Starting phenix.real_space_refine on Sun Sep 13 04:26:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pa7_20281/09_2026/6pa7_20281.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pa7_20281/09_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_20281/09_2026/6pa7_20281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pa7_20281/09_2026/6pa7_20281.map" model { file = "/net/cci-nas-00/data/ceres_data/6pa7_20281/09_2026/6pa7_20281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pa7_20281/09_2026/6pa7_20281.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pa7_20281/09_2026/6pa7_20281.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pa7_20281/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.24, per 1000 atoms: 0.20 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: 1.44 Conformation dependent library (CDL) restraints added in 631.1 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: 2.76 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: 4.94 Time building geometry restraints manager: 2.10 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=" C3' DG I 104 " pdb=" O3' DG I 104 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.46e+01 bond pdb=" C3' DT J 138 " pdb=" O3' DT J 138 " ideal model delta sigma weight residual 1.435 1.482 -0.047 1.30e-02 5.92e+03 1.33e+01 bond pdb=" C3' DT I 12 " pdb=" O3' DT I 12 " ideal model delta sigma weight residual 1.435 1.482 -0.047 1.30e-02 5.92e+03 1.30e+01 ... (remaining 22137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 29452 1.84 - 3.67: 1742 3.67 - 5.51: 114 5.51 - 7.35: 24 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=" O4' DC J 136 " pdb=" C4' DC J 136 " pdb=" C3' DC J 136 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" C3' DG I 104 " pdb=" O3' DG I 104 " pdb=" P DC I 105 " ideal model delta sigma weight residual 119.70 125.20 -5.50 1.20e+00 6.94e-01 2.10e+01 angle pdb=" C3' DT I 12 " pdb=" O3' DT I 12 " pdb=" P DG I 13 " ideal model delta sigma weight residual 119.70 125.18 -5.48 1.20e+00 6.94e-01 2.09e+01 angle pdb=" O5' DA I 49 " pdb=" C5' DA I 49 " pdb=" C4' DA I 49 " ideal model delta sigma weight residual 109.40 113.05 -3.65 8.00e-01 1.56e+00 2.08e+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: 2282 0.046 - 0.092: 936 0.092 - 0.138: 216 0.138 - 0.184: 33 0.184 - 0.230: 10 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=" P DG I 5 " pdb=" OP1 DG I 5 " pdb=" OP2 DG I 5 " pdb=" O5' DG I 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.54 -0.21 2.00e-01 2.50e+01 1.07e+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 ... (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: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.160 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 22142 Z= 0.470 Angle : 0.905 9.185 31352 Z= 0.682 Chirality : 0.051 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/Z covalent geometry : bond 0.00586 / 0.47 (22142) covalent geometry : angle 0.90478 / 0.68 (31352) hydrogen bonds : bond 0.13638 / 8.90 ( 1098) hydrogen bonds : angle 6.10372 / 4.38 ( 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 : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 THR cc_start: 0.7776 (p) cc_final: 0.7477 (t) REVERT: D 57 SER cc_start: 0.8637 (m) cc_final: 0.8378 (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: 0.7555 (t) REVERT: H 64 ASN cc_start: 0.8786 (m-40) cc_final: 0.8488 (m-40) REVERT: K 698 TRP cc_start: 0.7024 (m-10) cc_final: 0.6358 (m-10) REVERT: K 735 TYR cc_start: 0.8212 (t80) cc_final: 0.7956 (t80) REVERT: K 882 ARG cc_start: 0.6575 (tmm-80) cc_final: 0.6216 (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: 0.8246 (t80) REVERT: N 675 MET cc_start: 0.8231 (tmm) cc_final: 0.7095 (tmt) REVERT: N 676 PHE cc_start: 0.6855 (t80) cc_final: 0.6385 (t80) REVERT: N 756 ILE cc_start: 0.8131 (mm) cc_final: 0.7623 (pt) REVERT: P 623 TYR cc_start: 0.7607 (m-80) cc_final: 0.7350 (m-10) REVERT: S 568 TYR cc_start: 0.7429 (t80) cc_final: 0.7198 (t80) REVERT: S 623 ASP cc_start: 0.7906 (m-30) cc_final: 0.7601 (m-30) 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: 0.7194 time to fit residues: 472.4054 Evaluate side-chains 289 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 287 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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: 8.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 24 GLN 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.134199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.096061 restraints weight = 51647.384| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.70 r_work: 0.3383 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22142 Z= 0.188 Angle : 0.737 8.791 31352 Z= 0.403 Chirality : 0.049 0.268 3477 Planarity : 0.006 0.084 2845 Dihedral : 29.222 176.990 5576 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.93 % Allowed : 18.20 % Favored : 77.87 % 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: -0.99 (0.18), residues: 1736 helix: 0.23 (0.16), residues: 885 sheet: -0.51 (0.48), residues: 109 loop : -1.76 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 688 TYR 0.039 0.002 TYR S 714 PHE 0.032 0.003 PHE N 652 TRP 0.018 0.001 TRP N 716 HIS 0.010 0.002 HIS K 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (22142) covalent geometry : angle 0.73723 / 0.40 (31352) hydrogen bonds : bond 0.05116 / 3.40 ( 1098) hydrogen bonds : angle 4.14021 / 2.93 ( 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 380 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 321 time to evaluate : 0.683 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: B 24 ASP cc_start: 0.7868 (m-30) cc_final: 0.7462 (p0) REVERT: C 76 THR cc_start: 0.8154 (p) cc_final: 0.7848 (t) REVERT: D 76 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7756 (mtp85) REVERT: D 102 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7941 (mm-30) REVERT: D 105 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8083 (ptpp) REVERT: E 131 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8565 (mtt180) REVERT: F 79 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8506 (mmtm) REVERT: G 36 LYS cc_start: 0.8744 (pttt) cc_final: 0.8309 (mmtt) REVERT: G 76 THR cc_start: 0.8395 (p) cc_final: 0.7967 (t) REVERT: G 92 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8056 (mt-10) REVERT: K 656 GLN cc_start: 0.9118 (mp10) cc_final: 0.8849 (mp-120) REVERT: K 682 MET cc_start: 0.7546 (tmm) cc_final: 0.7127 (tmm) REVERT: N 551 ARG cc_start: 0.6498 (OUTLIER) cc_final: 0.6217 (ptp-110) REVERT: N 561 PHE cc_start: 0.6677 (t80) cc_final: 0.6287 (t80) REVERT: N 617 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8228 (pp20) REVERT: N 618 GLU cc_start: 0.8694 (pt0) cc_final: 0.8205 (pp20) REVERT: N 622 PHE cc_start: 0.7576 (m-80) cc_final: 0.6936 (m-80) REVERT: N 654 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8765 (mm-30) REVERT: N 660 ASN cc_start: 0.7961 (p0) cc_final: 0.7695 (p0) REVERT: N 722 MET cc_start: 0.5254 (mpt) cc_final: 0.5049 (mpt) REVERT: P 717 ASN cc_start: 0.5688 (m-40) cc_final: 0.5458 (t0) REVERT: P 731 PHE cc_start: 0.8194 (t80) cc_final: 0.7898 (t80) REVERT: S 656 TYR cc_start: 0.9070 (t80) cc_final: 0.8842 (t80) REVERT: S 660 ASN cc_start: 0.8784 (m-40) cc_final: 0.8180 (m-40) REVERT: S 722 MET cc_start: 0.6576 (ppp) cc_final: 0.6224 (ppp) REVERT: S 737 ASN cc_start: 0.5676 (m-40) cc_final: 0.5472 (m-40) outliers start: 59 outliers final: 20 residues processed: 352 average time/residue: 0.6277 time to fit residues: 249.7441 Evaluate side-chains 304 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 279 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 102 GLU Chi-restraints excluded: chain D residue 105 LYS 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 E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 113 LYS 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 551 ARG 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 S residue 617 GLU 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: 10.0000 chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN 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 810 ASN ** P 847 HIS ** 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 = 0.4260 r_free = 0.4260 target = 0.132614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.093582 restraints weight = 51433.736| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.64 r_work: 0.3342 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 22142 Z= 0.163 Angle : 0.668 9.429 31352 Z= 0.369 Chirality : 0.046 0.265 3477 Planarity : 0.005 0.051 2845 Dihedral : 29.395 177.529 5571 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: -0.26 (0.19), residues: 1736 helix: 0.96 (0.17), residues: 885 sheet: -0.66 (0.46), residues: 117 loop : -1.52 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 650 TYR 0.022 0.002 TYR P 793 PHE 0.026 0.002 PHE N 652 TRP 0.008 0.001 TRP N 674 HIS 0.009 0.001 HIS S 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (22142) covalent geometry : angle 0.66843 / 0.37 (31352) hydrogen bonds : bond 0.04440 / 2.93 ( 1098) hydrogen bonds : angle 3.88744 / 2.73 ( 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 350 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 287 time to evaluate : 0.703 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 59 GLU cc_start: 0.8826 (pm20) cc_final: 0.8597 (pm20) REVERT: C 76 THR cc_start: 0.8264 (p) cc_final: 0.7967 (t) REVERT: D 59 MET cc_start: 0.9475 (mmm) cc_final: 0.9274 (mmt) REVERT: D 76 ARG cc_start: 0.8024 (mtp85) cc_final: 0.7813 (mtp180) REVERT: D 102 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8052 (mm-30) REVERT: D 105 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8266 (ptpp) REVERT: E 53 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8086 (ttt-90) REVERT: E 73 GLU cc_start: 0.8919 (tt0) cc_final: 0.8588 (tt0) REVERT: E 122 LYS cc_start: 0.8725 (mtmm) cc_final: 0.8519 (ptmt) REVERT: E 131 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8589 (mtt180) REVERT: F 79 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8539 (mmtm) REVERT: G 36 LYS cc_start: 0.8810 (pttt) cc_final: 0.8226 (mmtt) REVERT: G 76 THR cc_start: 0.8445 (p) cc_final: 0.8038 (t) REVERT: G 92 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8055 (mt-10) REVERT: K 656 GLN cc_start: 0.9135 (mp10) cc_final: 0.8447 (mp10) REVERT: K 682 MET cc_start: 0.7553 (tmm) cc_final: 0.7104 (tmm) REVERT: N 617 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8185 (pp20) REVERT: N 618 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8375 (pp20) REVERT: N 622 PHE cc_start: 0.7842 (m-80) cc_final: 0.7115 (m-80) REVERT: N 654 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8785 (mm-30) REVERT: N 722 MET cc_start: 0.5469 (mpt) cc_final: 0.5230 (mpt) REVERT: N 738 MET cc_start: 0.4696 (OUTLIER) cc_final: 0.4457 (ppp) REVERT: P 731 PHE cc_start: 0.8182 (t80) cc_final: 0.7884 (t80) REVERT: P 793 TYR cc_start: 0.7565 (m-80) cc_final: 0.7317 (m-80) REVERT: S 619 TRP cc_start: 0.8417 (m-10) cc_final: 0.8213 (m-10) REVERT: S 660 ASN cc_start: 0.8853 (m-40) cc_final: 0.8282 (m-40) REVERT: S 680 VAL cc_start: 0.7433 (OUTLIER) cc_final: 0.7137 (m) REVERT: S 718 ASN cc_start: 0.8073 (t0) cc_final: 0.7762 (t0) outliers start: 63 outliers final: 27 residues processed: 321 average time/residue: 0.6191 time to fit residues: 225.7875 Evaluate side-chains 297 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 105 LYS 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 86 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 622 VAL 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 N residue 618 GLU Chi-restraints excluded: chain N residue 701 ILE Chi-restraints excluded: chain N residue 719 LEU Chi-restraints excluded: chain N residue 738 MET Chi-restraints excluded: chain P residue 684 VAL 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 S residue 680 VAL Chi-restraints excluded: chain S residue 696 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 80 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 132 optimal weight: 0.1980 chunk 56 optimal weight: 0.4980 chunk 89 optimal weight: 40.0000 chunk 196 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 692 GLN ** K 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 847 HIS ** 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 = 0.4250 r_free = 0.4250 target = 0.131969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.093490 restraints weight = 51446.693| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.73 r_work: 0.3331 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22142 Z= 0.161 Angle : 0.661 8.497 31352 Z= 0.363 Chirality : 0.045 0.290 3477 Planarity : 0.005 0.075 2845 Dihedral : 29.426 177.740 5571 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.27 % Allowed : 20.67 % Favored : 75.07 % 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: 0.07 (0.20), residues: 1736 helix: 1.27 (0.17), residues: 884 sheet: -0.87 (0.47), residues: 117 loop : -1.33 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 35 TYR 0.027 0.002 TYR S 714 PHE 0.023 0.002 PHE N 652 TRP 0.006 0.001 TRP N 751 HIS 0.011 0.001 HIS N 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (22142) covalent geometry : angle 0.66089 / 0.36 (31352) hydrogen bonds : bond 0.04206 / 2.78 ( 1098) hydrogen bonds : angle 3.79239 / 2.67 ( 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 350 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 286 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9238 (mp) cc_final: 0.9027 (mm) REVERT: A 56 LYS cc_start: 0.8639 (ttmm) cc_final: 0.8234 (tttp) REVERT: B 59 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8656 (ttmt) REVERT: C 76 THR cc_start: 0.8328 (p) cc_final: 0.8052 (t) REVERT: C 92 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7753 (mt-10) REVERT: D 59 MET cc_start: 0.9450 (mmm) cc_final: 0.9156 (tpp) REVERT: D 102 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8053 (mm-30) REVERT: D 105 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8429 (ptpp) REVERT: D 110 GLU cc_start: 0.8335 (tt0) cc_final: 0.8048 (tp30) REVERT: E 53 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8101 (ttt-90) REVERT: E 73 GLU cc_start: 0.8978 (tt0) cc_final: 0.8605 (tt0) REVERT: E 131 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8612 (mtt180) REVERT: F 79 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8522 (mmtm) REVERT: G 36 LYS cc_start: 0.8700 (pttt) cc_final: 0.8227 (mmmm) REVERT: G 76 THR cc_start: 0.8412 (p) cc_final: 0.8025 (t) REVERT: G 92 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8060 (mt-10) REVERT: H 65 ASP cc_start: 0.9177 (t70) cc_final: 0.8890 (t0) REVERT: K 656 GLN cc_start: 0.9193 (mp10) cc_final: 0.8567 (mp10) REVERT: K 682 MET cc_start: 0.7575 (tmm) cc_final: 0.7071 (tmm) REVERT: K 688 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7195 (mmm-85) REVERT: K 779 MET cc_start: 0.8204 (tmm) cc_final: 0.7871 (tmm) REVERT: N 622 PHE cc_start: 0.7907 (m-80) cc_final: 0.7272 (m-80) REVERT: N 654 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8767 (mm-30) REVERT: N 682 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8093 (tmm) REVERT: N 688 ARG cc_start: 0.8764 (ttm110) cc_final: 0.8495 (mmm160) REVERT: N 689 ASP cc_start: 0.7816 (p0) cc_final: 0.7407 (p0) REVERT: N 738 MET cc_start: 0.4748 (tmm) cc_final: 0.4500 (ppp) REVERT: P 793 TYR cc_start: 0.7656 (m-80) cc_final: 0.7284 (m-80) REVERT: P 831 ARG cc_start: 0.7328 (mmt180) cc_final: 0.7060 (pmt170) REVERT: S 568 TYR cc_start: 0.8008 (t80) cc_final: 0.7692 (t80) REVERT: S 656 TYR cc_start: 0.8946 (t80) cc_final: 0.8694 (t80) REVERT: S 660 ASN cc_start: 0.8855 (m-40) cc_final: 0.8171 (m-40) REVERT: S 688 ARG cc_start: 0.9247 (ptm160) cc_final: 0.8920 (ptt-90) outliers start: 64 outliers final: 28 residues processed: 323 average time/residue: 0.6371 time to fit residues: 232.2649 Evaluate side-chains 293 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 257 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS 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 D residue 102 GLU Chi-restraints excluded: chain D residue 105 LYS 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 E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 79 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 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 688 ARG Chi-restraints excluded: chain K residue 691 THR 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 560 LEU Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 682 MET Chi-restraints excluded: chain P residue 684 VAL 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 S residue 617 GLU Chi-restraints excluded: chain S residue 696 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 21 optimal weight: 0.9980 chunk 152 optimal weight: 30.0000 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 139 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 88 optimal weight: 40.0000 chunk 115 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS G 73 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 696 GLN ** P 847 HIS ** 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 = 0.4215 r_free = 0.4215 target = 0.129669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.090417 restraints weight = 50964.053| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.62 r_work: 0.3269 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22142 Z= 0.206 Angle : 0.690 8.338 31352 Z= 0.375 Chirality : 0.047 0.287 3477 Planarity : 0.005 0.051 2845 Dihedral : 29.552 177.358 5571 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.47 % Allowed : 20.53 % Favored : 75.00 % 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: 0.20 (0.20), residues: 1736 helix: 1.31 (0.17), residues: 883 sheet: -0.83 (0.47), residues: 115 loop : -1.16 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 35 TYR 0.023 0.002 TYR H 80 PHE 0.033 0.002 PHE S 652 TRP 0.032 0.002 TRP N 619 HIS 0.008 0.001 HIS S 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (22142) covalent geometry : angle 0.68985 / 0.37 (31352) hydrogen bonds : bond 0.04641 / 3.06 ( 1098) hydrogen bonds : angle 3.79732 / 2.68 ( 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 334 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 267 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8483 (mtt) REVERT: B 59 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8648 (ttmt) REVERT: C 76 THR cc_start: 0.8363 (p) cc_final: 0.8113 (t) REVERT: C 99 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7738 (mtp85) REVERT: D 59 MET cc_start: 0.9506 (mmm) cc_final: 0.9153 (mmt) REVERT: D 102 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8115 (mm-30) REVERT: D 110 GLU cc_start: 0.8418 (tp30) cc_final: 0.8164 (tp30) REVERT: E 53 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8147 (ttt-90) REVERT: E 56 LYS cc_start: 0.8826 (mtpp) cc_final: 0.8368 (mtmt) REVERT: E 73 GLU cc_start: 0.8999 (tt0) cc_final: 0.8772 (tt0) REVERT: E 120 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8595 (mtm) REVERT: E 131 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8667 (mtt180) REVERT: G 36 LYS cc_start: 0.8771 (pttt) cc_final: 0.8527 (mmtt) REVERT: G 76 THR cc_start: 0.8425 (p) cc_final: 0.8076 (t) REVERT: G 92 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8076 (mt-10) REVERT: H 65 ASP cc_start: 0.9188 (t70) cc_final: 0.8971 (t0) REVERT: K 656 GLN cc_start: 0.9200 (mp10) cc_final: 0.8576 (mp10) REVERT: K 682 MET cc_start: 0.7849 (tmm) cc_final: 0.7416 (tmm) REVERT: K 688 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7298 (mmm-85) REVERT: K 779 MET cc_start: 0.8389 (tmm) cc_final: 0.8100 (tmm) REVERT: N 617 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8053 (pp20) REVERT: N 622 PHE cc_start: 0.8083 (m-80) cc_final: 0.7490 (m-10) REVERT: N 654 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8775 (mm-30) REVERT: N 682 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8039 (tmm) REVERT: N 688 ARG cc_start: 0.8768 (ttm110) cc_final: 0.8498 (mmm160) REVERT: N 689 ASP cc_start: 0.7834 (p0) cc_final: 0.7466 (p0) REVERT: P 775 SER cc_start: 0.8517 (t) cc_final: 0.8261 (p) REVERT: P 831 ARG cc_start: 0.7348 (mmt180) cc_final: 0.7077 (pmt170) REVERT: S 568 TYR cc_start: 0.8077 (t80) cc_final: 0.7704 (t80) REVERT: S 656 TYR cc_start: 0.9061 (t80) cc_final: 0.8779 (t80) REVERT: S 660 ASN cc_start: 0.8902 (m-40) cc_final: 0.8164 (m-40) outliers start: 67 outliers final: 31 residues processed: 310 average time/residue: 0.6315 time to fit residues: 220.4832 Evaluate side-chains 295 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 102 GLU 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 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 95 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 H residue 113 LYS 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 802 ASN Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 682 MET 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 862 THR Chi-restraints excluded: chain S residue 648 THR Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 719 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 48 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 195 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P 847 HIS ** P 879 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 = 0.4228 r_free = 0.4228 target = 0.130494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.091735 restraints weight = 50877.110| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.80 r_work: 0.3288 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22142 Z= 0.145 Angle : 0.649 7.924 31352 Z= 0.357 Chirality : 0.045 0.261 3477 Planarity : 0.004 0.052 2845 Dihedral : 29.486 176.185 5571 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.53 % Allowed : 21.73 % Favored : 74.73 % 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: 0.45 (0.20), residues: 1736 helix: 1.54 (0.17), residues: 882 sheet: -0.69 (0.47), residues: 113 loop : -1.07 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 35 TYR 0.028 0.002 TYR S 714 PHE 0.030 0.002 PHE S 652 TRP 0.007 0.001 TRP K 795 HIS 0.009 0.001 HIS S 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (22142) covalent geometry : angle 0.64904 / 0.36 (31352) hydrogen bonds : bond 0.03909 / 2.59 ( 1098) hydrogen bonds : angle 3.69334 / 2.60 ( 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 317 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 0.628 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: 0.9236 (OUTLIER) cc_final: 0.8675 (ttmt) REVERT: C 76 THR cc_start: 0.8386 (p) cc_final: 0.8149 (t) REVERT: C 92 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7829 (mt-10) REVERT: C 99 ARG cc_start: 0.7985 (mmm160) cc_final: 0.7721 (mtp85) REVERT: C 110 ASN cc_start: 0.8327 (t0) cc_final: 0.7862 (t0) REVERT: D 59 MET cc_start: 0.9494 (mmm) cc_final: 0.9149 (tpp) REVERT: D 110 GLU cc_start: 0.8380 (tp30) cc_final: 0.8149 (tp30) REVERT: E 56 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8398 (mtmt) REVERT: E 73 GLU cc_start: 0.8991 (tt0) cc_final: 0.8745 (tt0) REVERT: E 120 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8519 (mtm) REVERT: G 36 LYS cc_start: 0.8803 (pttt) cc_final: 0.8544 (mmtt) REVERT: G 76 THR cc_start: 0.8401 (p) cc_final: 0.8050 (t) REVERT: G 92 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8029 (mt-10) REVERT: H 65 ASP cc_start: 0.9151 (t70) cc_final: 0.8848 (t0) REVERT: K 656 GLN cc_start: 0.9285 (mp10) cc_final: 0.8718 (mp10) REVERT: K 682 MET cc_start: 0.7827 (tmm) cc_final: 0.7402 (tmm) REVERT: K 688 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7265 (mmm-85) REVERT: K 779 MET cc_start: 0.8436 (tmm) cc_final: 0.8114 (tmm) REVERT: N 617 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8069 (pp20) REVERT: N 622 PHE cc_start: 0.8111 (m-80) cc_final: 0.7590 (m-10) REVERT: N 654 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8741 (mm-30) REVERT: N 689 ASP cc_start: 0.7812 (p0) cc_final: 0.7536 (p0) REVERT: N 738 MET cc_start: 0.4385 (tmm) cc_final: 0.4143 (ppp) REVERT: P 831 ARG cc_start: 0.7362 (mmt180) cc_final: 0.7108 (pmt170) REVERT: P 852 MET cc_start: 0.7995 (ttp) cc_final: 0.7595 (ttp) REVERT: S 568 TYR cc_start: 0.8091 (t80) cc_final: 0.7817 (t80) REVERT: S 656 TYR cc_start: 0.9071 (t80) cc_final: 0.8725 (t80) REVERT: S 660 ASN cc_start: 0.8892 (m-40) cc_final: 0.8126 (m-40) REVERT: S 678 ASN cc_start: 0.7160 (t0) cc_final: 0.6936 (m-40) outliers start: 53 outliers final: 29 residues processed: 296 average time/residue: 0.6135 time to fit residues: 206.0363 Evaluate side-chains 282 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 250 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 79 ILE 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 120 MET Chi-restraints excluded: chain E residue 133 GLU 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 36 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 688 ARG 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 789 HIS Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain S residue 617 GLU Chi-restraints excluded: chain S residue 648 THR Chi-restraints excluded: chain S residue 696 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 89 optimal weight: 40.0000 chunk 62 optimal weight: 0.8980 chunk 63 optimal weight: 0.0980 chunk 169 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 174 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 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 S 610 ASN S 718 ASN ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.131059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.092351 restraints weight = 50958.049| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.69 r_work: 0.3307 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22142 Z= 0.136 Angle : 0.643 9.117 31352 Z= 0.355 Chirality : 0.044 0.270 3477 Planarity : 0.004 0.052 2845 Dihedral : 29.410 176.447 5571 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.20 % Allowed : 23.13 % Favored : 73.67 % 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: 0.61 (0.20), residues: 1736 helix: 1.65 (0.17), residues: 890 sheet: -0.75 (0.47), residues: 115 loop : -0.97 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 35 TYR 0.028 0.002 TYR H 80 PHE 0.037 0.002 PHE P 731 TRP 0.009 0.001 TRP K 795 HIS 0.012 0.001 HIS N 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (22142) covalent geometry : angle 0.64250 / 0.36 (31352) hydrogen bonds : bond 0.03788 / 2.51 ( 1098) hydrogen bonds : angle 3.64287 / 2.56 ( 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 317 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 269 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9198 (mp) cc_final: 0.8991 (mm) REVERT: B 59 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8692 (ttmt) REVERT: C 76 THR cc_start: 0.8362 (p) cc_final: 0.8144 (t) REVERT: C 92 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7829 (mt-10) REVERT: C 99 ARG cc_start: 0.7971 (mmm160) cc_final: 0.7704 (mtp85) REVERT: C 110 ASN cc_start: 0.8340 (t0) cc_final: 0.7927 (t0) REVERT: D 59 MET cc_start: 0.9506 (mmm) cc_final: 0.9159 (tpp) REVERT: D 110 GLU cc_start: 0.8371 (tp30) cc_final: 0.8140 (tp30) REVERT: E 56 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8473 (mtmt) REVERT: E 73 GLU cc_start: 0.8991 (tt0) cc_final: 0.8741 (tt0) REVERT: E 120 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: G 36 LYS cc_start: 0.8786 (pttt) cc_final: 0.8549 (mmtt) REVERT: G 76 THR cc_start: 0.8392 (p) cc_final: 0.8048 (t) REVERT: G 92 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8061 (mt-10) REVERT: H 65 ASP cc_start: 0.9122 (t70) cc_final: 0.8844 (t0) REVERT: K 656 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8708 (mp10) REVERT: K 682 MET cc_start: 0.7776 (tmm) cc_final: 0.7357 (tmm) REVERT: K 688 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7291 (mmm-85) REVERT: K 779 MET cc_start: 0.8438 (tmm) cc_final: 0.8100 (tmm) REVERT: N 561 PHE cc_start: 0.6852 (t80) cc_final: 0.6614 (t80) REVERT: N 617 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8025 (pp20) REVERT: N 622 PHE cc_start: 0.8142 (m-80) cc_final: 0.7634 (m-80) REVERT: N 630 PRO cc_start: 0.3193 (Cg_endo) cc_final: 0.2675 (Cg_exo) REVERT: N 654 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8747 (mm-30) REVERT: N 682 MET cc_start: 0.8103 (tmm) cc_final: 0.7855 (tmm) REVERT: N 689 ASP cc_start: 0.7911 (p0) cc_final: 0.7704 (p0) REVERT: P 831 ARG cc_start: 0.7349 (mmt180) cc_final: 0.7138 (pmt170) REVERT: P 852 MET cc_start: 0.8111 (ttp) cc_final: 0.7657 (ttp) REVERT: S 568 TYR cc_start: 0.8012 (t80) cc_final: 0.7777 (t80) REVERT: S 656 TYR cc_start: 0.9059 (t80) cc_final: 0.8700 (t80) REVERT: S 660 ASN cc_start: 0.8943 (m-40) cc_final: 0.8110 (m-40) REVERT: S 678 ASN cc_start: 0.7061 (t0) cc_final: 0.6832 (m-40) REVERT: S 718 ASN cc_start: 0.8259 (t0) cc_final: 0.7751 (p0) outliers start: 48 outliers final: 28 residues processed: 302 average time/residue: 0.6181 time to fit residues: 211.5278 Evaluate side-chains 287 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 255 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 79 ILE 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 E residue 133 GLU 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 36 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 113 LYS 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 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 759 VAL Chi-restraints excluded: chain P residue 789 HIS Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain S residue 617 GLU Chi-restraints excluded: chain S residue 648 THR Chi-restraints excluded: chain S residue 696 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 194 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** 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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.129866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.091041 restraints weight = 50823.371| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.65 r_work: 0.3273 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22142 Z= 0.172 Angle : 0.667 11.379 31352 Z= 0.364 Chirality : 0.045 0.258 3477 Planarity : 0.005 0.089 2845 Dihedral : 29.468 176.388 5571 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.27 % Allowed : 23.33 % Favored : 73.40 % 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: 0.60 (0.20), residues: 1736 helix: 1.58 (0.17), residues: 891 sheet: -0.83 (0.47), residues: 115 loop : -0.87 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG P 767 TYR 0.032 0.002 TYR H 80 PHE 0.029 0.002 PHE P 731 TRP 0.008 0.001 TRP K 698 HIS 0.009 0.001 HIS S 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (22142) covalent geometry : angle 0.66737 / 0.36 (31352) hydrogen bonds : bond 0.04088 / 2.69 ( 1098) hydrogen bonds : angle 3.67752 / 2.60 ( 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 306 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 0.643 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: 0.9246 (mp) cc_final: 0.9044 (mm) REVERT: B 59 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8705 (ttmt) REVERT: C 76 THR cc_start: 0.8399 (p) cc_final: 0.8174 (t) REVERT: C 99 ARG cc_start: 0.8057 (mmm160) cc_final: 0.7788 (mtp85) REVERT: C 110 ASN cc_start: 0.8354 (t0) cc_final: 0.8003 (t0) REVERT: D 59 MET cc_start: 0.9514 (mmm) cc_final: 0.9244 (mmt) REVERT: D 110 GLU cc_start: 0.8397 (tp30) cc_final: 0.8183 (tp30) REVERT: E 56 LYS cc_start: 0.8919 (mtpp) cc_final: 0.8478 (mtmt) REVERT: E 73 GLU cc_start: 0.9003 (tt0) cc_final: 0.8769 (tt0) REVERT: E 120 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8524 (mtm) REVERT: E 131 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8699 (mtt180) REVERT: G 36 LYS cc_start: 0.8811 (pttt) cc_final: 0.8594 (mmtt) REVERT: G 76 THR cc_start: 0.8411 (p) cc_final: 0.8098 (t) REVERT: G 92 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8038 (mt-10) REVERT: H 65 ASP cc_start: 0.9166 (t70) cc_final: 0.8881 (t0) REVERT: K 656 GLN cc_start: 0.9315 (mp10) cc_final: 0.8700 (mp10) REVERT: K 670 ILE cc_start: 0.8976 (mm) cc_final: 0.7731 (mp) REVERT: K 682 MET cc_start: 0.7861 (tmm) cc_final: 0.7433 (tmm) REVERT: K 688 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7274 (mmm-85) REVERT: K 779 MET cc_start: 0.8503 (tmm) cc_final: 0.8198 (tmm) REVERT: N 585 GLU cc_start: 0.3244 (mm-30) cc_final: 0.1818 (mt-10) REVERT: N 617 GLU cc_start: 0.8917 (mm-30) cc_final: 0.7995 (pp20) REVERT: N 622 PHE cc_start: 0.8229 (m-80) cc_final: 0.7768 (m-80) REVERT: N 630 PRO cc_start: 0.3598 (Cg_endo) cc_final: 0.3052 (Cg_exo) REVERT: N 654 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8742 (mm-30) REVERT: N 682 MET cc_start: 0.8090 (tmm) cc_final: 0.7799 (tmm) REVERT: N 689 ASP cc_start: 0.7924 (p0) cc_final: 0.7661 (p0) REVERT: N 714 TYR cc_start: 0.5719 (OUTLIER) cc_final: 0.5296 (p90) REVERT: N 738 MET cc_start: 0.5974 (pp-130) cc_final: 0.5653 (ppp) REVERT: P 775 SER cc_start: 0.8517 (t) cc_final: 0.8229 (p) REVERT: P 831 ARG cc_start: 0.7386 (mmt180) cc_final: 0.7139 (pmt170) REVERT: S 568 TYR cc_start: 0.8012 (t80) cc_final: 0.7751 (t80) REVERT: S 604 TYR cc_start: 0.8059 (m-80) cc_final: 0.7397 (t80) REVERT: S 656 TYR cc_start: 0.9107 (t80) cc_final: 0.8739 (t80) REVERT: S 660 ASN cc_start: 0.8954 (m-40) cc_final: 0.8180 (m-40) REVERT: S 678 ASN cc_start: 0.7183 (t0) cc_final: 0.6971 (m-40) outliers start: 49 outliers final: 31 residues processed: 293 average time/residue: 0.6279 time to fit residues: 208.5461 Evaluate side-chains 283 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 79 ILE 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 E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS 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 688 ARG Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 802 ASN Chi-restraints excluded: chain K residue 875 THR Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 560 LEU 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 S residue 617 GLU Chi-restraints excluded: chain S residue 648 THR Chi-restraints excluded: chain S residue 696 CYS 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: 5.9990 chunk 107 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 160 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** 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 718 ASN ** 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 = 0.4230 r_free = 0.4230 target = 0.130650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.091631 restraints weight = 50543.000| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.79 r_work: 0.3291 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22142 Z= 0.144 Angle : 0.666 10.974 31352 Z= 0.364 Chirality : 0.044 0.257 3477 Planarity : 0.005 0.085 2845 Dihedral : 29.423 176.983 5571 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.80 % Allowed : 24.87 % 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: 0.72 (0.20), residues: 1736 helix: 1.65 (0.17), residues: 893 sheet: -0.91 (0.47), residues: 117 loop : -0.76 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 767 TYR 0.032 0.002 TYR K 735 PHE 0.034 0.002 PHE S 652 TRP 0.010 0.001 TRP K 795 HIS 0.010 0.001 HIS S 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (22142) covalent geometry : angle 0.66604 / 0.36 (31352) hydrogen bonds : bond 0.03789 / 2.50 ( 1098) hydrogen bonds : angle 3.65729 / 2.58 ( 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 305 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 0.646 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: C 76 THR cc_start: 0.8407 (p) cc_final: 0.8201 (t) REVERT: C 99 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7777 (mtp85) REVERT: C 110 ASN cc_start: 0.8350 (t0) cc_final: 0.8000 (t0) REVERT: D 59 MET cc_start: 0.9507 (mmm) cc_final: 0.9161 (tpp) REVERT: E 56 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8426 (mtmt) REVERT: E 73 GLU cc_start: 0.9004 (tt0) cc_final: 0.8756 (tt0) REVERT: E 120 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8510 (mtm) REVERT: F 35 ARG cc_start: 0.9134 (mtp-110) cc_final: 0.8744 (ttp80) REVERT: G 36 LYS cc_start: 0.8793 (pttt) cc_final: 0.8583 (mmtt) REVERT: G 76 THR cc_start: 0.8392 (p) cc_final: 0.8081 (t) REVERT: G 92 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8080 (mt-10) REVERT: H 65 ASP cc_start: 0.9118 (t70) cc_final: 0.8836 (t0) REVERT: K 656 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.8762 (mp10) REVERT: K 674 MET cc_start: 0.8742 (mpt) cc_final: 0.8406 (mpt) REVERT: K 682 MET cc_start: 0.7918 (tmm) cc_final: 0.7353 (tmm) REVERT: K 688 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7306 (mmm-85) REVERT: K 779 MET cc_start: 0.8521 (tmm) cc_final: 0.8210 (tmm) REVERT: N 585 GLU cc_start: 0.3080 (mm-30) cc_final: 0.1706 (mt-10) REVERT: N 617 GLU cc_start: 0.8931 (mm-30) cc_final: 0.7936 (pp20) REVERT: N 622 PHE cc_start: 0.8399 (m-80) cc_final: 0.7997 (m-80) REVERT: N 630 PRO cc_start: 0.3707 (Cg_endo) cc_final: 0.3221 (Cg_exo) REVERT: N 654 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8747 (mm-30) REVERT: N 682 MET cc_start: 0.8104 (tmm) cc_final: 0.7799 (tmm) REVERT: N 689 ASP cc_start: 0.7941 (p0) cc_final: 0.7681 (p0) REVERT: N 714 TYR cc_start: 0.5746 (OUTLIER) cc_final: 0.5045 (p90) REVERT: P 775 SER cc_start: 0.8444 (t) cc_final: 0.8191 (p) REVERT: P 831 ARG cc_start: 0.7338 (mmt180) cc_final: 0.7110 (pmt170) REVERT: S 604 TYR cc_start: 0.8038 (m-80) cc_final: 0.7410 (t80) REVERT: S 656 TYR cc_start: 0.9106 (t80) cc_final: 0.8694 (t80) REVERT: S 660 ASN cc_start: 0.8950 (m-40) cc_final: 0.8161 (m-40) REVERT: S 678 ASN cc_start: 0.7155 (t0) cc_final: 0.6950 (m-40) REVERT: S 718 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7783 (p0) outliers start: 42 outliers final: 25 residues processed: 294 average time/residue: 0.6447 time to fit residues: 214.8534 Evaluate side-chains 285 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 79 ILE 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 E residue 133 GLU 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 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 802 ASN Chi-restraints excluded: chain K residue 875 THR Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 661 TYR 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 738 LEU Chi-restraints excluded: chain P residue 759 VAL Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain S residue 648 THR Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 718 ASN Chi-restraints excluded: chain S residue 719 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 94 optimal weight: 10.0000 chunk 202 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 152 optimal weight: 0.5980 chunk 199 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 91 optimal weight: 30.0000 chunk 160 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** 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 758 HIS S 718 ASN ** 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 = 0.4226 r_free = 0.4226 target = 0.130379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.091432 restraints weight = 51016.542| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.63 r_work: 0.3293 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22142 Z= 0.153 Angle : 0.680 11.085 31352 Z= 0.370 Chirality : 0.045 0.256 3477 Planarity : 0.005 0.068 2845 Dihedral : 29.410 176.851 5571 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.20 % Allowed : 25.73 % Favored : 72.07 % 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: 0.71 (0.20), residues: 1736 helix: 1.65 (0.17), residues: 893 sheet: -0.98 (0.47), residues: 117 loop : -0.75 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG P 767 TYR 0.033 0.002 TYR K 735 PHE 0.033 0.002 PHE N 760 TRP 0.010 0.001 TRP K 795 HIS 0.014 0.001 HIS N 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (22142) covalent geometry : angle 0.68047 / 0.37 (31352) hydrogen bonds : bond 0.03875 / 2.55 ( 1098) hydrogen bonds : angle 3.68237 / 2.61 ( 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 284 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 0.644 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: 0.8018 (mmm160) cc_final: 0.7778 (mtp85) REVERT: C 110 ASN cc_start: 0.8386 (t0) cc_final: 0.8048 (t0) REVERT: D 59 MET cc_start: 0.9500 (mmm) cc_final: 0.9154 (tpp) REVERT: E 56 LYS cc_start: 0.8915 (mtpp) cc_final: 0.8432 (mtmt) REVERT: E 73 GLU cc_start: 0.8964 (tt0) cc_final: 0.8732 (tt0) REVERT: E 120 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8496 (mtm) REVERT: E 131 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8673 (mtt180) REVERT: F 35 ARG cc_start: 0.9121 (mtp-110) cc_final: 0.8732 (ttp80) REVERT: G 76 THR cc_start: 0.8355 (p) cc_final: 0.8057 (t) REVERT: G 92 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8055 (mt-10) REVERT: H 65 ASP cc_start: 0.9099 (t70) cc_final: 0.8825 (t0) REVERT: K 656 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.8751 (mp10) REVERT: K 674 MET cc_start: 0.8663 (mpt) cc_final: 0.8420 (mpt) REVERT: K 682 MET cc_start: 0.7929 (tmm) cc_final: 0.7405 (tmm) REVERT: K 688 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7311 (mmm-85) REVERT: K 779 MET cc_start: 0.8530 (tmm) cc_final: 0.8228 (tmm) REVERT: N 585 GLU cc_start: 0.3015 (mm-30) cc_final: 0.1758 (mt-10) REVERT: N 617 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8645 (mm-30) REVERT: N 622 PHE cc_start: 0.8435 (m-80) cc_final: 0.8033 (m-80) REVERT: N 654 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8742 (mm-30) REVERT: N 682 MET cc_start: 0.8085 (tmm) cc_final: 0.7789 (tmm) REVERT: N 689 ASP cc_start: 0.7977 (p0) cc_final: 0.7701 (p0) REVERT: N 714 TYR cc_start: 0.5697 (OUTLIER) cc_final: 0.4923 (p90) REVERT: P 775 SER cc_start: 0.8491 (t) cc_final: 0.8170 (p) REVERT: S 568 TYR cc_start: 0.7987 (t80) cc_final: 0.7768 (t80) REVERT: S 604 TYR cc_start: 0.8041 (m-80) cc_final: 0.7459 (t80) REVERT: S 656 TYR cc_start: 0.9069 (t80) cc_final: 0.8653 (t80) REVERT: S 660 ASN cc_start: 0.8947 (m-40) cc_final: 0.8160 (m-40) outliers start: 33 outliers final: 21 residues processed: 270 average time/residue: 0.6729 time to fit residues: 205.1868 Evaluate side-chains 272 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 79 ILE 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 E residue 131 ARG Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL 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 875 THR Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 661 TYR 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 862 THR Chi-restraints excluded: chain S residue 648 THR Chi-restraints excluded: chain S residue 696 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 2 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 29 optimal weight: 0.0970 chunk 175 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 141 optimal weight: 0.0270 chunk 53 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 598 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 = 0.4241 r_free = 0.4241 target = 0.131207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.092780 restraints weight = 51102.985| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.61 r_work: 0.3323 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22142 Z= 0.134 Angle : 0.673 13.793 31352 Z= 0.367 Chirality : 0.044 0.254 3477 Planarity : 0.005 0.061 2845 Dihedral : 29.326 177.409 5571 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.93 % Allowed : 26.13 % Favored : 71.93 % 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: 0.82 (0.20), residues: 1736 helix: 1.74 (0.17), residues: 893 sheet: -0.94 (0.47), residues: 117 loop : -0.70 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 767 TYR 0.036 0.002 TYR K 735 PHE 0.040 0.002 PHE S 652 TRP 0.012 0.001 TRP K 795 HIS 0.010 0.001 HIS S 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (22142) covalent geometry : angle 0.67264 / 0.37 (31352) hydrogen bonds : bond 0.03688 / 2.44 ( 1098) hydrogen bonds : angle 3.66255 / 2.61 ( 2815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8736.82 seconds wall clock time: 149 minutes 6.77 seconds (8946.77 seconds total)