Starting phenix.real_space_refine on Tue Nov 18 19:53:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbr_7848/11_2025/6dbr_7848_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbr_7848/11_2025/6dbr_7848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dbr_7848/11_2025/6dbr_7848_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbr_7848/11_2025/6dbr_7848_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dbr_7848/11_2025/6dbr_7848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbr_7848/11_2025/6dbr_7848.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 2 6.06 5 P 136 5.49 5 S 106 5.16 5 C 10290 2.51 5 N 3011 2.21 5 O 3491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17040 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4437 Classifications: {'peptide': 550} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 526} Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "C" Number of atoms: 4381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4381 Classifications: {'peptide': 542} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 517} Chain breaks: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "F" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "G" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 694 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "H" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 700 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2118 SG CYS A 749 58.000 80.244 22.558 1.00 57.87 S ATOM 2139 SG CYS A 752 55.870 81.445 19.736 1.00 76.36 S ATOM 9204 SG CYS C 749 62.134 58.237 102.464 1.00 61.27 S ATOM 9225 SG CYS C 752 60.643 58.094 105.519 1.00 59.68 S Time building chain proxies: 4.16, per 1000 atoms: 0.24 Number of scatterers: 17040 At special positions: 0 Unit cell: (129.99, 146.084, 123.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 4 19.99 S 106 16.00 P 136 15.00 O 3491 8.00 N 3011 7.00 C 10290 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 652.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 752 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 752 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " Number of angles added : 4 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 18 sheets defined 33.9% alpha, 23.0% beta 62 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.591A pdb=" N SER A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 527 removed outlier: 3.595A pdb=" N LYS A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 601 removed outlier: 4.625A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 704 Proline residue: A 696 - end of helix Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.858A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 799 Processing helix chain 'A' and resid 819 through 835 removed outlier: 3.543A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 862 Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 894 through 912 Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.736A pdb=" N ARG A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 917 " --> pdb=" O PRO A 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 917' Processing helix chain 'A' and resid 924 through 946 removed outlier: 3.684A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N TYR A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.533A pdb=" N HIS A 959 " --> pdb=" O THR A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 975 through 979 removed outlier: 3.594A pdb=" N ALA A 979 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 5.039A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1017 Processing helix chain 'A' and resid 1018 through 1024 Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.525A pdb=" N SER B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 526 removed outlier: 3.637A pdb=" N LEU C 522 " --> pdb=" O PRO C 518 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN C 524 " --> pdb=" O HIS C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 600 removed outlier: 5.245A pdb=" N GLU C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.620A pdb=" N SER C 673 " --> pdb=" O SER C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.539A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 757 through 762 removed outlier: 3.988A pdb=" N GLN C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 757 through 762' Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 799 Processing helix chain 'C' and resid 815 through 835 removed outlier: 3.948A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 removed outlier: 3.512A pdb=" N ARG C 848 " --> pdb=" O SER C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 881 removed outlier: 3.751A pdb=" N THR C 881 " --> pdb=" O ARG C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 889 removed outlier: 3.801A pdb=" N VAL C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 892 No H-bonds generated for 'chain 'C' and resid 890 through 892' Processing helix chain 'C' and resid 894 through 912 Processing helix chain 'C' and resid 912 through 917 removed outlier: 3.608A pdb=" N ARG C 916 " --> pdb=" O LYS C 912 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 917 " --> pdb=" O PRO C 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 912 through 917' Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 removed outlier: 3.895A pdb=" N LEU C 928 " --> pdb=" O CYS C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 964 through 972 Processing helix chain 'C' and resid 980 through 985 Processing helix chain 'C' and resid 987 through 996 removed outlier: 3.634A pdb=" N ARG C 994 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS C 995 " --> pdb=" O ARG C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1016 removed outlier: 3.835A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 Processing helix chain 'D' and resid 308 through 314 removed outlier: 3.709A pdb=" N SER D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 539 removed outlier: 4.031A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A 617 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU A 677 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 539 removed outlier: 4.031A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A 617 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE A 651 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR A 661 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 5.703A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.254A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.774A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS B 89 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB1, first strand: chain 'C' and resid 536 through 539 removed outlier: 3.696A pdb=" N ARG C 708 " --> pdb=" O GLN C 539 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 611 " --> pdb=" O SER C 719 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR C 727 " --> pdb=" O GLU C 617 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N CYS C 619 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 648 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS C 616 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE C 646 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER C 618 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE C 644 " --> pdb=" O SER C 618 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASP C 620 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE C 642 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET C 622 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL C 640 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 536 through 539 removed outlier: 3.696A pdb=" N ARG C 708 " --> pdb=" O GLN C 539 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 611 " --> pdb=" O SER C 719 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR C 727 " --> pdb=" O GLU C 617 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N CYS C 619 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 648 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS C 616 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE C 646 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER C 618 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE C 644 " --> pdb=" O SER C 618 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASP C 620 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE C 642 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET C 622 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL C 640 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N MET C 647 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLN C 664 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE C 649 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 23 removed outlier: 4.414A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE D 318 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 61 through 62 removed outlier: 6.706A pdb=" N SER D 61 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N CYS D 124 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 96 through 97 removed outlier: 3.926A pdb=" N GLU D 101 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB8, first strand: chain 'D' and resid 210 through 211 Processing sheet with id=AB9, first strand: chain 'D' and resid 263 through 265 627 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 156 hydrogen bonds 308 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2491 1.27 - 1.40: 4716 1.40 - 1.54: 9938 1.54 - 1.68: 387 1.68 - 1.81: 158 Bond restraints: 17690 Sorted by residual: bond pdb=" CG ASN A 983 " pdb=" OD1 ASN A 983 " ideal model delta sigma weight residual 1.231 1.133 0.098 1.90e-02 2.77e+03 2.69e+01 bond pdb=" CG ASN C 524 " pdb=" OD1 ASN C 524 " ideal model delta sigma weight residual 1.231 1.142 0.089 1.90e-02 2.77e+03 2.21e+01 bond pdb=" CG ASN C 956 " pdb=" ND2 ASN C 956 " ideal model delta sigma weight residual 1.328 1.425 -0.097 2.10e-02 2.27e+03 2.14e+01 bond pdb=" CD GLN D 33 " pdb=" OE1 GLN D 33 " ideal model delta sigma weight residual 1.231 1.146 0.085 1.90e-02 2.77e+03 2.01e+01 bond pdb=" CA ALA A1027 " pdb=" C ALA A1027 " ideal model delta sigma weight residual 1.523 1.589 -0.067 1.49e-02 4.50e+03 2.00e+01 ... (remaining 17685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.27: 24479 11.27 - 22.53: 11 22.53 - 33.80: 3 33.80 - 45.07: 3 45.07 - 56.33: 1 Bond angle restraints: 24497 Sorted by residual: angle pdb=" CB ASN C 524 " pdb=" CG ASN C 524 " pdb=" OD1 ASN C 524 " ideal model delta sigma weight residual 120.80 177.13 -56.33 2.00e+00 2.50e-01 7.93e+02 angle pdb=" CB ASN C 956 " pdb=" CG ASN C 956 " pdb=" ND2 ASN C 956 " ideal model delta sigma weight residual 116.40 75.42 40.98 1.50e+00 4.44e-01 7.46e+02 angle pdb=" CB ASN C 524 " pdb=" CG ASN C 524 " pdb=" ND2 ASN C 524 " ideal model delta sigma weight residual 116.40 76.96 39.44 1.50e+00 4.44e-01 6.91e+02 angle pdb=" OD1 ASN C 956 " pdb=" CG ASN C 956 " pdb=" ND2 ASN C 956 " ideal model delta sigma weight residual 122.60 97.64 24.96 1.00e+00 1.00e+00 6.23e+02 angle pdb=" CB ASN C 956 " pdb=" CG ASN C 956 " pdb=" OD1 ASN C 956 " ideal model delta sigma weight residual 120.80 165.20 -44.40 2.00e+00 2.50e-01 4.93e+02 ... (remaining 24492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 9447 35.52 - 71.04: 831 71.04 - 106.57: 20 106.57 - 142.09: 0 142.09 - 177.61: 2 Dihedral angle restraints: 10300 sinusoidal: 5109 harmonic: 5191 Sorted by residual: dihedral pdb=" N HIS A1028 " pdb=" C HIS A1028 " pdb=" CA HIS A1028 " pdb=" CB HIS A1028 " ideal model delta harmonic sigma weight residual 122.80 97.75 25.05 0 2.50e+00 1.60e-01 1.00e+02 dihedral pdb=" N ASN A 983 " pdb=" C ASN A 983 " pdb=" CA ASN A 983 " pdb=" CB ASN A 983 " ideal model delta harmonic sigma weight residual 122.80 140.40 -17.60 0 2.50e+00 1.60e-01 4.96e+01 dihedral pdb=" CA ARG C 523 " pdb=" C ARG C 523 " pdb=" N ASN C 524 " pdb=" CA ASN C 524 " ideal model delta harmonic sigma weight residual 180.00 149.16 30.84 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 10297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2556 0.096 - 0.193: 113 0.193 - 0.289: 4 0.289 - 0.386: 3 0.386 - 0.482: 2 Chirality restraints: 2678 Sorted by residual: chirality pdb=" CG LEU C 751 " pdb=" CB LEU C 751 " pdb=" CD1 LEU C 751 " pdb=" CD2 LEU C 751 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CA ASN A 983 " pdb=" N ASN A 983 " pdb=" C ASN A 983 " pdb=" CB ASN A 983 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CB VAL A 713 " pdb=" CA VAL A 713 " pdb=" CG1 VAL A 713 " pdb=" CG2 VAL A 713 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.37 2.00e-01 2.50e+01 3.52e+00 ... (remaining 2675 not shown) Planarity restraints: 2691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 983 " -0.098 2.00e-02 2.50e+03 1.97e-01 3.87e+02 pdb=" CG ASN A 983 " 0.337 2.00e-02 2.50e+03 pdb=" OD1 ASN A 983 " -0.158 2.00e-02 2.50e+03 pdb=" ND2 ASN A 983 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 539 " 0.078 2.00e-02 2.50e+03 1.71e-01 2.92e+02 pdb=" CD GLN A 539 " -0.295 2.00e-02 2.50e+03 pdb=" OE1 GLN A 539 " 0.125 2.00e-02 2.50e+03 pdb=" NE2 GLN A 539 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1028 " -0.032 2.00e-02 2.50e+03 1.29e-01 2.49e+02 pdb=" CG HIS A1028 " 0.194 2.00e-02 2.50e+03 pdb=" ND1 HIS A1028 " -0.186 2.00e-02 2.50e+03 pdb=" CD2 HIS A1028 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 HIS A1028 " 0.140 2.00e-02 2.50e+03 pdb=" NE2 HIS A1028 " -0.068 2.00e-02 2.50e+03 ... (remaining 2688 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 136 2.43 - 3.05: 10916 3.05 - 3.66: 27516 3.66 - 4.28: 38691 4.28 - 4.90: 60661 Nonbonded interactions: 137920 Sorted by model distance: nonbonded pdb=" OE2 GLU C 774 " pdb=" NH1 ARG C 778 " model vdw 1.811 3.120 nonbonded pdb=" OD2 ASP C 566 " pdb=" OH TYR D 138 " model vdw 1.905 3.040 nonbonded pdb=" OG1 THR B 97 " pdb=" OE2 GLU B 101 " model vdw 1.929 3.040 nonbonded pdb=" NZ LYS A 628 " pdb=" OP1 DT F 17 " model vdw 1.939 3.120 nonbonded pdb=" OD2 ASP A 832 " pdb=" NH1 ARG A 949 " model vdw 1.973 3.120 ... (remaining 137915 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 480 through 626 or resid 635 through 1103)) selection = (chain 'C' and (resid 480 through 1028 or resid 1101 through 1103)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 22.880 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 0.274 17699 Z= 0.257 Angle : 1.054 56.334 24501 Z= 0.644 Chirality : 0.047 0.482 2678 Planarity : 0.008 0.197 2691 Dihedral : 21.294 177.612 6960 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.90 % Favored : 91.98 % Rotamer: Outliers : 0.25 % Allowed : 22.36 % Favored : 77.39 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.16), residues: 1784 helix: -2.26 (0.17), residues: 561 sheet: -2.44 (0.25), residues: 330 loop : -3.23 (0.16), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 675 TYR 0.014 0.002 TYR C 948 PHE 0.018 0.002 PHE A1024 TRP 0.016 0.002 TRP A 538 HIS 0.201 0.004 HIS A1028 Details of bonding type rmsd covalent geometry : bond 0.00485 (17690) covalent geometry : angle 1.04553 (24497) hydrogen bonds : bond 0.11526 ( 747) hydrogen bonds : angle 6.36585 ( 2057) metal coordination : bond 0.12919 ( 8) metal coordination : angle 10.48515 ( 4) Misc. bond : bond 0.05386 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 388 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 MET cc_start: 0.7701 (mtt) cc_final: 0.7362 (mtm) REVERT: A 871 MET cc_start: 0.8035 (mpp) cc_final: 0.7794 (mmt) REVERT: A 886 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8576 (tm-30) REVERT: A 987 ASN cc_start: 0.8316 (m-40) cc_final: 0.7902 (m-40) REVERT: A 1007 GLU cc_start: 0.9265 (tt0) cc_final: 0.9044 (tm-30) REVERT: B 127 LYS cc_start: 0.9134 (tptp) cc_final: 0.8638 (tptt) REVERT: B 189 PHE cc_start: 0.8805 (m-80) cc_final: 0.8605 (m-80) REVERT: C 832 ASP cc_start: 0.8804 (m-30) cc_final: 0.8398 (m-30) REVERT: C 850 ARG cc_start: 0.9132 (ttm-80) cc_final: 0.8657 (ptm160) REVERT: D 65 ASN cc_start: 0.8435 (p0) cc_final: 0.7722 (p0) REVERT: D 200 LEU cc_start: 0.8816 (mp) cc_final: 0.8596 (mm) REVERT: D 285 MET cc_start: 0.6822 (mmt) cc_final: 0.6549 (mmt) outliers start: 4 outliers final: 2 residues processed: 390 average time/residue: 0.1646 time to fit residues: 91.0754 Evaluate side-chains 197 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 996 MET Chi-restraints excluded: chain C residue 824 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN A 514 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 499 GLN C 524 ASN C 539 GLN C 544 ASN C 687 HIS C 762 ASN C 766 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN D 253 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.090919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.067239 restraints weight = 55410.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.069039 restraints weight = 31474.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070166 restraints weight = 22581.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.070822 restraints weight = 18649.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071118 restraints weight = 16745.418| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17699 Z= 0.161 Angle : 0.713 9.044 24501 Z= 0.387 Chirality : 0.044 0.219 2678 Planarity : 0.005 0.062 2691 Dihedral : 24.081 175.406 3461 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 6.46 % Allowed : 19.89 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % 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: -2.91 (0.18), residues: 1784 helix: -0.94 (0.20), residues: 561 sheet: -1.97 (0.26), residues: 338 loop : -2.59 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 598 TYR 0.028 0.002 TYR B 268 PHE 0.020 0.001 PHE C 938 TRP 0.037 0.002 TRP A 538 HIS 0.014 0.001 HIS A1028 Details of bonding type rmsd covalent geometry : bond 0.00349 (17690) covalent geometry : angle 0.71197 (24497) hydrogen bonds : bond 0.04566 ( 747) hydrogen bonds : angle 5.07266 ( 2057) metal coordination : bond 0.02051 ( 8) metal coordination : angle 3.55443 ( 4) Misc. bond : bond 0.00289 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 240 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 871 MET cc_start: 0.7843 (mpp) cc_final: 0.7491 (mmt) REVERT: A 902 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8863 (mt) REVERT: A 987 ASN cc_start: 0.8055 (m-40) cc_final: 0.7070 (m-40) REVERT: B 101 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7283 (pm20) REVERT: B 250 THR cc_start: 0.7565 (OUTLIER) cc_final: 0.7333 (p) REVERT: C 711 ILE cc_start: 0.8873 (mm) cc_final: 0.8659 (mm) REVERT: C 755 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8953 (t) REVERT: C 825 GLU cc_start: 0.8172 (tp30) cc_final: 0.7861 (tp30) REVERT: C 871 MET cc_start: 0.7983 (mtt) cc_final: 0.7742 (mtt) REVERT: D 64 ASN cc_start: 0.8622 (m-40) cc_final: 0.7903 (t0) REVERT: D 65 ASN cc_start: 0.8793 (p0) cc_final: 0.8442 (p0) REVERT: D 173 ASN cc_start: 0.8582 (m-40) cc_final: 0.8380 (m110) REVERT: D 212 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7502 (ttt-90) outliers start: 102 outliers final: 32 residues processed: 325 average time/residue: 0.1235 time to fit residues: 62.5674 Evaluate side-chains 223 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 102 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN A 535 GLN A 539 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 GLN C 858 GLN D 222 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.090056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.066495 restraints weight = 56694.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.068254 restraints weight = 32532.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069342 restraints weight = 23330.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070020 restraints weight = 19256.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070322 restraints weight = 17238.285| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17699 Z= 0.175 Angle : 0.690 8.941 24501 Z= 0.373 Chirality : 0.043 0.202 2678 Planarity : 0.005 0.059 2691 Dihedral : 23.916 173.300 3457 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.88 % Allowed : 22.36 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % 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: -2.35 (0.18), residues: 1784 helix: -0.42 (0.21), residues: 564 sheet: -1.58 (0.27), residues: 312 loop : -2.33 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 212 TYR 0.021 0.002 TYR B 268 PHE 0.020 0.001 PHE B 274 TRP 0.013 0.001 TRP A 538 HIS 0.005 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00384 (17690) covalent geometry : angle 0.68593 (24497) hydrogen bonds : bond 0.04198 ( 747) hydrogen bonds : angle 4.86031 ( 2057) metal coordination : bond 0.02507 ( 8) metal coordination : angle 5.64177 ( 4) Misc. bond : bond 0.00114 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 192 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8129 (m) cc_final: 0.7884 (m) REVERT: A 617 GLU cc_start: 0.8147 (pm20) cc_final: 0.7105 (pm20) REVERT: A 869 MET cc_start: 0.5842 (OUTLIER) cc_final: 0.4022 (ppp) REVERT: A 871 MET cc_start: 0.7753 (mpp) cc_final: 0.7490 (mmt) REVERT: A 898 ARG cc_start: 0.8483 (mtt180) cc_final: 0.8116 (mtt180) REVERT: A 902 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8998 (mt) REVERT: A 903 LYS cc_start: 0.9460 (ptmt) cc_final: 0.9256 (ptpt) REVERT: A 905 MET cc_start: 0.9024 (mmm) cc_final: 0.8369 (tpt) REVERT: A 987 ASN cc_start: 0.8337 (m-40) cc_final: 0.7766 (m-40) REVERT: C 733 MET cc_start: 0.7709 (tpp) cc_final: 0.7224 (mpp) REVERT: C 781 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8434 (mp) REVERT: C 831 GLN cc_start: 0.8457 (pt0) cc_final: 0.8109 (pt0) REVERT: D 64 ASN cc_start: 0.8681 (m-40) cc_final: 0.7939 (t0) REVERT: D 65 ASN cc_start: 0.8686 (p0) cc_final: 0.8222 (p0) REVERT: D 84 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7324 (p0) REVERT: D 148 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8059 (ptp90) REVERT: D 212 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7595 (ttt-90) REVERT: D 253 HIS cc_start: 0.7694 (t-90) cc_final: 0.7258 (t-90) outliers start: 77 outliers final: 42 residues processed: 254 average time/residue: 0.1273 time to fit residues: 50.5527 Evaluate side-chains 210 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 85 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 125 optimal weight: 30.0000 chunk 190 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064003 restraints weight = 56718.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.065635 restraints weight = 33766.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.066650 restraints weight = 24769.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.067240 restraints weight = 20706.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.067530 restraints weight = 18704.443| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 17699 Z= 0.281 Angle : 0.754 12.561 24501 Z= 0.401 Chirality : 0.045 0.188 2678 Planarity : 0.005 0.060 2691 Dihedral : 23.940 172.926 3457 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 6.40 % Allowed : 21.98 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % 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: -2.29 (0.19), residues: 1784 helix: -0.34 (0.21), residues: 557 sheet: -1.69 (0.28), residues: 332 loop : -2.24 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 701 TYR 0.020 0.002 TYR C 500 PHE 0.017 0.002 PHE B 274 TRP 0.017 0.002 TRP C 560 HIS 0.006 0.002 HIS C 687 Details of bonding type rmsd covalent geometry : bond 0.00606 (17690) covalent geometry : angle 0.74426 (24497) hydrogen bonds : bond 0.04652 ( 747) hydrogen bonds : angle 4.96992 ( 2057) metal coordination : bond 0.04293 ( 8) metal coordination : angle 9.70556 ( 4) Misc. bond : bond 0.00104 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 170 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8308 (m) cc_final: 0.8046 (m) REVERT: A 622 MET cc_start: 0.8335 (mtp) cc_final: 0.8070 (mtp) REVERT: A 902 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8958 (mt) REVERT: A 903 LYS cc_start: 0.9526 (ptmt) cc_final: 0.9300 (ptpt) REVERT: A 905 MET cc_start: 0.9200 (mmm) cc_final: 0.8455 (tpt) REVERT: A 987 ASN cc_start: 0.8371 (m-40) cc_final: 0.8164 (m-40) REVERT: B 213 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6618 (pt0) REVERT: C 622 MET cc_start: 0.7688 (ttp) cc_final: 0.7352 (ttm) REVERT: C 711 ILE cc_start: 0.8940 (mm) cc_final: 0.8696 (mm) REVERT: C 733 MET cc_start: 0.7958 (tpp) cc_final: 0.7274 (mpp) REVERT: C 778 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8109 (ttm-80) REVERT: C 781 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8502 (mp) REVERT: C 831 GLN cc_start: 0.8564 (pt0) cc_final: 0.8158 (pt0) REVERT: C 850 ARG cc_start: 0.8714 (ttp-170) cc_final: 0.8216 (ptm160) REVERT: D 64 ASN cc_start: 0.8767 (m-40) cc_final: 0.8141 (t0) REVERT: D 65 ASN cc_start: 0.8769 (p0) cc_final: 0.8345 (p0) REVERT: D 84 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6914 (p0) REVERT: D 137 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8560 (ptp90) REVERT: D 159 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8874 (mtt90) REVERT: D 197 LEU cc_start: 0.8310 (tp) cc_final: 0.8072 (tp) REVERT: D 212 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7597 (ttt-90) REVERT: D 285 MET cc_start: 0.7648 (mmt) cc_final: 0.7421 (mmt) outliers start: 101 outliers final: 65 residues processed: 251 average time/residue: 0.1195 time to fit residues: 48.1135 Evaluate side-chains 222 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 149 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 746 THR Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 778 ARG Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 996 MET Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 183 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 GLN A 858 GLN B 347 GLN D 253 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.090452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.066203 restraints weight = 55432.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.067994 restraints weight = 31815.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069123 restraints weight = 22781.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069792 restraints weight = 18818.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.070182 restraints weight = 16853.735| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17699 Z= 0.147 Angle : 0.673 15.120 24501 Z= 0.359 Chirality : 0.043 0.190 2678 Planarity : 0.005 0.059 2691 Dihedral : 23.750 172.650 3457 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.56 % Allowed : 23.50 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.19), residues: 1784 helix: 0.12 (0.22), residues: 558 sheet: -1.55 (0.28), residues: 330 loop : -2.04 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 850 TYR 0.020 0.002 TYR C 933 PHE 0.018 0.001 PHE D 218 TRP 0.009 0.001 TRP D 317 HIS 0.007 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00320 (17690) covalent geometry : angle 0.67073 (24497) hydrogen bonds : bond 0.03862 ( 747) hydrogen bonds : angle 4.65565 ( 2057) metal coordination : bond 0.01156 ( 8) metal coordination : angle 4.20624 ( 4) Misc. bond : bond 0.00104 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 182 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8225 (m) cc_final: 0.7921 (m) REVERT: A 606 MET cc_start: 0.8199 (mmm) cc_final: 0.7067 (ppp) REVERT: A 851 TRP cc_start: 0.7866 (m-10) cc_final: 0.6701 (m-10) REVERT: A 898 ARG cc_start: 0.8529 (mtt180) cc_final: 0.8158 (mtt180) REVERT: A 902 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8935 (mt) REVERT: A 905 MET cc_start: 0.9044 (mmm) cc_final: 0.8218 (tpt) REVERT: A 987 ASN cc_start: 0.8333 (m-40) cc_final: 0.7988 (m-40) REVERT: C 606 MET cc_start: 0.6892 (ppp) cc_final: 0.6150 (ppp) REVERT: C 778 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8107 (ttm-80) REVERT: C 831 GLN cc_start: 0.8539 (pt0) cc_final: 0.8189 (pt0) REVERT: C 850 ARG cc_start: 0.8670 (ttp-170) cc_final: 0.8255 (ptm160) REVERT: C 869 MET cc_start: 0.7770 (mpp) cc_final: 0.7462 (mpp) REVERT: C 1025 MET cc_start: 0.8436 (tpt) cc_final: 0.8213 (tpp) REVERT: D 64 ASN cc_start: 0.8583 (m-40) cc_final: 0.7866 (t0) REVERT: D 65 ASN cc_start: 0.8718 (p0) cc_final: 0.8283 (p0) REVERT: D 84 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7092 (p0) REVERT: D 197 LEU cc_start: 0.8569 (tp) cc_final: 0.8345 (pt) REVERT: D 212 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7786 (ttt-90) REVERT: D 285 MET cc_start: 0.7752 (mmt) cc_final: 0.7523 (mmt) REVERT: D 347 GLN cc_start: 0.8547 (tt0) cc_final: 0.8137 (mt0) outliers start: 72 outliers final: 41 residues processed: 240 average time/residue: 0.1194 time to fit residues: 45.7830 Evaluate side-chains 206 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 778 ARG Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 177 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.087183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.063699 restraints weight = 56156.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.065303 restraints weight = 33716.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.066314 restraints weight = 24864.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.066935 restraints weight = 20768.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.067147 restraints weight = 18699.474| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 17699 Z= 0.269 Angle : 0.743 12.069 24501 Z= 0.394 Chirality : 0.044 0.172 2678 Planarity : 0.005 0.069 2691 Dihedral : 23.765 172.497 3457 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.94 % Allowed : 23.88 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.19), residues: 1784 helix: 0.08 (0.22), residues: 558 sheet: -1.46 (0.28), residues: 323 loop : -2.06 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 123 TYR 0.020 0.002 TYR C 500 PHE 0.016 0.002 PHE A 494 TRP 0.014 0.002 TRP A 538 HIS 0.011 0.002 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00588 (17690) covalent geometry : angle 0.73360 (24497) hydrogen bonds : bond 0.04583 ( 747) hydrogen bonds : angle 4.84934 ( 2057) metal coordination : bond 0.04163 ( 8) metal coordination : angle 9.45390 ( 4) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 163 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8344 (m) cc_final: 0.8069 (m) REVERT: A 496 SER cc_start: 0.9434 (OUTLIER) cc_final: 0.9185 (t) REVERT: A 622 MET cc_start: 0.8169 (mtp) cc_final: 0.7935 (mtp) REVERT: A 851 TRP cc_start: 0.7954 (m-10) cc_final: 0.6822 (m-10) REVERT: A 863 MET cc_start: 0.7705 (mmm) cc_final: 0.7445 (tpp) REVERT: A 898 ARG cc_start: 0.8563 (mtt180) cc_final: 0.8195 (mtt180) REVERT: A 902 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8960 (mt) REVERT: A 984 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7208 (tt0) REVERT: B 213 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6822 (pt0) REVERT: C 606 MET cc_start: 0.7275 (ppp) cc_final: 0.6763 (ppp) REVERT: C 733 MET cc_start: 0.8654 (tpp) cc_final: 0.7788 (tpp) REVERT: C 778 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8152 (ttm-80) REVERT: C 781 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8495 (mp) REVERT: C 850 ARG cc_start: 0.8699 (ttp-170) cc_final: 0.8209 (ptm160) REVERT: C 869 MET cc_start: 0.7884 (mpp) cc_final: 0.7522 (mpp) REVERT: C 1006 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9221 (mm) REVERT: D 64 ASN cc_start: 0.8777 (m-40) cc_final: 0.8092 (t0) REVERT: D 65 ASN cc_start: 0.8736 (p0) cc_final: 0.8330 (p0) REVERT: D 137 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8629 (ptp90) REVERT: D 212 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7816 (ttt-90) REVERT: D 285 MET cc_start: 0.7518 (mmt) cc_final: 0.7190 (mmt) REVERT: D 347 GLN cc_start: 0.8648 (tt0) cc_final: 0.8210 (mt0) outliers start: 78 outliers final: 51 residues processed: 230 average time/residue: 0.1132 time to fit residues: 42.2060 Evaluate side-chains 210 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 778 ARG Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 959 HIS Chi-restraints excluded: chain C residue 1006 LEU Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 108 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 177 optimal weight: 0.0670 chunk 125 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.089109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.065667 restraints weight = 54890.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.067470 restraints weight = 31061.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068609 restraints weight = 22031.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069287 restraints weight = 18051.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.069634 restraints weight = 16110.781| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17699 Z= 0.160 Angle : 0.689 11.199 24501 Z= 0.365 Chirality : 0.042 0.175 2678 Planarity : 0.005 0.068 2691 Dihedral : 23.651 172.379 3457 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.86 % Allowed : 25.46 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.19), residues: 1784 helix: 0.27 (0.22), residues: 556 sheet: -1.40 (0.29), residues: 320 loop : -1.93 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 229 TYR 0.019 0.002 TYR C 933 PHE 0.019 0.001 PHE D 218 TRP 0.014 0.001 TRP A 538 HIS 0.006 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00354 (17690) covalent geometry : angle 0.68617 (24497) hydrogen bonds : bond 0.03886 ( 747) hydrogen bonds : angle 4.68287 ( 2057) metal coordination : bond 0.01568 ( 8) metal coordination : angle 4.64571 ( 4) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 166 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8265 (m) cc_final: 0.7955 (m) REVERT: A 733 MET cc_start: 0.8899 (mmm) cc_final: 0.8602 (tpp) REVERT: A 863 MET cc_start: 0.7601 (mmm) cc_final: 0.7295 (tpp) REVERT: A 898 ARG cc_start: 0.8563 (mtt180) cc_final: 0.8175 (mtt180) REVERT: A 902 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8970 (mt) REVERT: A 905 MET cc_start: 0.9254 (mmp) cc_final: 0.8451 (tpt) REVERT: B 210 LEU cc_start: 0.8555 (mt) cc_final: 0.8089 (mp) REVERT: C 605 SER cc_start: 0.8011 (OUTLIER) cc_final: 0.7431 (p) REVERT: C 606 MET cc_start: 0.7252 (ppp) cc_final: 0.6979 (ppp) REVERT: C 778 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8102 (ttm-80) REVERT: C 781 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8441 (mp) REVERT: C 831 GLN cc_start: 0.8534 (pt0) cc_final: 0.7886 (tm-30) REVERT: C 850 ARG cc_start: 0.8655 (ttp-170) cc_final: 0.8181 (ptm160) REVERT: C 869 MET cc_start: 0.7901 (mpp) cc_final: 0.7631 (mpp) REVERT: C 1006 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9161 (mm) REVERT: D 64 ASN cc_start: 0.8646 (m-40) cc_final: 0.8107 (t0) REVERT: D 65 ASN cc_start: 0.8773 (p0) cc_final: 0.8364 (p0) REVERT: D 285 MET cc_start: 0.7699 (mmt) cc_final: 0.7350 (mmt) REVERT: D 347 GLN cc_start: 0.8604 (tt0) cc_final: 0.8137 (mt0) outliers start: 61 outliers final: 46 residues processed: 217 average time/residue: 0.1159 time to fit residues: 41.0012 Evaluate side-chains 205 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 778 ARG Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 1006 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 67 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 44 optimal weight: 0.0270 chunk 72 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN D 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.090614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.067069 restraints weight = 55008.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068903 restraints weight = 30881.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.070044 restraints weight = 21892.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070761 restraints weight = 17896.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071200 restraints weight = 15919.696| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17699 Z= 0.138 Angle : 0.687 10.925 24501 Z= 0.359 Chirality : 0.042 0.203 2678 Planarity : 0.004 0.069 2691 Dihedral : 23.451 172.586 3457 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.42 % Allowed : 25.90 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.19), residues: 1784 helix: 0.26 (0.22), residues: 566 sheet: -1.32 (0.29), residues: 322 loop : -1.84 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 212 TYR 0.019 0.001 TYR C 933 PHE 0.019 0.001 PHE C 720 TRP 0.015 0.001 TRP A 851 HIS 0.005 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00306 (17690) covalent geometry : angle 0.68528 (24497) hydrogen bonds : bond 0.03682 ( 747) hydrogen bonds : angle 4.54996 ( 2057) metal coordination : bond 0.00995 ( 8) metal coordination : angle 3.65414 ( 4) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8189 (m) cc_final: 0.7928 (m) REVERT: A 489 ILE cc_start: 0.9578 (tp) cc_final: 0.9244 (pt) REVERT: A 496 SER cc_start: 0.9377 (OUTLIER) cc_final: 0.9150 (t) REVERT: A 733 MET cc_start: 0.8883 (mmm) cc_final: 0.8559 (tpp) REVERT: A 863 MET cc_start: 0.7630 (mmm) cc_final: 0.7351 (tpp) REVERT: A 898 ARG cc_start: 0.8565 (mtt180) cc_final: 0.8128 (mtt-85) REVERT: A 902 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8991 (mt) REVERT: A 905 MET cc_start: 0.9125 (mmp) cc_final: 0.8284 (tpt) REVERT: A 951 ASP cc_start: 0.7339 (p0) cc_final: 0.6501 (m-30) REVERT: B 210 LEU cc_start: 0.8466 (mt) cc_final: 0.8023 (mp) REVERT: B 224 LEU cc_start: 0.8418 (tp) cc_final: 0.8109 (tt) REVERT: C 594 MET cc_start: 0.8366 (mmm) cc_final: 0.8131 (mmt) REVERT: C 606 MET cc_start: 0.7261 (ppp) cc_final: 0.6972 (ppp) REVERT: C 622 MET cc_start: 0.7493 (ttp) cc_final: 0.7139 (ttm) REVERT: C 737 MET cc_start: 0.8008 (ttm) cc_final: 0.7662 (mtp) REVERT: C 778 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8057 (ttm-80) REVERT: C 825 GLU cc_start: 0.8070 (tp30) cc_final: 0.7831 (tp30) REVERT: C 850 ARG cc_start: 0.8593 (ttp-170) cc_final: 0.8198 (ptm160) REVERT: C 1006 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9167 (mm) REVERT: D 64 ASN cc_start: 0.8534 (m-40) cc_final: 0.7845 (t0) REVERT: D 65 ASN cc_start: 0.8739 (p0) cc_final: 0.8311 (p0) REVERT: D 285 MET cc_start: 0.7660 (mmt) cc_final: 0.7331 (mmt) REVERT: D 347 GLN cc_start: 0.8572 (tt0) cc_final: 0.8080 (mt0) outliers start: 54 outliers final: 48 residues processed: 218 average time/residue: 0.1166 time to fit residues: 41.3722 Evaluate side-chains 212 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 778 ARG Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 959 HIS Chi-restraints excluded: chain C residue 1006 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 184 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 147 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 128 optimal weight: 0.0970 chunk 31 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.090062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.066277 restraints weight = 55901.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.068107 restraints weight = 32061.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.069253 restraints weight = 22990.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.069954 restraints weight = 18874.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.070179 restraints weight = 16826.963| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17699 Z= 0.159 Angle : 0.687 10.718 24501 Z= 0.360 Chirality : 0.042 0.172 2678 Planarity : 0.005 0.068 2691 Dihedral : 23.379 172.433 3457 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.61 % Allowed : 25.84 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.19), residues: 1784 helix: 0.29 (0.22), residues: 566 sheet: -1.25 (0.29), residues: 322 loop : -1.78 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 212 TYR 0.023 0.002 TYR C 931 PHE 0.017 0.001 PHE D 218 TRP 0.017 0.001 TRP A 538 HIS 0.005 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00354 (17690) covalent geometry : angle 0.68408 (24497) hydrogen bonds : bond 0.03759 ( 747) hydrogen bonds : angle 4.57062 ( 2057) metal coordination : bond 0.02077 ( 8) metal coordination : angle 5.31191 ( 4) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8189 (m) cc_final: 0.7944 (m) REVERT: A 496 SER cc_start: 0.9390 (OUTLIER) cc_final: 0.9158 (t) REVERT: A 733 MET cc_start: 0.8864 (mmm) cc_final: 0.8544 (tpp) REVERT: A 863 MET cc_start: 0.7542 (mmm) cc_final: 0.7270 (tpp) REVERT: A 898 ARG cc_start: 0.8578 (mtt180) cc_final: 0.8201 (mtt180) REVERT: A 902 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8922 (mt) REVERT: A 905 MET cc_start: 0.9149 (mmp) cc_final: 0.8352 (tpt) REVERT: A 951 ASP cc_start: 0.7402 (p0) cc_final: 0.6332 (m-30) REVERT: A 984 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7068 (tt0) REVERT: A 1007 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8141 (tm-30) REVERT: B 224 LEU cc_start: 0.8444 (tp) cc_final: 0.8133 (tt) REVERT: C 606 MET cc_start: 0.7336 (ppp) cc_final: 0.7130 (ppp) REVERT: C 622 MET cc_start: 0.7493 (ttp) cc_final: 0.7126 (ttm) REVERT: C 737 MET cc_start: 0.7974 (ttm) cc_final: 0.7639 (mtp) REVERT: C 778 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8031 (ttm-80) REVERT: C 781 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8469 (mp) REVERT: C 825 GLU cc_start: 0.8058 (tp30) cc_final: 0.7786 (tp30) REVERT: C 831 GLN cc_start: 0.8521 (pt0) cc_final: 0.7715 (tm-30) REVERT: C 850 ARG cc_start: 0.8607 (ttp-170) cc_final: 0.8174 (ptm160) REVERT: C 869 MET cc_start: 0.7894 (mpp) cc_final: 0.7487 (mpp) REVERT: C 1006 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9159 (mm) REVERT: D 64 ASN cc_start: 0.8590 (m-40) cc_final: 0.7903 (t0) REVERT: D 65 ASN cc_start: 0.8744 (p0) cc_final: 0.8313 (p0) REVERT: D 285 MET cc_start: 0.7658 (mmt) cc_final: 0.7316 (mmt) outliers start: 57 outliers final: 46 residues processed: 217 average time/residue: 0.1168 time to fit residues: 41.2307 Evaluate side-chains 210 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 778 ARG Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 959 HIS Chi-restraints excluded: chain C residue 1006 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 48 optimal weight: 0.0170 chunk 75 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.089964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.066129 restraints weight = 56078.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067926 restraints weight = 32444.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.069055 restraints weight = 23398.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.069720 restraints weight = 19308.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.070001 restraints weight = 17311.272| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17699 Z= 0.166 Angle : 0.703 10.700 24501 Z= 0.366 Chirality : 0.042 0.170 2678 Planarity : 0.005 0.068 2691 Dihedral : 23.327 172.509 3457 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.42 % Allowed : 26.09 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.19), residues: 1784 helix: 0.25 (0.22), residues: 564 sheet: -1.20 (0.29), residues: 321 loop : -1.73 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 212 TYR 0.021 0.002 TYR C 931 PHE 0.016 0.001 PHE D 274 TRP 0.013 0.001 TRP A 538 HIS 0.010 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00368 (17690) covalent geometry : angle 0.69991 (24497) hydrogen bonds : bond 0.03815 ( 747) hydrogen bonds : angle 4.61108 ( 2057) metal coordination : bond 0.02160 ( 8) metal coordination : angle 4.98601 ( 4) Misc. bond : bond 0.00052 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 160 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.7922 (m) cc_final: 0.7702 (m) REVERT: A 489 ILE cc_start: 0.9645 (tp) cc_final: 0.9390 (pt) REVERT: A 496 SER cc_start: 0.9334 (OUTLIER) cc_final: 0.9082 (t) REVERT: A 622 MET cc_start: 0.8194 (tpp) cc_final: 0.7960 (mmt) REVERT: A 733 MET cc_start: 0.8887 (mmm) cc_final: 0.8564 (tpp) REVERT: A 898 ARG cc_start: 0.8580 (mtt180) cc_final: 0.8200 (mtt180) REVERT: A 902 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8894 (mt) REVERT: A 905 MET cc_start: 0.9190 (mmp) cc_final: 0.8374 (tpt) REVERT: A 951 ASP cc_start: 0.7232 (p0) cc_final: 0.6384 (m-30) REVERT: A 984 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7066 (tt0) REVERT: B 224 LEU cc_start: 0.8448 (tp) cc_final: 0.8153 (tt) REVERT: C 594 MET cc_start: 0.8410 (mmm) cc_final: 0.8186 (mmt) REVERT: C 622 MET cc_start: 0.7512 (ttp) cc_final: 0.7117 (ttm) REVERT: C 778 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8049 (ttm-80) REVERT: C 781 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8439 (mp) REVERT: C 825 GLU cc_start: 0.8111 (tp30) cc_final: 0.7826 (tp30) REVERT: C 831 GLN cc_start: 0.8524 (pt0) cc_final: 0.7677 (tm-30) REVERT: C 850 ARG cc_start: 0.8648 (ttp-170) cc_final: 0.8208 (ptm160) REVERT: C 869 MET cc_start: 0.7943 (mpp) cc_final: 0.7517 (mpp) REVERT: C 1006 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9169 (mm) REVERT: D 64 ASN cc_start: 0.8630 (m-40) cc_final: 0.8158 (t0) REVERT: D 65 ASN cc_start: 0.8778 (p0) cc_final: 0.8365 (p0) REVERT: D 285 MET cc_start: 0.7654 (mmt) cc_final: 0.7279 (mmt) outliers start: 54 outliers final: 45 residues processed: 206 average time/residue: 0.1170 time to fit residues: 39.8089 Evaluate side-chains 204 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 778 ARG Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 959 HIS Chi-restraints excluded: chain C residue 1006 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 292 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 135 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.089289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.065086 restraints weight = 55793.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.066862 restraints weight = 32433.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067955 restraints weight = 23487.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068638 restraints weight = 19524.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069001 restraints weight = 17549.239| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17699 Z= 0.208 Angle : 0.731 12.708 24501 Z= 0.379 Chirality : 0.043 0.164 2678 Planarity : 0.005 0.068 2691 Dihedral : 23.345 172.349 3457 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.36 % Allowed : 26.79 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.19), residues: 1784 helix: 0.24 (0.22), residues: 558 sheet: -1.22 (0.29), residues: 320 loop : -1.76 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 212 TYR 0.029 0.002 TYR A 875 PHE 0.019 0.002 PHE D 218 TRP 0.011 0.001 TRP A 538 HIS 0.011 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00460 (17690) covalent geometry : angle 0.72592 (24497) hydrogen bonds : bond 0.03996 ( 747) hydrogen bonds : angle 4.68133 ( 2057) metal coordination : bond 0.03058 ( 8) metal coordination : angle 6.58637 ( 4) Misc. bond : bond 0.00061 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2593.38 seconds wall clock time: 45 minutes 52.35 seconds (2752.35 seconds total)