Starting phenix.real_space_refine on Sat Sep 12 16:04:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbr_7848/09_2026/6dbr_7848_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbr_7848/09_2026/6dbr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6dbr_7848/09_2026/6dbr_7848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbr_7848/09_2026/6dbr_7848.map" model { file = "/net/cci-nas-00/data/ceres_data/6dbr_7848/09_2026/6dbr_7848_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbr_7848/09_2026/6dbr_7848_neut.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.59, per 1000 atoms: 0.21 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: 1.73 Conformation dependent library (CDL) restraints added in 609.6 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: 2.00 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: 4.21 Time building geometry restraints manager: 2.09 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: 2520 0.096 - 0.193: 148 0.193 - 0.289: 5 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.250 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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= 0.401 Angle : 1.090 56.334 24501 Z= 0.736 Chirality : 0.050 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/Z covalent geometry : bond 0.00553 / 0.39 (17690) covalent geometry : angle 1.08173 / 0.74 (24497) hydrogen bonds : bond 0.11526 / 7.92 ( 747) hydrogen bonds : angle 6.36585 / 4.54 ( 2057) metal coordination : bond 0.12919 / 5.87 ( 8) metal coordination : angle 10.48515 / 7.95 ( 4) Misc. bond : bond 0.05386 / 2.83 ( 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 : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 MET cc_start: 0.7701 (mtt) cc_final: 0.7362 (mtm) REVERT: A 871 MET cc_start: 0.8035 (mpp) cc_final: 0.7783 (mmt) REVERT: A 886 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8576 (tm-30) REVERT: A 987 ASN cc_start: 0.8317 (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: 0.8436 (p0) cc_final: 0.7723 (p0) REVERT: D 200 LEU cc_start: 0.8816 (mp) cc_final: 0.8595 (mm) REVERT: D 285 MET cc_start: 0.6822 (mmt) cc_final: 0.6550 (mmt) outliers start: 4 outliers final: 2 residues processed: 390 average time/residue: 0.1618 time to fit residues: 90.8897 Evaluate side-chains 198 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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... A 499 GLN ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN C 492 ASN C 499 GLN C 539 GLN C 544 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.090541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.066955 restraints weight = 55515.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.068744 restraints weight = 31525.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069849 restraints weight = 22582.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070520 restraints weight = 18643.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.070841 restraints weight = 16690.779| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17699 Z= 0.166 Angle : 0.753 8.859 24501 Z= 0.411 Chirality : 0.049 0.439 2678 Planarity : 0.006 0.080 2691 Dihedral : 24.244 176.397 3461 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 6.40 % Allowed : 20.20 % Favored : 73.40 % 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: -3.13 (0.17), residues: 1784 helix: -1.18 (0.20), residues: 561 sheet: -2.07 (0.25), residues: 338 loop : -2.69 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 848 TYR 0.027 0.002 TYR B 268 PHE 0.021 0.001 PHE B 31 TRP 0.027 0.002 TRP A 538 HIS 0.008 0.001 HIS C 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (17690) covalent geometry : angle 0.75010 / 0.41 (24497) hydrogen bonds : bond 0.05221 / 3.47 ( 747) hydrogen bonds : angle 5.21612 / 3.77 ( 2057) metal coordination : bond 0.02733 / 1.33 ( 8) metal coordination : angle 4.79642 / 3.96 ( 4) Misc. bond : bond 0.00877 / 0.46 ( 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 328 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 227 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.5635 (OUTLIER) cc_final: 0.4881 (ppp) REVERT: A 871 MET cc_start: 0.7833 (mpp) cc_final: 0.7350 (mmt) REVERT: A 902 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.8876 (mt) REVERT: C 711 ILE cc_start: 0.8925 (mm) cc_final: 0.8690 (mm) REVERT: C 733 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7249 (mpp) REVERT: D 64 ASN cc_start: 0.8884 (m-40) cc_final: 0.8210 (t0) REVERT: D 65 ASN cc_start: 0.8711 (p0) cc_final: 0.8354 (p0) REVERT: D 212 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7532 (ttt-90) outliers start: 101 outliers final: 36 residues processed: 311 average time/residue: 0.1288 time to fit residues: 61.9786 Evaluate side-chains 221 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 848 ARG 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 101 GLU 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 212 ARG 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 733 MET Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 956 ASN 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: 9.9990 chunk 48 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 27 optimal weight: 0.0060 chunk 24 optimal weight: 0.8980 chunk 181 optimal weight: 30.0000 chunk 180 optimal weight: 40.0000 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.0170 chunk 15 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 overall best weight: 1.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 ASN ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 GLN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 GLN C 858 GLN C 910 GLN C 934 ASN D 173 ASN D 222 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.090791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.067248 restraints weight = 56428.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.069045 restraints weight = 32486.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070157 restraints weight = 23122.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.070814 restraints weight = 19104.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071130 restraints weight = 17118.520| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17699 Z= 0.154 Angle : 0.729 12.102 24501 Z= 0.395 Chirality : 0.048 0.370 2678 Planarity : 0.005 0.056 2691 Dihedral : 24.138 179.445 3458 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.69 % Allowed : 22.23 % Favored : 73.08 % 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: -2.53 (0.18), residues: 1784 helix: -0.61 (0.21), residues: 561 sheet: -1.65 (0.27), residues: 321 loop : -2.43 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 870 TYR 0.020 0.002 TYR C 500 PHE 0.019 0.001 PHE B 274 TRP 0.011 0.001 TRP A 538 HIS 0.006 0.001 HIS D 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (17690) covalent geometry : angle 0.72661 / 0.40 (24497) hydrogen bonds : bond 0.04611 / 3.09 ( 747) hydrogen bonds : angle 4.99692 / 3.64 ( 2057) metal coordination : bond 0.03223 / 1.53 ( 8) metal coordination : angle 4.82509 / 3.65 ( 4) Misc. bond : bond 0.00240 / 0.13 ( 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 283 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 209 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8065 (m) cc_final: 0.7757 (m) REVERT: A 851 TRP cc_start: 0.7767 (m-10) cc_final: 0.6731 (m-10) REVERT: A 870 ARG cc_start: 0.8096 (ptp90) cc_final: 0.7624 (mtm-85) REVERT: A 871 MET cc_start: 0.7927 (mpp) cc_final: 0.7539 (mmt) REVERT: A 898 ARG cc_start: 0.8467 (mtt180) cc_final: 0.8091 (mtt180) REVERT: A 902 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8978 (mt) REVERT: A 905 MET cc_start: 0.9127 (mmp) cc_final: 0.8395 (tpt) REVERT: A 987 ASN cc_start: 0.8208 (m-40) cc_final: 0.7701 (m-40) REVERT: C 491 VAL cc_start: 0.9491 (m) cc_final: 0.9289 (p) REVERT: C 711 ILE cc_start: 0.8937 (mm) cc_final: 0.8733 (mm) REVERT: C 825 GLU cc_start: 0.8185 (tp30) cc_final: 0.7979 (tp30) REVERT: C 831 GLN cc_start: 0.8524 (pt0) cc_final: 0.8200 (pt0) REVERT: C 1025 MET cc_start: 0.8178 (tpt) cc_final: 0.7952 (tpp) REVERT: D 64 ASN cc_start: 0.8647 (m-40) cc_final: 0.7953 (t0) REVERT: D 65 ASN cc_start: 0.8764 (p0) cc_final: 0.8269 (p0) REVERT: D 212 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7507 (ttt-90) outliers start: 74 outliers final: 41 residues processed: 266 average time/residue: 0.1139 time to fit residues: 49.6628 Evaluate side-chains 219 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 856 ASP 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 A residue 997 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 216 VAL 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 544 ASN 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 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 1024 PHE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 130 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 85 optimal weight: 7.9990 chunk 139 optimal weight: 0.0020 chunk 125 optimal weight: 20.0000 chunk 190 optimal weight: 30.0000 chunk 72 optimal weight: 0.9990 chunk 137 optimal weight: 0.0370 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 154 optimal weight: 0.0670 chunk 101 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 GLN A 858 GLN A 983 ASN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.091816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.068193 restraints weight = 55804.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070013 restraints weight = 31501.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.071129 restraints weight = 22470.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.071821 restraints weight = 18479.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072174 restraints weight = 16541.466| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17699 Z= 0.137 Angle : 0.708 11.449 24501 Z= 0.381 Chirality : 0.046 0.348 2678 Planarity : 0.004 0.059 2691 Dihedral : 23.996 177.094 3457 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.75 % Allowed : 22.99 % Favored : 72.26 % 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: -2.20 (0.19), residues: 1784 helix: -0.32 (0.21), residues: 557 sheet: -1.52 (0.27), residues: 316 loop : -2.20 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 523 TYR 0.022 0.002 TYR C 933 PHE 0.020 0.001 PHE B 31 TRP 0.010 0.001 TRP A 538 HIS 0.008 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (17690) covalent geometry : angle 0.70602 / 0.38 (24497) hydrogen bonds : bond 0.04359 / 2.93 ( 747) hydrogen bonds : angle 4.73613 / 3.45 ( 2057) metal coordination : bond 0.01274 / 0.61 ( 8) metal coordination : angle 3.73423 / 2.76 ( 4) Misc. bond : bond 0.00068 / 0.04 ( 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 276 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 201 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.7999 (m) cc_final: 0.7755 (m) REVERT: A 851 TRP cc_start: 0.7751 (m-10) cc_final: 0.6643 (m-10) REVERT: A 871 MET cc_start: 0.7859 (mpp) cc_final: 0.7549 (mmt) REVERT: A 898 ARG cc_start: 0.8449 (mtt180) cc_final: 0.8096 (mtt180) REVERT: A 902 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8994 (mt) REVERT: A 905 MET cc_start: 0.9065 (mmp) cc_final: 0.8328 (tpt) REVERT: A 951 ASP cc_start: 0.7220 (p0) cc_final: 0.6239 (m-30) REVERT: A 984 GLU cc_start: 0.7543 (tt0) cc_final: 0.7159 (tt0) REVERT: A 987 ASN cc_start: 0.7941 (m-40) cc_final: 0.7690 (m-40) REVERT: B 224 LEU cc_start: 0.8170 (tp) cc_final: 0.7918 (tt) REVERT: B 268 TYR cc_start: 0.7566 (t80) cc_final: 0.7339 (t80) REVERT: C 622 MET cc_start: 0.7666 (ttp) cc_final: 0.7416 (ttp) REVERT: C 711 ILE cc_start: 0.8888 (mm) cc_final: 0.8649 (mm) REVERT: C 733 MET cc_start: 0.7706 (tpp) cc_final: 0.7167 (mpp) REVERT: C 831 GLN cc_start: 0.8514 (pt0) cc_final: 0.8147 (pt0) REVERT: D 64 ASN cc_start: 0.8483 (m-40) cc_final: 0.7735 (t0) REVERT: D 65 ASN cc_start: 0.8667 (p0) cc_final: 0.8179 (p0) REVERT: D 84 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.6965 (p0) REVERT: D 207 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.7396 (p90) REVERT: D 212 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7465 (ttt-90) outliers start: 75 outliers final: 42 residues processed: 263 average time/residue: 0.1182 time to fit residues: 50.4354 Evaluate side-chains 215 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 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 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 212 ARG Chi-restraints excluded: chain B residue 216 VAL 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 551 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 740 LEU 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 909 LEU Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1015 LEU 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 207 HIS 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 252 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 272 ILE 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: 30.0000 chunk 143 optimal weight: 0.1980 chunk 129 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 GLN B 64 ASN B 347 GLN C 687 HIS ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.092150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.068675 restraints weight = 55786.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070498 restraints weight = 31570.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.071643 restraints weight = 22594.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072342 restraints weight = 18511.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.072505 restraints weight = 16516.123| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17699 Z= 0.131 Angle : 0.689 8.808 24501 Z= 0.369 Chirality : 0.045 0.327 2678 Planarity : 0.004 0.057 2691 Dihedral : 23.887 176.560 3457 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.62 % Allowed : 23.24 % Favored : 72.13 % 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: -1.90 (0.19), residues: 1784 helix: -0.02 (0.22), residues: 555 sheet: -1.32 (0.27), residues: 311 loop : -2.07 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 870 TYR 0.023 0.001 TYR C 933 PHE 0.020 0.001 PHE D 218 TRP 0.011 0.001 TRP A 538 HIS 0.006 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (17690) covalent geometry : angle 0.68689 / 0.37 (24497) hydrogen bonds : bond 0.04203 / 2.84 ( 747) hydrogen bonds : angle 4.62147 / 3.37 ( 2057) metal coordination : bond 0.01182 / 0.58 ( 8) metal coordination : angle 3.92622 / 2.84 ( 4) Misc. bond : bond 0.00038 / 0.02 ( 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 265 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 192 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 VAL cc_start: 0.9490 (t) cc_final: 0.9287 (p) REVERT: A 606 MET cc_start: 0.8211 (mmm) cc_final: 0.7140 (ppp) REVERT: A 851 TRP cc_start: 0.7773 (m-10) cc_final: 0.6655 (m-10) REVERT: A 871 MET cc_start: 0.7747 (mpp) cc_final: 0.7479 (mmt) REVERT: A 898 ARG cc_start: 0.8445 (mtt180) cc_final: 0.8000 (mtt-85) REVERT: A 902 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9026 (mt) REVERT: A 905 MET cc_start: 0.8942 (mmp) cc_final: 0.8146 (tpt) REVERT: A 951 ASP cc_start: 0.7121 (p0) cc_final: 0.6240 (m-30) REVERT: A 984 GLU cc_start: 0.7527 (tt0) cc_final: 0.7280 (tt0) REVERT: A 987 ASN cc_start: 0.8126 (m-40) cc_final: 0.7223 (m-40) REVERT: B 224 LEU cc_start: 0.8192 (tp) cc_final: 0.7933 (tt) REVERT: B 268 TYR cc_start: 0.7607 (t80) cc_final: 0.7363 (t80) REVERT: C 733 MET cc_start: 0.7754 (tpp) cc_final: 0.7230 (mpp) REVERT: C 831 GLN cc_start: 0.8482 (pt0) cc_final: 0.8127 (pt0) REVERT: C 850 ARG cc_start: 0.8592 (ttp-170) cc_final: 0.8176 (ptm160) REVERT: D 64 ASN cc_start: 0.8551 (m-40) cc_final: 0.7787 (t0) REVERT: D 84 ASP cc_start: 0.7512 (m-30) cc_final: 0.6940 (p0) outliers start: 73 outliers final: 47 residues processed: 252 average time/residue: 0.1236 time to fit residues: 49.8442 Evaluate side-chains 215 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 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 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 212 ARG Chi-restraints excluded: chain B residue 216 VAL 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 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 740 LEU 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 909 LEU Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 958 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 91 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 219 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 281 THR 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: 7.9990 chunk 134 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 117 optimal weight: 0.0980 chunk 105 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 GLN D 99 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.067118 restraints weight = 55619.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068789 restraints weight = 33114.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.069833 restraints weight = 24228.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070461 restraints weight = 20163.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070714 restraints weight = 18154.939| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17699 Z= 0.183 Angle : 0.725 14.312 24501 Z= 0.382 Chirality : 0.045 0.327 2678 Planarity : 0.005 0.064 2691 Dihedral : 23.856 175.259 3457 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.12 % Allowed : 24.45 % Favored : 71.44 % 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: -1.85 (0.19), residues: 1784 helix: 0.05 (0.22), residues: 556 sheet: -1.38 (0.27), residues: 330 loop : -2.02 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 212 TYR 0.020 0.002 TYR C 933 PHE 0.019 0.001 PHE D 218 TRP 0.010 0.001 TRP C 560 HIS 0.006 0.001 HIS D 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (17690) covalent geometry : angle 0.71981 / 0.38 (24497) hydrogen bonds : bond 0.04324 / 2.91 ( 747) hydrogen bonds : angle 4.63925 / 3.37 ( 2057) metal coordination : bond 0.02698 / 1.32 ( 8) metal coordination : angle 6.99361 / 5.97 ( 4) Misc. bond : bond 0.00078 / 0.04 ( 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 240 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 175 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 MET cc_start: 0.8249 (mmm) cc_final: 0.7086 (ppp) REVERT: A 871 MET cc_start: 0.7780 (mpp) cc_final: 0.7465 (mmt) REVERT: A 898 ARG cc_start: 0.8463 (mtt180) cc_final: 0.8039 (mtt-85) REVERT: A 902 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9012 (mt) REVERT: A 905 MET cc_start: 0.9066 (mmp) cc_final: 0.8083 (tpt) REVERT: A 909 LEU cc_start: 0.8755 (mm) cc_final: 0.8446 (mm) REVERT: A 951 ASP cc_start: 0.7295 (p0) cc_final: 0.6326 (m-30) REVERT: A 984 GLU cc_start: 0.7633 (tt0) cc_final: 0.7292 (tt0) REVERT: A 987 ASN cc_start: 0.8090 (m-40) cc_final: 0.7882 (m-40) REVERT: C 733 MET cc_start: 0.7864 (tpp) cc_final: 0.7242 (mpp) REVERT: C 781 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8414 (mp) REVERT: C 831 GLN cc_start: 0.8525 (pt0) cc_final: 0.8146 (pt0) REVERT: C 850 ARG cc_start: 0.8654 (ttp-170) cc_final: 0.8190 (ptm160) REVERT: C 1025 MET cc_start: 0.8282 (tpt) cc_final: 0.8034 (tpp) REVERT: D 64 ASN cc_start: 0.8566 (m-40) cc_final: 0.7856 (t0) REVERT: D 84 ASP cc_start: 0.7569 (m-30) cc_final: 0.6907 (p0) REVERT: D 347 GLN cc_start: 0.8367 (tt0) cc_final: 0.7865 (mt0) outliers start: 65 outliers final: 49 residues processed: 228 average time/residue: 0.1087 time to fit residues: 41.0693 Evaluate side-chains 215 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 592 ASP 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 812 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 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 295 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 892 VAL Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 958 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 91 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 227 ASP 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 281 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 108 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 186 optimal weight: 30.0000 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 775 ASN A 997 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.090181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.066717 restraints weight = 55277.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068515 restraints weight = 31479.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.069636 restraints weight = 22452.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070339 restraints weight = 18442.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070678 restraints weight = 16444.465| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17699 Z= 0.171 Angle : 0.707 13.037 24501 Z= 0.374 Chirality : 0.045 0.310 2678 Planarity : 0.005 0.064 2691 Dihedral : 23.799 174.578 3457 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.50 % Allowed : 24.26 % Favored : 71.25 % 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: 0.20 (0.22), residues: 552 sheet: -1.27 (0.27), residues: 329 loop : -1.91 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 212 TYR 0.021 0.002 TYR C 933 PHE 0.026 0.002 PHE D 218 TRP 0.013 0.001 TRP A 851 HIS 0.005 0.001 HIS D 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (17690) covalent geometry : angle 0.70235 / 0.37 (24497) hydrogen bonds : bond 0.04162 / 2.79 ( 747) hydrogen bonds : angle 4.64791 / 3.37 ( 2057) metal coordination : bond 0.02378 / 1.17 ( 8) metal coordination : angle 6.49703 / 5.47 ( 4) Misc. bond : bond 0.00121 / 0.06 ( 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 237 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 166 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 MET cc_start: 0.8084 (mmm) cc_final: 0.7038 (ppp) REVERT: A 622 MET cc_start: 0.8764 (tpp) cc_final: 0.8253 (tpp) REVERT: A 871 MET cc_start: 0.7692 (mpp) cc_final: 0.7419 (mmt) REVERT: A 898 ARG cc_start: 0.8525 (mtt180) cc_final: 0.8114 (mtt-85) REVERT: A 902 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9028 (mt) REVERT: A 905 MET cc_start: 0.8991 (mmp) cc_final: 0.8013 (tpt) REVERT: A 909 LEU cc_start: 0.8779 (mm) cc_final: 0.8442 (mm) REVERT: A 951 ASP cc_start: 0.7216 (p0) cc_final: 0.6267 (m-30) REVERT: A 984 GLU cc_start: 0.7553 (tt0) cc_final: 0.7228 (tt0) REVERT: A 1002 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8440 (tppp) REVERT: B 210 LEU cc_start: 0.8602 (mt) cc_final: 0.8064 (mp) REVERT: B 268 TYR cc_start: 0.7637 (t80) cc_final: 0.7208 (t80) REVERT: C 733 MET cc_start: 0.7862 (tpp) cc_final: 0.7060 (mpp) REVERT: C 781 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8453 (mp) REVERT: C 831 GLN cc_start: 0.8469 (pt0) cc_final: 0.8072 (pt0) REVERT: C 850 ARG cc_start: 0.8668 (ttp-170) cc_final: 0.8220 (ptm160) REVERT: C 1025 MET cc_start: 0.8286 (tpt) cc_final: 0.8048 (tpp) REVERT: D 64 ASN cc_start: 0.8566 (m-40) cc_final: 0.7946 (t0) REVERT: D 84 ASP cc_start: 0.7506 (m-30) cc_final: 0.6884 (p0) REVERT: D 159 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8748 (mtt90) outliers start: 71 outliers final: 54 residues processed: 223 average time/residue: 0.1160 time to fit residues: 41.9882 Evaluate side-chains 214 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 812 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 A residue 1002 LYS 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 212 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 295 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 612 THR Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 694 LEU 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 909 LEU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 996 MET 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 91 LEU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 227 ASP 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 281 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 67 optimal weight: 3.9990 chunk 180 optimal weight: 40.0000 chunk 146 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 ASN C 492 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.088963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.065622 restraints weight = 56032.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.067293 restraints weight = 33475.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068332 restraints weight = 24534.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068890 restraints weight = 20426.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069335 restraints weight = 18476.802| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17699 Z= 0.216 Angle : 0.736 12.817 24501 Z= 0.387 Chirality : 0.046 0.313 2678 Planarity : 0.005 0.064 2691 Dihedral : 23.800 173.796 3457 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.43 % Allowed : 24.32 % Favored : 71.25 % 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: -1.66 (0.19), residues: 1784 helix: 0.14 (0.22), residues: 560 sheet: -1.21 (0.28), residues: 327 loop : -1.88 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 73 TYR 0.021 0.002 TYR C 500 PHE 0.024 0.002 PHE D 274 TRP 0.015 0.002 TRP C 560 HIS 0.006 0.001 HIS D 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.22 (17690) covalent geometry : angle 0.72833 / 0.39 (24497) hydrogen bonds : bond 0.04343 / 2.91 ( 747) hydrogen bonds : angle 4.69837 / 3.40 ( 2057) metal coordination : bond 0.03325 / 1.63 ( 8) metal coordination : angle 8.35261 / 7.12 ( 4) Misc. bond : bond 0.00038 / 0.02 ( 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 231 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 161 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 506 THR cc_start: 0.8843 (m) cc_final: 0.8477 (m) REVERT: A 704 MET cc_start: 0.8973 (tpp) cc_final: 0.8531 (tpt) REVERT: A 871 MET cc_start: 0.7765 (mpp) cc_final: 0.7480 (mmt) REVERT: A 898 ARG cc_start: 0.8487 (mtt180) cc_final: 0.8117 (mtt180) REVERT: A 902 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8894 (mt) REVERT: A 905 MET cc_start: 0.9055 (mmp) cc_final: 0.8147 (tpt) REVERT: A 909 LEU cc_start: 0.8812 (mm) cc_final: 0.8606 (mm) REVERT: A 984 GLU cc_start: 0.7681 (tt0) cc_final: 0.7332 (tt0) REVERT: B 210 LEU cc_start: 0.8709 (mt) cc_final: 0.8203 (mp) REVERT: C 489 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9154 (mt) REVERT: C 606 MET cc_start: 0.7179 (ppp) cc_final: 0.6229 (ppp) REVERT: C 781 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8498 (mp) REVERT: C 850 ARG cc_start: 0.8709 (ttp-170) cc_final: 0.8267 (ptm160) REVERT: C 1025 MET cc_start: 0.8303 (tpt) cc_final: 0.8029 (tpp) REVERT: D 64 ASN cc_start: 0.8608 (m-40) cc_final: 0.8008 (t0) REVERT: D 84 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.6840 (p0) REVERT: D 159 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8741 (mtt90) outliers start: 70 outliers final: 58 residues processed: 216 average time/residue: 0.1159 time to fit residues: 40.7749 Evaluate side-chains 217 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 154 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 711 ILE 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 812 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 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 246 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 564 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 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 892 VAL Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 996 MET 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 73 ARG Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 227 ASP 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 281 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 184 optimal weight: 50.0000 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.089489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.066010 restraints weight = 55697.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.067730 restraints weight = 32283.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068885 restraints weight = 23315.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069474 restraints weight = 19147.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.069932 restraints weight = 17232.724| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17699 Z= 0.179 Angle : 0.725 11.991 24501 Z= 0.381 Chirality : 0.045 0.301 2678 Planarity : 0.005 0.064 2691 Dihedral : 23.765 173.561 3457 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.99 % Allowed : 25.46 % 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: -1.56 (0.19), residues: 1784 helix: 0.26 (0.22), residues: 558 sheet: -1.22 (0.28), residues: 327 loop : -1.82 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 212 TYR 0.020 0.002 TYR C 933 PHE 0.024 0.002 PHE D 274 TRP 0.010 0.001 TRP A 851 HIS 0.009 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (17690) covalent geometry : angle 0.71961 / 0.38 (24497) hydrogen bonds : bond 0.04188 / 2.78 ( 747) hydrogen bonds : angle 4.69465 / 3.40 ( 2057) metal coordination : bond 0.02583 / 1.27 ( 8) metal coordination : angle 6.74930 / 5.75 ( 4) Misc. bond : bond 0.00117 / 0.06 ( 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: 63 poor density : 162 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 THR cc_start: 0.8809 (m) cc_final: 0.8404 (m) REVERT: A 733 MET cc_start: 0.8755 (mmm) cc_final: 0.8305 (ttm) REVERT: A 871 MET cc_start: 0.7708 (mpp) cc_final: 0.7410 (mmt) REVERT: A 898 ARG cc_start: 0.8519 (mtt180) cc_final: 0.8143 (mtt180) REVERT: A 902 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8919 (mt) REVERT: A 905 MET cc_start: 0.9064 (mmp) cc_final: 0.8199 (tpt) REVERT: A 909 LEU cc_start: 0.8793 (mm) cc_final: 0.8517 (mm) REVERT: A 984 GLU cc_start: 0.7570 (tt0) cc_final: 0.7250 (tt0) REVERT: B 210 LEU cc_start: 0.8605 (mt) cc_final: 0.8112 (mp) REVERT: B 212 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6104 (mtp180) REVERT: C 489 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9092 (mt) REVERT: C 606 MET cc_start: 0.7103 (ppp) cc_final: 0.6263 (ppp) REVERT: C 781 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8490 (mp) REVERT: C 831 GLN cc_start: 0.8499 (pt0) cc_final: 0.8228 (pt0) REVERT: C 850 ARG cc_start: 0.8615 (ttp-170) cc_final: 0.8245 (ptm160) REVERT: C 1025 MET cc_start: 0.8237 (tpt) cc_final: 0.7954 (tpp) REVERT: D 64 ASN cc_start: 0.8605 (m-40) cc_final: 0.7996 (t0) REVERT: D 84 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.6878 (p0) outliers start: 63 outliers final: 52 residues processed: 211 average time/residue: 0.1116 time to fit residues: 38.7561 Evaluate side-chains 212 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 155 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 812 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 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 212 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 489 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 680 MET 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 958 LEU Chi-restraints excluded: chain C residue 996 MET 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 73 ARG Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 227 ASP 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 281 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.0040 chunk 112 optimal weight: 4.9990 chunk 187 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 524 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 HIS ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.091147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067562 restraints weight = 55726.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.069378 restraints weight = 32181.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070534 restraints weight = 23162.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071248 restraints weight = 19031.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071658 restraints weight = 16966.747| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17699 Z= 0.134 Angle : 0.721 11.764 24501 Z= 0.374 Chirality : 0.044 0.287 2678 Planarity : 0.005 0.066 2691 Dihedral : 23.670 173.499 3457 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.98 % Allowed : 26.66 % Favored : 70.36 % 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: -1.45 (0.19), residues: 1784 helix: 0.44 (0.22), residues: 552 sheet: -1.22 (0.28), residues: 329 loop : -1.77 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 73 TYR 0.020 0.001 TYR C 933 PHE 0.014 0.001 PHE D 218 TRP 0.011 0.001 TRP A 851 HIS 0.006 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (17690) covalent geometry : angle 0.71941 / 0.37 (24497) hydrogen bonds : bond 0.03998 / 2.65 ( 747) hydrogen bonds : angle 4.61126 / 3.35 ( 2057) metal coordination : bond 0.01086 / 0.54 ( 8) metal coordination : angle 4.34107 / 3.58 ( 4) Misc. bond : bond 0.00145 / 0.08 ( 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 226 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 704 MET cc_start: 0.8916 (tpp) cc_final: 0.8493 (tpt) REVERT: A 871 MET cc_start: 0.7622 (mpp) cc_final: 0.7344 (mmt) REVERT: A 898 ARG cc_start: 0.8509 (mtt180) cc_final: 0.8053 (mtt-85) REVERT: A 902 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9034 (mt) REVERT: A 905 MET cc_start: 0.9085 (mmp) cc_final: 0.8160 (tpt) REVERT: A 909 LEU cc_start: 0.8782 (mm) cc_final: 0.8507 (mm) REVERT: A 951 ASP cc_start: 0.7309 (p0) cc_final: 0.6500 (m-30) REVERT: A 984 GLU cc_start: 0.7616 (tt0) cc_final: 0.7273 (tt0) REVERT: B 212 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.6071 (mtp180) REVERT: B 224 LEU cc_start: 0.8349 (tp) cc_final: 0.8101 (tt) REVERT: C 606 MET cc_start: 0.7004 (ppp) cc_final: 0.6236 (ppp) REVERT: C 622 MET cc_start: 0.7971 (mtm) cc_final: 0.7579 (mtm) REVERT: C 733 MET cc_start: 0.8518 (tpp) cc_final: 0.7821 (tpp) REVERT: C 831 GLN cc_start: 0.8470 (pt0) cc_final: 0.8220 (pt0) REVERT: C 850 ARG cc_start: 0.8610 (ttp-170) cc_final: 0.8236 (ptm160) REVERT: C 987 ASN cc_start: 0.8896 (m-40) cc_final: 0.8115 (t0) REVERT: C 1025 MET cc_start: 0.8181 (tpt) cc_final: 0.7914 (tpp) REVERT: D 64 ASN cc_start: 0.8537 (m-40) cc_final: 0.8014 (t0) REVERT: D 84 ASP cc_start: 0.7408 (m-30) cc_final: 0.7083 (p0) outliers start: 47 outliers final: 37 residues processed: 213 average time/residue: 0.1135 time to fit residues: 39.4430 Evaluate side-chains 202 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 902 LEU Chi-restraints excluded: chain A residue 956 ASN 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 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 290 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 612 THR Chi-restraints excluded: chain C residue 680 MET 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 958 LEU Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain D residue 91 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 281 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 135 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 182 optimal weight: 50.0000 chunk 70 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.090132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.066280 restraints weight = 56377.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.068098 restraints weight = 32263.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069256 restraints weight = 23099.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069958 restraints weight = 18983.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.070379 restraints weight = 16914.013| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17699 Z= 0.173 Angle : 0.727 11.800 24501 Z= 0.377 Chirality : 0.045 0.292 2678 Planarity : 0.005 0.072 2691 Dihedral : 23.677 173.696 3457 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.23 % Allowed : 26.79 % Favored : 69.98 % 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: -1.38 (0.19), residues: 1784 helix: 0.46 (0.22), residues: 558 sheet: -1.25 (0.28), residues: 330 loop : -1.69 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 860 TYR 0.021 0.002 TYR C 500 PHE 0.014 0.002 PHE D 218 TRP 0.010 0.001 TRP C 560 HIS 0.006 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (17690) covalent geometry : angle 0.72094 / 0.38 (24497) hydrogen bonds : bond 0.04122 / 2.74 ( 747) hydrogen bonds : angle 4.63222 / 3.35 ( 2057) metal coordination : bond 0.02603 / 1.28 ( 8) metal coordination : angle 7.14524 / 6.06 ( 4) Misc. bond : bond 0.00137 / 0.07 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2658.70 seconds wall clock time: 47 minutes 3.44 seconds (2823.44 seconds total)