final: 0.7555 (m-80) REVERT: N 630 PRO cc_start: 0.2780 (Cg_endo) cc_final: 0.2233 (Cg_exo) REVERT: N 654 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8781 (mm-30) REVERT: N 682 MET cc_start: 0.7955 (tmm) cc_final: 0.7724 (tmm) REVERT: N 714 TYR cc_start: 0.5616 (OUTLIER) cc_final: 0.5282 (p90) REVERT: P 775 SER cc_start: 0.8518 (t) cc_final: 0.8231 (p) REVERT: P 831 ARG cc_start: 0.7318 (mmt180) cc_final: 0.7090 (pmt170) REVERT: S 560 LEU cc_start: 0.8202 (mm) cc_final: 0.7648 (tm) REVERT: S 568 TYR cc_start: 0.7742 (t80) cc_final: 0.7536 (t80) REVERT: S 604 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7429 (t80) REVERT: S 656 TYR cc_start: 0.9036 (t80) cc_final: 0.8534 (t80) REVERT: S 660 ASN cc_start: 0.8909 (m-40) cc_final: 0.8069 (m-40) REVERT: S 722 MET cc_start: 0.7231 (ptm) cc_final: 0.6742 (mtp) outliers start: 49 outliers final: 26 residues processed: 288 average time/residue: 0.6367 time to fit residues: 206.6622 Evaluate side-chains 281 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 721 LYS Chi-restraints excluded: chain K residue 812 LYS Chi-restraints excluded: chain K residue 886 GLN Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 714 TYR Chi-restraints excluded: chain P residue 626 VAL Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 759 VAL Chi-restraints excluded: chain P residue 824 ILE Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain P residue 888 LEU Chi-restraints excluded: chain S residue 604 TYR Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 753 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 89 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 660 ASN N 758 HIS P 696 GLN P 810 ASN ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.130232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.091209 restraints weight = 51043.112| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.60 r_work: 0.3279 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22142 Z= 0.170 Angle : 0.609 11.359 31352 Z= 0.340 Chirality : 0.038 0.242 3477 Planarity : 0.004 0.044 2845 Dihedral : 29.114 179.659 5571 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.53 % Allowed : 23.33 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1736 helix: 1.68 (0.17), residues: 892 sheet: -0.68 (0.47), residues: 117 loop : -0.66 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 767 TYR 0.024 0.002 TYR K 735 PHE 0.030 0.002 PHE S 652 TRP 0.008 0.001 TRP K 795 HIS 0.013 0.001 HIS N 758 Details of bonding type rmsd covalent geometry : bond 0.00380 (22142) covalent geometry : angle 0.60860 (31352) hydrogen bonds : bond 0.03483 ( 1098) hydrogen bonds : angle 3.54507 ( 2815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 260 time to evaluate : 0.658 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: C 99 ARG cc_start: 0.8081 (mmm160) cc_final: 0.7831 (mtp85) REVERT: C 110 ASN cc_start: 0.8412 (t0) cc_final: 0.8057 (t0) REVERT: D 34 TYR cc_start: 0.9306 (m-80) cc_final: 0.8980 (m-80) REVERT: D 76 ARG cc_start: 0.8100 (mtp85) cc_final: 0.7831 (mtp180) REVERT: D 102 GLU cc_start: 0.8074 (tp30) cc_final: 0.7859 (mp0) REVERT: E 56 LYS cc_start: 0.8892 (mtpp) cc_final: 0.8459 (mtmt) REVERT: E 73 GLU cc_start: 0.8929 (tt0) cc_final: 0.8650 (tt0) REVERT: E 131 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8670 (mtt180) REVERT: G 41 GLU cc_start: 0.8338 (tt0) cc_final: 0.8111 (pt0) REVERT: G 76 THR cc_start: 0.8388 (p) cc_final: 0.8099 (t) REVERT: G 92 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8124 (mt-10) REVERT: H 31 LYS cc_start: 0.7920 (tppt) cc_final: 0.7644 (mmmt) REVERT: K 656 GLN cc_start: 0.9376 (mp10) cc_final: 0.8729 (mp10) REVERT: K 670 ILE cc_start: 0.9018 (mm) cc_final: 0.7919 (mp) REVERT: K 682 MET cc_start: 0.7813 (tmm) cc_final: 0.7167 (tmm) REVERT: K 688 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7270 (mmm-85) REVERT: K 779 MET cc_start: 0.8519 (tmm) cc_final: 0.8206 (tmm) REVERT: K 848 PHE cc_start: 0.7401 (m-80) cc_final: 0.7049 (m-80) REVERT: K 882 ARG cc_start: 0.7095 (tmm-80) cc_final: 0.6595 (ptt180) REVERT: K 886 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7319 (mm110) REVERT: N 585 GLU cc_start: 0.3187 (mm-30) cc_final: 0.2209 (mt-10) REVERT: N 617 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8656 (mm-30) REVERT: N 622 PHE cc_start: 0.8320 (m-80) cc_final: 0.7596 (m-80) REVERT: N 630 PRO cc_start: 0.3577 (Cg_endo) cc_final: 0.2985 (Cg_exo) REVERT: N 654 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8829 (mm-30) REVERT: N 689 ASP cc_start: 0.8001 (p0) cc_final: 0.7751 (p0) REVERT: N 714 TYR cc_start: 0.5687 (OUTLIER) cc_final: 0.4919 (p90) REVERT: P 775 SER cc_start: 0.8477 (t) cc_final: 0.8192 (p) REVERT: P 793 TYR cc_start: 0.8124 (m-80) cc_final: 0.7904 (m-80) REVERT: P 831 ARG cc_start: 0.7332 (mmt180) cc_final: 0.7089 (pmt170) REVERT: S 560 LEU cc_start: 0.8274 (mm) cc_final: 0.7687 (tm) REVERT: S 568 TYR cc_start: 0.7767 (t80) cc_final: 0.7528 (t80) REVERT: S 604 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7503 (t80) REVERT: S 656 TYR cc_start: 0.9053 (t80) cc_final: 0.8576 (t80) REVERT: S 660 ASN cc_start: 0.8991 (m-40) cc_final: 0.8134 (m-40) REVERT: S 722 MET cc_start: 0.7227 (ptm) cc_final: 0.6706 (mtp) outliers start: 53 outliers final: 30 residues processed: 290 average time/residue: 0.6290 time to fit residues: 205.5360 Evaluate side-chains 279 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 688 ARG Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 886 GLN Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 661 TYR Chi-restraints excluded: chain N residue 701 ILE Chi-restraints excluded: chain N residue 714 TYR Chi-restraints excluded: chain P residue 626 VAL Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 759 VAL Chi-restraints excluded: chain P residue 789 HIS Chi-restraints excluded: chain P residue 824 ILE Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain S residue 604 TYR Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 719 LEU Chi-restraints excluded: chain S residue 753 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 610 ASN ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.129917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.090825 restraints weight = 50896.810| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.63 r_work: 0.3261 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22142 Z= 0.177 Angle : 0.629 12.582 31352 Z= 0.347 Chirality : 0.038 0.254 3477 Planarity : 0.004 0.044 2845 Dihedral : 29.125 179.600 5571 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.27 % Allowed : 24.13 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1736 helix: 1.62 (0.17), residues: 891 sheet: -0.65 (0.48), residues: 117 loop : -0.62 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 35 TYR 0.030 0.002 TYR K 735 PHE 0.063 0.002 PHE N 760 TRP 0.026 0.001 TRP S 751 HIS 0.010 0.001 HIS S 758 Details of bonding type rmsd covalent geometry : bond 0.00398 (22142) covalent geometry : angle 0.62859 (31352) hydrogen bonds : bond 0.03570 ( 1098) hydrogen bonds : angle 3.57029 ( 2815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 254 time to evaluate : 0.648 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: C 99 ARG cc_start: 0.8106 (mmm160) cc_final: 0.7831 (mtp85) REVERT: C 110 ASN cc_start: 0.8433 (t0) cc_final: 0.8037 (t0) REVERT: D 34 TYR cc_start: 0.9321 (m-80) cc_final: 0.9055 (m-80) REVERT: D 76 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7858 (mtp180) REVERT: D 102 GLU cc_start: 0.8122 (tp30) cc_final: 0.7761 (mp0) REVERT: E 56 LYS cc_start: 0.8894 (mtpp) cc_final: 0.8461 (mtmt) REVERT: E 73 GLU cc_start: 0.8954 (tt0) cc_final: 0.8678 (tt0) REVERT: E 131 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8802 (mtt180) REVERT: G 76 THR cc_start: 0.8387 (p) cc_final: 0.8094 (t) REVERT: G 92 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8126 (mt-10) REVERT: H 31 LYS cc_start: 0.7967 (tppt) cc_final: 0.7623 (mmmt) REVERT: H 32 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7533 (pt0) REVERT: H 65 ASP cc_start: 0.9239 (t70) cc_final: 0.8939 (t0) REVERT: K 656 GLN cc_start: 0.9415 (OUTLIER) cc_final: 0.8738 (mp10) REVERT: K 682 MET cc_start: 0.7900 (tmm) cc_final: 0.7207 (tmm) REVERT: K 688 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7310 (mmm-85) REVERT: K 779 MET cc_start: 0.8627 (tmm) cc_final: 0.8308 (tmm) REVERT: K 848 PHE cc_start: 0.7434 (m-80) cc_final: 0.7109 (m-80) REVERT: K 882 ARG cc_start: 0.7137 (tmm-80) cc_final: 0.6618 (ptt180) REVERT: K 886 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7354 (mm110) REVERT: N 585 GLU cc_start: 0.3277 (mm-30) cc_final: 0.2304 (mt-10) REVERT: N 617 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8657 (mm-30) REVERT: N 622 PHE cc_start: 0.8339 (m-80) cc_final: 0.7642 (m-80) REVERT: N 630 PRO cc_start: 0.3569 (Cg_endo) cc_final: 0.2965 (Cg_exo) REVERT: N 654 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8819 (mm-30) REVERT: N 689 ASP cc_start: 0.7986 (p0) cc_final: 0.7710 (p0) REVERT: N 714 TYR cc_start: 0.5926 (OUTLIER) cc_final: 0.4915 (p90) REVERT: N 738 MET cc_start: 0.5140 (pp-130) cc_final: 0.4859 (tmm) REVERT: P 775 SER cc_start: 0.8582 (t) cc_final: 0.8233 (p) REVERT: P 831 ARG cc_start: 0.7353 (mmt180) cc_final: 0.7138 (pmt170) REVERT: S 560 LEU cc_start: 0.8325 (mm) cc_final: 0.7762 (tm) REVERT: S 568 TYR cc_start: 0.7775 (t80) cc_final: 0.7568 (t80) REVERT: S 604 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7238 (t80) REVERT: S 660 ASN cc_start: 0.9015 (m-40) cc_final: 0.8334 (m-40) REVERT: S 722 MET cc_start: 0.7253 (ptm) cc_final: 0.6689 (mtp) outliers start: 49 outliers final: 31 residues processed: 283 average time/residue: 0.6376 time to fit residues: 203.2949 Evaluate side-chains 284 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 656 GLN Chi-restraints excluded: chain K residue 688 ARG Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 886 GLN Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 661 TYR Chi-restraints excluded: chain N residue 701 ILE Chi-restraints excluded: chain N residue 714 TYR Chi-restraints excluded: chain P residue 626 VAL Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 759 VAL Chi-restraints excluded: chain P residue 789 HIS Chi-restraints excluded: chain P residue 824 ILE Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain S residue 604 TYR Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 719 LEU Chi-restraints excluded: chain S residue 753 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 130 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 chunk 160 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 598 HIS ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.130744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.092007 restraints weight = 50882.554| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.69 r_work: 0.3288 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22142 Z= 0.153 Angle : 0.621 13.824 31352 Z= 0.346 Chirality : 0.038 0.229 3477 Planarity : 0.004 0.045 2845 Dihedral : 29.029 179.114 5571 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.73 % Allowed : 24.93 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1736 helix: 1.73 (0.17), residues: 893 sheet: -0.78 (0.47), residues: 119 loop : -0.53 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 35 TYR 0.031 0.002 TYR K 735 PHE 0.037 0.001 PHE S 652 TRP 0.009 0.001 TRP K 795 HIS 0.011 0.001 HIS S 758 Details of bonding type rmsd covalent geometry : bond 0.00342 (22142) covalent geometry : angle 0.62125 (31352) hydrogen bonds : bond 0.03339 ( 1098) hydrogen bonds : angle 3.58157 ( 2815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 0.573 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: C 99 ARG cc_start: 0.8103 (mmm160) cc_final: 0.7826 (mtp85) REVERT: C 110 ASN cc_start: 0.8430 (t0) cc_final: 0.8060 (t0) REVERT: D 34 TYR cc_start: 0.9325 (m-80) cc_final: 0.8965 (m-80) REVERT: D 76 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7820 (mtp180) REVERT: D 102 GLU cc_start: 0.8035 (tp30) cc_final: 0.7810 (mp0) REVERT: E 56 LYS cc_start: 0.8875 (mtpp) cc_final: 0.8452 (mtmt) REVERT: E 73 GLU cc_start: 0.8945 (tt0) cc_final: 0.8635 (tt0) REVERT: E 131 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8687 (mtt180) REVERT: G 76 THR cc_start: 0.8386 (p) cc_final: 0.8099 (t) REVERT: G 92 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8120 (mt-10) REVERT: H 31 LYS cc_start: 0.7961 (tppt) cc_final: 0.7628 (mmmt) REVERT: H 65 ASP cc_start: 0.9188 (t70) cc_final: 0.8894 (t0) REVERT: K 656 GLN cc_start: 0.9436 (OUTLIER) cc_final: 0.8781 (mp10) REVERT: K 682 MET cc_start: 0.7823 (tmm) cc_final: 0.7123 (tmm) REVERT: K 721 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6709 (ptmm) REVERT: K 779 MET cc_start: 0.8651 (tmm) cc_final: 0.8330 (tmm) REVERT: K 848 PHE cc_start: 0.7403 (m-80) cc_final: 0.7126 (m-80) REVERT: K 882 ARG cc_start: 0.7110 (tmm-80) cc_final: 0.6671 (ptt180) REVERT: K 886 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7272 (mm110) REVERT: N 585 GLU cc_start: 0.3133 (mm-30) cc_final: 0.2120 (mt-10) REVERT: N 617 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8677 (mm-30) REVERT: N 622 PHE cc_start: 0.8529 (m-80) cc_final: 0.7888 (m-80) REVERT: N 654 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8807 (mm-30) REVERT: N 714 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.4914 (p90) REVERT: N 738 MET cc_start: 0.5080 (pp-130) cc_final: 0.4759 (tmm) REVERT: P 775 SER cc_start: 0.8551 (t) cc_final: 0.8191 (p) REVERT: P 793 TYR cc_start: 0.8011 (m-80) cc_final: 0.7745 (m-80) REVERT: P 831 ARG cc_start: 0.7288 (mmt180) cc_final: 0.7013 (pmt170) REVERT: S 560 LEU cc_start: 0.8264 (mm) cc_final: 0.7765 (tm) REVERT: S 568 TYR cc_start: 0.7751 (t80) cc_final: 0.7517 (t80) REVERT: S 604 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7289 (t80) REVERT: S 656 TYR cc_start: 0.9028 (t80) cc_final: 0.8734 (t80) REVERT: S 660 ASN cc_start: 0.8936 (m-40) cc_final: 0.8072 (m-40) REVERT: S 722 MET cc_start: 0.7043 (ptm) cc_final: 0.6638 (mtp) outliers start: 41 outliers final: 28 residues processed: 289 average time/residue: 0.6563 time to fit residues: 212.9140 Evaluate side-chains 278 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 656 GLN Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 721 LYS Chi-restraints excluded: chain K residue 805 LEU Chi-restraints excluded: chain K residue 886 GLN Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 661 TYR Chi-restraints excluded: chain N residue 701 ILE Chi-restraints excluded: chain N residue 714 TYR Chi-restraints excluded: chain P residue 626 VAL Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 759 VAL Chi-restraints excluded: chain P residue 789 HIS Chi-restraints excluded: chain P residue 824 ILE Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain S residue 604 TYR Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 753 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 94 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 127 optimal weight: 0.0970 chunk 152 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 chunk 71 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 160 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 60 ASN H 44 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 758 HIS P 696 GLN ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.129232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.090089 restraints weight = 51110.408| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.65 r_work: 0.3250 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22142 Z= 0.181 Angle : 0.641 12.626 31352 Z= 0.356 Chirality : 0.038 0.232 3477 Planarity : 0.004 0.043 2845 Dihedral : 29.104 179.368 5571 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.00 % Allowed : 25.33 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1736 helix: 1.64 (0.17), residues: 895 sheet: -0.56 (0.44), residues: 134 loop : -0.51 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 35 TYR 0.032 0.002 TYR K 735 PHE 0.020 0.002 PHE P 731 TRP 0.006 0.001 TRP N 751 HIS 0.013 0.001 HIS N 758 Details of bonding type rmsd covalent geometry : bond 0.00410 (22142) covalent geometry : angle 0.64081 (31352) hydrogen bonds : bond 0.03700 ( 1098) hydrogen bonds : angle 3.62947 ( 2815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 257 time to evaluate : 0.662 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: B 59 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8738 (ttmt) REVERT: C 99 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7867 (mtp85) REVERT: C 110 ASN cc_start: 0.8467 (t0) cc_final: 0.8050 (t0) REVERT: D 34 TYR cc_start: 0.9343 (m-80) cc_final: 0.9017 (m-80) REVERT: D 59 MET cc_start: 0.9539 (mmm) cc_final: 0.9127 (tpp) REVERT: D 76 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7874 (mtp180) REVERT: D 102 GLU cc_start: 0.8151 (tp30) cc_final: 0.7870 (mp0) REVERT: E 56 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8474 (mtmt) REVERT: E 73 GLU cc_start: 0.8950 (tt0) cc_final: 0.8659 (tt0) REVERT: E 131 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8705 (mtt180) REVERT: G 76 THR cc_start: 0.8383 (p) cc_final: 0.8107 (t) REVERT: G 92 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8112 (mt-10) REVERT: H 31 LYS cc_start: 0.7973 (tppt) cc_final: 0.7618 (mmmt) REVERT: H 44 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8881 (tt0) REVERT: H 65 ASP cc_start: 0.9243 (t70) cc_final: 0.8947 (t0) REVERT: K 656 GLN cc_start: 0.9452 (OUTLIER) cc_final: 0.8817 (mp10) REVERT: K 682 MET cc_start: 0.7870 (tmm) cc_final: 0.7191 (tmm) REVERT: K 779 MET cc_start: 0.8671 (tmm) cc_final: 0.8352 (tmm) REVERT: K 848 PHE cc_start: 0.7409 (m-80) cc_final: 0.7125 (m-80) REVERT: K 886 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7318 (mm110) REVERT: N 585 GLU cc_start: 0.3194 (mm-30) cc_final: 0.2111 (mt-10) REVERT: N 617 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8667 (mm-30) REVERT: N 622 PHE cc_start: 0.8470 (m-80) cc_final: 0.7938 (m-80) REVERT: N 654 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8769 (mm-30) REVERT: N 714 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.4257 (p90) REVERT: N 738 MET cc_start: 0.5001 (pp-130) cc_final: 0.4614 (tmm) REVERT: P 775 SER cc_start: 0.8629 (t) cc_final: 0.8224 (p) REVERT: S 560 LEU cc_start: 0.8145 (mm) cc_final: 0.7655 (tm) REVERT: S 568 TYR cc_start: 0.7835 (t80) cc_final: 0.7630 (t80) REVERT: S 604 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7374 (t80) REVERT: S 660 ASN cc_start: 0.9015 (m-40) cc_final: 0.8259 (m-40) REVERT: S 722 MET cc_start: 0.6945 (ptm) cc_final: 0.6509 (mtp) REVERT: S 738 MET cc_start: 0.3503 (OUTLIER) cc_final: 0.3225 (ppp) outliers start: 45 outliers final: 30 residues processed: 282 average time/residue: 0.6551 time to fit residues: 207.3133 Evaluate side-chains 284 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 656 GLN Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 739 HIS Chi-restraints excluded: chain K residue 805 LEU Chi-restraints excluded: chain K residue 886 GLN Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 661 TYR Chi-restraints excluded: chain N residue 701 ILE Chi-restraints excluded: chain N residue 714 TYR Chi-restraints excluded: chain P residue 626 VAL Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 759 VAL Chi-restraints excluded: chain P residue 824 ILE Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain P residue 864 MET Chi-restraints excluded: chain S residue 604 TYR Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 738 MET Chi-restraints excluded: chain S residue 753 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 2 optimal weight: 0.0050 chunk 101 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 175 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 172 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.130350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.091653 restraints weight = 51100.050| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.86 r_work: 0.3269 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22142 Z= 0.155 Angle : 0.635 11.228 31352 Z= 0.352 Chirality : 0.038 0.229 3477 Planarity : 0.004 0.067 2845 Dihedral : 29.044 178.744 5571 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.67 % Allowed : 26.07 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1736 helix: 1.72 (0.17), residues: 891 sheet: -0.51 (0.43), residues: 134 loop : -0.50 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 83 TYR 0.035 0.001 TYR K 735 PHE 0.043 0.002 PHE S 652 TRP 0.011 0.001 TRP K 795 HIS 0.012 0.001 HIS S 758 Details of bonding type rmsd covalent geometry : bond 0.00347 (22142) covalent geometry : angle 0.63526 (31352) hydrogen bonds : bond 0.03392 ( 1098) hydrogen bonds : angle 3.64746 ( 2815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9065.74 seconds wall clock time: 154 minutes 8.29 seconds (9248.29 seconds total)