Starting phenix.real_space_refine on Mon Aug 25 19:31:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jby_6488/08_2025/3jby_6488.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jby_6488/08_2025/3jby_6488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3jby_6488/08_2025/3jby_6488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jby_6488/08_2025/3jby_6488.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jby_6488/08_2025/3jby_6488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jby_6488/08_2025/3jby_6488.map" } resolution = 3.7 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16846 atoms to isotropic. 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 124 5.49 5 S 106 5.16 5 C 10202 2.51 5 N 2978 2.21 5 O 3430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16846 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4435 Classifications: {'peptide': 550} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 524} 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: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4435 Classifications: {'peptide': 550} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 524} 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: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "F" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 639 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "G" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 639 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "H" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "I" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 326 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "J" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 326 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} 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 2107 SG CYS A 749 96.116 79.954 64.147 1.00 7.90 S ATOM 9256 SG CYS C 749 56.429 25.315 64.298 1.00 9.51 S Time building chain proxies: 4.37, per 1000 atoms: 0.26 Number of scatterers: 16846 At special positions: 0 Unit cell: (153.75, 107.01, 121.77, 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 124 15.00 O 3430 8.00 N 2978 7.00 C 10202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 672.6 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 19 sheets defined 34.6% alpha, 23.2% beta 34 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 518 through 524 Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 589 through 600 Processing helix chain 'A' and resid 686 through 707 removed outlier: 3.938A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix removed outlier: 4.564A pdb=" N GLU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.513A 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 removed outlier: 3.747A pdb=" N ASP A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 835 removed outlier: 3.510A pdb=" N CYS A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 4.112A 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 removed outlier: 3.802A pdb=" N MET A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 894 through 917 removed outlier: 3.755A pdb=" N GLU A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 930 Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 946 through 951 removed outlier: 3.698A pdb=" N TYR A 950 " --> pdb=" O PHE A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 980 through 996 removed outlier: 3.600A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1017 removed outlier: 4.616A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A1008 " --> pdb=" O PHE A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1024 removed outlier: 3.520A pdb=" N GLN A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A1024 " --> pdb=" O TYR A1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 524 removed outlier: 3.547A pdb=" N ASN C 524 " --> pdb=" O HIS C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 529 removed outlier: 3.987A pdb=" N GLU C 528 " --> pdb=" O ALA C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 600 removed outlier: 4.995A pdb=" N GLU C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.755A 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 738 Processing helix chain 'C' and resid 757 through 762 Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 814 through 835 removed outlier: 3.512A pdb=" N CYS C 818 " --> pdb=" O ASP C 814 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 890 removed outlier: 3.681A pdb=" N ALA C 887 " --> pdb=" O GLU C 883 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 888 " --> pdb=" O ALA C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 917 Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 946 through 951 removed outlier: 3.522A pdb=" N TYR C 950 " --> pdb=" O PHE C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 980 through 993 removed outlier: 4.642A pdb=" N GLY C 986 " --> pdb=" O GLY C 982 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 4.519A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 removed outlier: 3.583A pdb=" N GLN C1022 " --> pdb=" O SER C1018 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C1024 " --> pdb=" O TYR C1020 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C1027 " --> pdb=" O LYS C1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 Processing sheet with id=A, first strand: chain 'A' and resid 536 through 539 removed outlier: 3.531A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU A 677 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 536 through 539 removed outlier: 3.531A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N MET A 647 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN A 664 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A 649 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'B' and resid 2 through 6 removed outlier: 3.819A pdb=" N PHE B 345 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.568A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.787A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=G, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=H, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=I, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=J, first strand: chain 'C' and resid 536 through 539 removed outlier: 6.574A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'C' and resid 536 through 539 removed outlier: 6.574A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N MET C 647 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN C 664 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 649 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'D' and resid 2 through 6 removed outlier: 3.906A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'D' and resid 20 through 23 removed outlier: 4.547A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 76 through 80 removed outlier: 4.490A pdb=" N LEU D 106 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'D' and resid 96 through 97 removed outlier: 3.773A pdb=" N GLU D 101 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=Q, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=R, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=S, first strand: chain 'D' and resid 263 through 265 removed outlier: 4.088A pdb=" N CYS D 287 " --> pdb=" O ARG D 302 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2888 1.32 - 1.45: 6125 1.45 - 1.59: 8094 1.59 - 1.72: 201 1.72 - 1.86: 158 Bond restraints: 17466 Sorted by residual: bond pdb=" CA PRO D 339 " pdb=" C PRO D 339 " ideal model delta sigma weight residual 1.517 1.576 -0.059 9.30e-03 1.16e+04 4.03e+01 bond pdb=" C1' DG F 15 " pdb=" N9 DG F 15 " ideal model delta sigma weight residual 1.460 1.342 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" CA PRO B 339 " pdb=" C PRO B 339 " ideal model delta sigma weight residual 1.517 1.568 -0.051 9.30e-03 1.16e+04 2.97e+01 bond pdb=" C SER A 985 " pdb=" N GLY A 986 " ideal model delta sigma weight residual 1.333 1.402 -0.070 1.31e-02 5.83e+03 2.83e+01 bond pdb=" CA ASN C 983 " pdb=" C ASN C 983 " ideal model delta sigma weight residual 1.525 1.479 0.046 1.02e-02 9.61e+03 2.02e+01 ... (remaining 17461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 22428 2.74 - 5.48: 1386 5.48 - 8.23: 241 8.23 - 10.97: 65 10.97 - 13.71: 16 Bond angle restraints: 24136 Sorted by residual: angle pdb=" N PRO D 339 " pdb=" CA PRO D 339 " pdb=" C PRO D 339 " ideal model delta sigma weight residual 110.70 121.88 -11.18 1.22e+00 6.72e-01 8.40e+01 angle pdb=" N ARG A 999 " pdb=" CA ARG A 999 " pdb=" C ARG A 999 " ideal model delta sigma weight residual 111.14 120.34 -9.20 1.08e+00 8.57e-01 7.26e+01 angle pdb=" C THR D 338 " pdb=" N PRO D 339 " pdb=" CA PRO D 339 " ideal model delta sigma weight residual 120.38 128.86 -8.48 1.03e+00 9.43e-01 6.77e+01 angle pdb=" N PRO B 339 " pdb=" CA PRO B 339 " pdb=" C PRO B 339 " ideal model delta sigma weight residual 110.70 120.21 -9.51 1.22e+00 6.72e-01 6.07e+01 angle pdb=" N ARG C 999 " pdb=" CA ARG C 999 " pdb=" C ARG C 999 " ideal model delta sigma weight residual 111.40 119.25 -7.85 1.22e+00 6.72e-01 4.15e+01 ... (remaining 24131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.34: 9194 29.34 - 58.68: 948 58.68 - 88.02: 46 88.02 - 117.35: 6 117.35 - 146.69: 4 Dihedral angle restraints: 10198 sinusoidal: 4986 harmonic: 5212 Sorted by residual: dihedral pdb=" CA ASP A 658 " pdb=" C ASP A 658 " pdb=" N GLY A 659 " pdb=" CA GLY A 659 " ideal model delta harmonic sigma weight residual 180.00 137.23 42.77 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA ASP C 658 " pdb=" C ASP C 658 " pdb=" N GLY C 659 " pdb=" CA GLY C 659 " ideal model delta harmonic sigma weight residual 180.00 142.38 37.62 0 5.00e+00 4.00e-02 5.66e+01 dihedral pdb=" CA PHE A1004 " pdb=" C PHE A1004 " pdb=" N GLU A1005 " pdb=" CA GLU A1005 " ideal model delta harmonic sigma weight residual -180.00 -145.84 -34.16 0 5.00e+00 4.00e-02 4.67e+01 ... (remaining 10195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1802 0.065 - 0.129: 655 0.129 - 0.193: 152 0.193 - 0.258: 20 0.258 - 0.322: 7 Chirality restraints: 2636 Sorted by residual: chirality pdb=" CB ILE D 272 " pdb=" CA ILE D 272 " pdb=" CG1 ILE D 272 " pdb=" CG2 ILE D 272 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA THR C 493 " pdb=" N THR C 493 " pdb=" C THR C 493 " pdb=" CB THR C 493 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' DG H 7 " pdb=" C4' DG H 7 " pdb=" O3' DG H 7 " pdb=" C2' DG H 7 " both_signs ideal model delta sigma weight residual False -2.66 -2.37 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2633 not shown) Planarity restraints: 2690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG F 1 " 0.033 2.00e-02 2.50e+03 2.58e-02 1.99e+01 pdb=" N9 DG F 1 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DG F 1 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG F 1 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG F 1 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG F 1 " -0.046 2.00e-02 2.50e+03 pdb=" O6 DG F 1 " 0.047 2.00e-02 2.50e+03 pdb=" N1 DG F 1 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DG F 1 " -0.039 2.00e-02 2.50e+03 pdb=" N2 DG F 1 " 0.026 2.00e-02 2.50e+03 pdb=" N3 DG F 1 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG F 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG G 1 " 0.047 2.00e-02 2.50e+03 2.53e-02 1.92e+01 pdb=" N9 DG G 1 " -0.032 2.00e-02 2.50e+03 pdb=" C8 DG G 1 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG G 1 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG G 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG G 1 " -0.033 2.00e-02 2.50e+03 pdb=" O6 DG G 1 " 0.047 2.00e-02 2.50e+03 pdb=" N1 DG G 1 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG G 1 " -0.024 2.00e-02 2.50e+03 pdb=" N2 DG G 1 " 0.020 2.00e-02 2.50e+03 pdb=" N3 DG G 1 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DG G 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG G 15 " -0.057 2.00e-02 2.50e+03 2.23e-02 1.49e+01 pdb=" N9 DG G 15 " 0.037 2.00e-02 2.50e+03 pdb=" C8 DG G 15 " 0.020 2.00e-02 2.50e+03 pdb=" N7 DG G 15 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG G 15 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG G 15 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG G 15 " -0.026 2.00e-02 2.50e+03 pdb=" N1 DG G 15 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG G 15 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG G 15 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG G 15 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DG G 15 " 0.005 2.00e-02 2.50e+03 ... (remaining 2687 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 276 2.59 - 3.17: 15173 3.17 - 3.75: 27503 3.75 - 4.32: 37786 4.32 - 4.90: 59813 Nonbonded interactions: 140551 Sorted by model distance: nonbonded pdb=" NE2 GLN A 858 " pdb=" O ALA A 887 " model vdw 2.015 3.120 nonbonded pdb=" OE2 GLU C 981 " pdb=" N2 DG F 15 " model vdw 2.100 3.120 nonbonded pdb=" OG SER C 760 " pdb=" O ASP C 951 " model vdw 2.116 3.040 nonbonded pdb=" NZ LYS A 508 " pdb=" OP1 DG F 5 " model vdw 2.133 3.120 nonbonded pdb=" O3' DA J 16 " pdb="CA CA C1103 " model vdw 2.175 2.510 ... (remaining 140546 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.030 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.016 0.313 17472 Z= 0.713 Angle : 1.574 13.709 24136 Z= 0.849 Chirality : 0.070 0.322 2636 Planarity : 0.009 0.090 2690 Dihedral : 20.891 146.691 6846 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 24.65 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.24 % Favored : 95.48 % Rotamer: Outliers : 5.74 % Allowed : 13.64 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.60 (0.15), residues: 1794 helix: -3.34 (0.14), residues: 540 sheet: -1.16 (0.26), residues: 314 loop : -2.20 (0.15), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 39 TYR 0.037 0.005 TYR A 875 PHE 0.029 0.005 PHE C 576 TRP 0.026 0.004 TRP B 172 HIS 0.019 0.004 HIS A1028 Details of bonding type rmsd covalent geometry : bond 0.01518 (17466) covalent geometry : angle 1.57416 (24136) hydrogen bonds : bond 0.15553 ( 688) hydrogen bonds : angle 9.77255 ( 1971) metal coordination : bond 0.18046 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 453 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8805 (mt) REVERT: A 858 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: A 905 MET cc_start: 0.9283 (tpp) cc_final: 0.8846 (tpp) REVERT: B 186 ASP cc_start: 0.7657 (t0) cc_final: 0.7445 (t0) REVERT: B 189 PHE cc_start: 0.7109 (m-80) cc_final: 0.6555 (m-80) REVERT: B 192 CYS cc_start: 0.7887 (m) cc_final: 0.7515 (t) REVERT: B 300 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6773 (tt0) REVERT: C 515 ILE cc_start: 0.8169 (mp) cc_final: 0.7921 (mp) REVERT: C 641 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7763 (mtp180) REVERT: C 674 CYS cc_start: 0.7769 (t) cc_final: 0.7283 (p) REVERT: C 737 MET cc_start: 0.7764 (mtm) cc_final: 0.7483 (ptp) REVERT: C 778 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8400 (mtt180) REVERT: C 806 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7549 (p90) REVERT: D 186 ASP cc_start: 0.7474 (t0) cc_final: 0.6828 (m-30) REVERT: D 192 CYS cc_start: 0.7917 (m) cc_final: 0.7621 (t) outliers start: 91 outliers final: 22 residues processed: 510 average time/residue: 0.1655 time to fit residues: 121.0401 Evaluate side-chains 271 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 778 ARG Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 860 ARG Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain D residue 231 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 HIS A 766 HIS A 910 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 278 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 HIS C 666 GLN ** C 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 687 HIS C 766 HIS C 831 GLN C 910 GLN C 937 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.120280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.096243 restraints weight = 32114.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.098841 restraints weight = 17676.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100516 restraints weight = 12148.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.101600 restraints weight = 9615.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102305 restraints weight = 8298.269| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17472 Z= 0.201 Angle : 0.768 8.322 24136 Z= 0.421 Chirality : 0.046 0.274 2636 Planarity : 0.006 0.079 2690 Dihedral : 22.925 155.598 3377 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.95 % Favored : 96.93 % Rotamer: Outliers : 4.73 % Allowed : 19.32 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.17), residues: 1794 helix: -0.99 (0.20), residues: 538 sheet: -0.37 (0.27), residues: 316 loop : -1.68 (0.16), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 850 TYR 0.025 0.002 TYR A 933 PHE 0.014 0.002 PHE B 62 TRP 0.020 0.001 TRP A 538 HIS 0.005 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00444 (17466) covalent geometry : angle 0.76807 (24136) hydrogen bonds : bond 0.04924 ( 688) hydrogen bonds : angle 5.91444 ( 1971) metal coordination : bond 0.00662 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 309 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 799 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8660 (mtpt) REVERT: A 974 SER cc_start: 0.7194 (OUTLIER) cc_final: 0.6878 (m) REVERT: B 177 ASP cc_start: 0.8605 (m-30) cc_final: 0.8381 (m-30) REVERT: B 189 PHE cc_start: 0.6739 (m-80) cc_final: 0.6255 (m-80) REVERT: B 210 LEU cc_start: 0.8919 (mt) cc_final: 0.8413 (mp) REVERT: C 526 GLU cc_start: 0.7678 (pm20) cc_final: 0.7077 (pt0) REVERT: C 705 MET cc_start: 0.8159 (mmm) cc_final: 0.7706 (mmm) REVERT: C 793 GLU cc_start: 0.7665 (mp0) cc_final: 0.7462 (mp0) REVERT: C 806 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.7667 (p90) REVERT: C 863 MET cc_start: 0.7297 (mmm) cc_final: 0.6874 (mmp) REVERT: C 947 LYS cc_start: 0.7974 (tppt) cc_final: 0.7659 (tppt) REVERT: D 33 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8048 (pt0) REVERT: D 258 ILE cc_start: 0.9009 (tp) cc_final: 0.8690 (pt) outliers start: 75 outliers final: 35 residues processed: 357 average time/residue: 0.1468 time to fit residues: 77.8604 Evaluate side-chains 262 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 155 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 153 optimal weight: 30.0000 chunk 178 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 187 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN B 65 ASN C 524 ASN C 669 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.122912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098155 restraints weight = 32342.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.100842 restraints weight = 17873.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.102588 restraints weight = 12372.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103726 restraints weight = 9874.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.104456 restraints weight = 8546.698| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17472 Z= 0.173 Angle : 0.690 8.865 24136 Z= 0.376 Chirality : 0.043 0.286 2636 Planarity : 0.005 0.069 2690 Dihedral : 22.597 158.877 3344 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.29 % Favored : 96.49 % Rotamer: Outliers : 4.42 % Allowed : 20.71 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.18), residues: 1794 helix: 0.18 (0.22), residues: 536 sheet: -0.26 (0.27), residues: 320 loop : -1.30 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 701 TYR 0.020 0.002 TYR A 933 PHE 0.021 0.001 PHE B 62 TRP 0.017 0.001 TRP A 538 HIS 0.007 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00385 (17466) covalent geometry : angle 0.68952 (24136) hydrogen bonds : bond 0.04057 ( 688) hydrogen bonds : angle 5.35653 ( 1971) metal coordination : bond 0.00326 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 271 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 799 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8581 (mtpt) REVERT: A 947 LYS cc_start: 0.7776 (tppt) cc_final: 0.7573 (tppt) REVERT: A 974 SER cc_start: 0.7358 (OUTLIER) cc_final: 0.7086 (m) REVERT: B 38 LYS cc_start: 0.7784 (mmmt) cc_final: 0.7527 (mmtm) REVERT: B 177 ASP cc_start: 0.8524 (m-30) cc_final: 0.8262 (m-30) REVERT: B 186 ASP cc_start: 0.6892 (t0) cc_final: 0.6628 (t0) REVERT: B 224 LEU cc_start: 0.8012 (mt) cc_final: 0.7806 (mt) REVERT: B 269 HIS cc_start: 0.6475 (m90) cc_final: 0.6237 (m170) REVERT: C 526 GLU cc_start: 0.7671 (pm20) cc_final: 0.7144 (pt0) REVERT: C 641 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7860 (mtp-110) REVERT: C 705 MET cc_start: 0.7989 (mmm) cc_final: 0.7752 (mmm) REVERT: C 839 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7177 (mt0) REVERT: C 863 MET cc_start: 0.7100 (mmm) cc_final: 0.6863 (mmp) REVERT: D 21 LEU cc_start: 0.9151 (mt) cc_final: 0.8269 (tp) REVERT: D 119 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7936 (mmtm) REVERT: D 258 ILE cc_start: 0.8889 (tp) cc_final: 0.8685 (pt) outliers start: 70 outliers final: 36 residues processed: 312 average time/residue: 0.1451 time to fit residues: 67.8902 Evaluate side-chains 254 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 ASN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 ASN D 173 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.125322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100433 restraints weight = 32189.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103281 restraints weight = 17376.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105175 restraints weight = 11838.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.106352 restraints weight = 9310.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106948 restraints weight = 8025.162| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17472 Z= 0.147 Angle : 0.653 8.672 24136 Z= 0.355 Chirality : 0.041 0.281 2636 Planarity : 0.005 0.076 2690 Dihedral : 22.444 160.417 3336 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.12 % Favored : 96.66 % Rotamer: Outliers : 4.67 % Allowed : 21.34 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.19), residues: 1794 helix: 0.63 (0.22), residues: 542 sheet: -0.07 (0.28), residues: 316 loop : -1.23 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 897 TYR 0.018 0.002 TYR A 933 PHE 0.023 0.001 PHE D 80 TRP 0.020 0.001 TRP A 538 HIS 0.014 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00319 (17466) covalent geometry : angle 0.65261 (24136) hydrogen bonds : bond 0.03629 ( 688) hydrogen bonds : angle 5.05620 ( 1971) metal coordination : bond 0.00193 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 262 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 650 SER cc_start: 0.9340 (p) cc_final: 0.8948 (t) REVERT: A 705 MET cc_start: 0.8076 (mmm) cc_final: 0.7505 (mmm) REVERT: A 733 MET cc_start: 0.8518 (tpp) cc_final: 0.8260 (tpp) REVERT: A 799 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8526 (mtpt) REVERT: A 905 MET cc_start: 0.8734 (tpp) cc_final: 0.8432 (tpp) REVERT: A 933 TYR cc_start: 0.7556 (t80) cc_final: 0.7249 (t80) REVERT: B 38 LYS cc_start: 0.7773 (mmmt) cc_final: 0.7533 (mmtm) REVERT: B 132 ASP cc_start: 0.7182 (t0) cc_final: 0.6963 (t0) REVERT: B 186 ASP cc_start: 0.7000 (t0) cc_final: 0.6719 (t0) REVERT: B 224 LEU cc_start: 0.8116 (mt) cc_final: 0.7805 (mt) REVERT: B 253 HIS cc_start: 0.7459 (t70) cc_final: 0.7247 (t70) REVERT: B 328 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8844 (tp) REVERT: C 526 GLU cc_start: 0.7514 (pm20) cc_final: 0.7040 (pt0) REVERT: C 641 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7896 (mtp180) REVERT: C 650 SER cc_start: 0.9455 (p) cc_final: 0.9135 (t) REVERT: C 839 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7168 (mt0) REVERT: C 902 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8218 (mt) REVERT: C 947 LYS cc_start: 0.8035 (tppt) cc_final: 0.7776 (tppt) REVERT: D 313 HIS cc_start: 0.8341 (m90) cc_final: 0.8009 (m90) outliers start: 74 outliers final: 43 residues processed: 307 average time/residue: 0.1400 time to fit residues: 65.1992 Evaluate side-chains 269 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 67 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** 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 = 0.3688 r_free = 0.3688 target = 0.123066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098282 restraints weight = 32079.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.101085 restraints weight = 17529.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102940 restraints weight = 11993.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104129 restraints weight = 9456.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.104860 restraints weight = 8153.707| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17472 Z= 0.176 Angle : 0.655 8.727 24136 Z= 0.354 Chirality : 0.042 0.277 2636 Planarity : 0.005 0.071 2690 Dihedral : 22.422 161.938 3335 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.51 % Favored : 96.27 % Rotamer: Outliers : 5.30 % Allowed : 20.96 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.19), residues: 1794 helix: 0.97 (0.23), residues: 532 sheet: -0.08 (0.28), residues: 316 loop : -1.22 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 598 TYR 0.017 0.002 TYR A 933 PHE 0.018 0.001 PHE C 663 TRP 0.016 0.001 TRP A 538 HIS 0.006 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00393 (17466) covalent geometry : angle 0.65496 (24136) hydrogen bonds : bond 0.03553 ( 688) hydrogen bonds : angle 4.92378 ( 1971) metal coordination : bond 0.00493 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 235 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 650 SER cc_start: 0.9344 (p) cc_final: 0.9113 (t) REVERT: A 705 MET cc_start: 0.8074 (mmm) cc_final: 0.7495 (mmm) REVERT: A 733 MET cc_start: 0.8547 (tpp) cc_final: 0.8344 (tpp) REVERT: A 902 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8756 (mt) REVERT: A 905 MET cc_start: 0.8795 (tpp) cc_final: 0.8507 (tpp) REVERT: A 933 TYR cc_start: 0.7622 (t80) cc_final: 0.7172 (t80) REVERT: A 947 LYS cc_start: 0.8122 (tppt) cc_final: 0.7890 (tppt) REVERT: B 54 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7817 (mt-10) REVERT: B 56 LYS cc_start: 0.8661 (mttp) cc_final: 0.8387 (mtpp) REVERT: B 80 PHE cc_start: 0.7891 (t80) cc_final: 0.7619 (t80) REVERT: B 119 LYS cc_start: 0.7888 (ttpt) cc_final: 0.7667 (ttmt) REVERT: B 177 ASP cc_start: 0.8482 (m-30) cc_final: 0.8172 (m-30) REVERT: B 224 LEU cc_start: 0.8238 (mt) cc_final: 0.8037 (mt) REVERT: B 253 HIS cc_start: 0.7469 (t70) cc_final: 0.7258 (t70) REVERT: B 328 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8806 (tp) REVERT: C 526 GLU cc_start: 0.7783 (pm20) cc_final: 0.7235 (pm20) REVERT: C 650 SER cc_start: 0.9373 (p) cc_final: 0.9075 (t) REVERT: C 733 MET cc_start: 0.8488 (tpp) cc_final: 0.7927 (tpp) REVERT: C 824 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8999 (t) REVERT: C 902 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8257 (mt) REVERT: D 280 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7273 (tm-30) REVERT: D 328 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8831 (tp) outliers start: 84 outliers final: 56 residues processed: 281 average time/residue: 0.1339 time to fit residues: 58.1603 Evaluate side-chains 274 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 213 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 328 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 168 optimal weight: 0.3980 chunk 117 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 237 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.122247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097891 restraints weight = 32160.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100576 restraints weight = 17797.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.102372 restraints weight = 12314.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.103501 restraints weight = 9755.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.104126 restraints weight = 8441.651| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17472 Z= 0.180 Angle : 0.657 8.928 24136 Z= 0.354 Chirality : 0.041 0.161 2636 Planarity : 0.005 0.073 2690 Dihedral : 22.369 163.185 3335 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.90 % Favored : 95.82 % Rotamer: Outliers : 4.73 % Allowed : 21.84 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.19), residues: 1794 helix: 0.96 (0.23), residues: 546 sheet: -0.12 (0.27), residues: 342 loop : -1.19 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 991 TYR 0.021 0.002 TYR C 933 PHE 0.014 0.001 PHE B 62 TRP 0.018 0.001 TRP C 978 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00404 (17466) covalent geometry : angle 0.65669 (24136) hydrogen bonds : bond 0.03470 ( 688) hydrogen bonds : angle 4.81820 ( 1971) metal coordination : bond 0.00463 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 224 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.8041 (mmm) cc_final: 0.7499 (mmm) REVERT: A 733 MET cc_start: 0.8644 (tpp) cc_final: 0.8324 (tpp) REVERT: A 737 MET cc_start: 0.7831 (mmm) cc_final: 0.7603 (mmm) REVERT: A 799 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8524 (mtpt) REVERT: A 905 MET cc_start: 0.8751 (tpp) cc_final: 0.8477 (tpp) REVERT: A 933 TYR cc_start: 0.7659 (t80) cc_final: 0.7205 (t80) REVERT: B 56 LYS cc_start: 0.8593 (mttp) cc_final: 0.8383 (mtpp) REVERT: B 80 PHE cc_start: 0.7902 (t80) cc_final: 0.7674 (t80) REVERT: B 119 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7636 (ttmt) REVERT: B 150 LYS cc_start: 0.8329 (tttp) cc_final: 0.8041 (tttp) REVERT: B 177 ASP cc_start: 0.8409 (m-30) cc_final: 0.8159 (m-30) REVERT: B 328 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8821 (tp) REVERT: C 526 GLU cc_start: 0.7816 (pm20) cc_final: 0.7508 (pm20) REVERT: C 705 MET cc_start: 0.7995 (mmm) cc_final: 0.7683 (mmm) REVERT: C 842 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7647 (p0) REVERT: C 902 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8284 (mt) REVERT: D 210 LEU cc_start: 0.8706 (mt) cc_final: 0.8438 (mt) REVERT: D 328 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8813 (tp) outliers start: 75 outliers final: 53 residues processed: 268 average time/residue: 0.1293 time to fit residues: 53.6271 Evaluate side-chains 265 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 207 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 842 ASN Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 328 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 52 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** 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 = 0.3657 r_free = 0.3657 target = 0.121150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096730 restraints weight = 32226.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.099392 restraints weight = 17970.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.101158 restraints weight = 12465.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102190 restraints weight = 9902.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.102957 restraints weight = 8634.067| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17472 Z= 0.199 Angle : 0.677 9.197 24136 Z= 0.362 Chirality : 0.042 0.164 2636 Planarity : 0.005 0.071 2690 Dihedral : 22.361 164.154 3333 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.62 % Favored : 96.10 % Rotamer: Outliers : 4.36 % Allowed : 22.35 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.19), residues: 1794 helix: 0.93 (0.22), residues: 548 sheet: -0.12 (0.27), residues: 326 loop : -1.14 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 574 TYR 0.019 0.002 TYR C 933 PHE 0.012 0.002 PHE D 274 TRP 0.013 0.001 TRP A 538 HIS 0.007 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00448 (17466) covalent geometry : angle 0.67675 (24136) hydrogen bonds : bond 0.03507 ( 688) hydrogen bonds : angle 4.79450 ( 1971) metal coordination : bond 0.00553 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 222 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.8010 (mmm) cc_final: 0.7754 (mmm) REVERT: A 733 MET cc_start: 0.8663 (tpp) cc_final: 0.8393 (tpp) REVERT: A 737 MET cc_start: 0.7847 (mmm) cc_final: 0.7603 (mmm) REVERT: A 799 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8467 (mtpt) REVERT: A 849 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7672 (mtm-85) REVERT: A 905 MET cc_start: 0.8801 (tpp) cc_final: 0.8541 (tpp) REVERT: A 933 TYR cc_start: 0.7667 (t80) cc_final: 0.7052 (t80) REVERT: B 69 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8378 (mm) REVERT: B 80 PHE cc_start: 0.7979 (t80) cc_final: 0.7687 (t80) REVERT: B 90 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: B 119 LYS cc_start: 0.7885 (ttpt) cc_final: 0.7603 (ttmt) REVERT: B 328 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8807 (tp) REVERT: C 792 ASP cc_start: 0.7867 (t0) cc_final: 0.7628 (t0) REVERT: C 842 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7643 (p0) REVERT: C 902 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8337 (mt) REVERT: D 328 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8840 (tp) outliers start: 69 outliers final: 53 residues processed: 263 average time/residue: 0.1306 time to fit residues: 53.0364 Evaluate side-chains 265 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 204 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 842 ASN Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 328 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 125 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** 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 = 0.3599 r_free = 0.3599 target = 0.118163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.092984 restraints weight = 33015.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095780 restraints weight = 17564.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097641 restraints weight = 11873.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098838 restraints weight = 9291.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099582 restraints weight = 7979.843| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17472 Z= 0.181 Angle : 0.666 9.089 24136 Z= 0.358 Chirality : 0.042 0.243 2636 Planarity : 0.005 0.071 2690 Dihedral : 22.277 164.937 3333 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.96 % Favored : 95.76 % Rotamer: Outliers : 4.73 % Allowed : 22.29 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.19), residues: 1794 helix: 0.96 (0.23), residues: 548 sheet: -0.05 (0.28), residues: 316 loop : -1.17 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 991 TYR 0.023 0.002 TYR A 500 PHE 0.013 0.001 PHE D 274 TRP 0.012 0.001 TRP A 538 HIS 0.007 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00406 (17466) covalent geometry : angle 0.66628 (24136) hydrogen bonds : bond 0.03398 ( 688) hydrogen bonds : angle 4.76769 ( 1971) metal coordination : bond 0.00470 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 219 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.8097 (mmm) cc_final: 0.7849 (mmm) REVERT: A 799 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8464 (mtpt) REVERT: A 849 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7719 (mtm-85) REVERT: A 905 MET cc_start: 0.8732 (tpp) cc_final: 0.8464 (tpp) REVERT: A 933 TYR cc_start: 0.7631 (t80) cc_final: 0.7020 (t80) REVERT: B 69 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8322 (mm) REVERT: B 80 PHE cc_start: 0.8126 (t80) cc_final: 0.7580 (t80) REVERT: B 90 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7111 (m-80) REVERT: B 119 LYS cc_start: 0.7889 (ttpt) cc_final: 0.7567 (ttmt) REVERT: B 328 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8837 (tp) REVERT: C 792 ASP cc_start: 0.7945 (t0) cc_final: 0.7697 (t0) REVERT: C 842 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7721 (p0) REVERT: C 902 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8319 (mt) REVERT: C 947 LYS cc_start: 0.8229 (tppt) cc_final: 0.8014 (tppt) REVERT: D 80 PHE cc_start: 0.8049 (t80) cc_final: 0.7794 (t80) REVERT: D 210 LEU cc_start: 0.8921 (mt) cc_final: 0.8539 (mp) REVERT: D 328 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8801 (tp) outliers start: 75 outliers final: 55 residues processed: 264 average time/residue: 0.1337 time to fit residues: 54.7926 Evaluate side-chains 273 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 842 ASN Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 328 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 78 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 chunk 20 optimal weight: 0.0370 chunk 51 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 7 optimal weight: 0.0670 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 overall best weight: 2.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.092265 restraints weight = 33029.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094965 restraints weight = 17862.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.096754 restraints weight = 12202.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.097880 restraints weight = 9614.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098623 restraints weight = 8305.892| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17472 Z= 0.205 Angle : 0.690 12.450 24136 Z= 0.369 Chirality : 0.042 0.165 2636 Planarity : 0.005 0.070 2690 Dihedral : 22.318 165.495 3333 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.18 % Favored : 95.54 % Rotamer: Outliers : 4.80 % Allowed : 22.54 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.19), residues: 1794 helix: 0.88 (0.23), residues: 548 sheet: -0.13 (0.27), residues: 326 loop : -1.13 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 159 TYR 0.019 0.002 TYR A 500 PHE 0.020 0.002 PHE D 46 TRP 0.013 0.001 TRP B 317 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00464 (17466) covalent geometry : angle 0.68989 (24136) hydrogen bonds : bond 0.03511 ( 688) hydrogen bonds : angle 4.78802 ( 1971) metal coordination : bond 0.00606 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 215 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 ASP cc_start: 0.8082 (m-30) cc_final: 0.7813 (t0) REVERT: A 705 MET cc_start: 0.8052 (mmm) cc_final: 0.7812 (mmm) REVERT: A 799 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8479 (mtpt) REVERT: A 849 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7777 (mtm-85) REVERT: A 905 MET cc_start: 0.8733 (tpp) cc_final: 0.8493 (tpp) REVERT: A 933 TYR cc_start: 0.7628 (t80) cc_final: 0.7007 (t80) REVERT: B 69 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8260 (mm) REVERT: B 80 PHE cc_start: 0.8141 (t80) cc_final: 0.7605 (t80) REVERT: B 90 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7174 (m-80) REVERT: B 119 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7606 (ttmt) REVERT: B 328 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8820 (tp) REVERT: C 792 ASP cc_start: 0.7947 (t0) cc_final: 0.7699 (t0) REVERT: C 842 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7694 (p0) REVERT: C 902 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8316 (mt) REVERT: D 260 SER cc_start: 0.9038 (OUTLIER) cc_final: 0.8811 (p) REVERT: D 298 HIS cc_start: 0.7844 (m90) cc_final: 0.7528 (t70) REVERT: D 328 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8755 (tp) outliers start: 76 outliers final: 56 residues processed: 260 average time/residue: 0.1312 time to fit residues: 52.7982 Evaluate side-chains 269 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 204 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 842 ASN Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 328 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 184 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** 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 = 0.3645 r_free = 0.3645 target = 0.121411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096675 restraints weight = 32743.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099469 restraints weight = 17619.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.101319 restraints weight = 11978.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.102522 restraints weight = 9402.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.103280 restraints weight = 8072.706| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17472 Z= 0.140 Angle : 0.655 11.737 24136 Z= 0.351 Chirality : 0.040 0.161 2636 Planarity : 0.005 0.070 2690 Dihedral : 22.049 166.730 3333 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.85 % Favored : 95.88 % Rotamer: Outliers : 3.09 % Allowed : 24.31 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.19), residues: 1794 helix: 1.06 (0.23), residues: 546 sheet: 0.15 (0.29), residues: 312 loop : -1.20 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 523 TYR 0.019 0.002 TYR C 933 PHE 0.017 0.001 PHE C 516 TRP 0.014 0.001 TRP A 538 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00309 (17466) covalent geometry : angle 0.65532 (24136) hydrogen bonds : bond 0.03248 ( 688) hydrogen bonds : angle 4.70932 ( 1971) metal coordination : bond 0.00177 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 232 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 ASP cc_start: 0.8057 (m-30) cc_final: 0.7777 (t0) REVERT: A 584 SER cc_start: 0.8925 (t) cc_final: 0.8674 (m) REVERT: A 705 MET cc_start: 0.8148 (mmm) cc_final: 0.7748 (mmm) REVERT: A 799 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8390 (mtpt) REVERT: B 69 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8308 (mm) REVERT: B 80 PHE cc_start: 0.8142 (t80) cc_final: 0.7636 (t80) REVERT: B 90 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: B 328 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8849 (tp) REVERT: C 622 MET cc_start: 0.8610 (ptm) cc_final: 0.8329 (ptp) REVERT: C 842 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7639 (p0) REVERT: C 902 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8161 (mt) REVERT: D 204 GLN cc_start: 0.8073 (pt0) cc_final: 0.7855 (pm20) REVERT: D 210 LEU cc_start: 0.8855 (mt) cc_final: 0.8491 (mt) REVERT: D 260 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8738 (p) REVERT: D 280 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7317 (tm-30) REVERT: D 298 HIS cc_start: 0.7801 (m90) cc_final: 0.7433 (t70) outliers start: 49 outliers final: 37 residues processed: 261 average time/residue: 0.1302 time to fit residues: 52.2788 Evaluate side-chains 258 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 842 ASN Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 286 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 40 optimal weight: 8.9990 chunk 126 optimal weight: 0.1980 chunk 177 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 95 optimal weight: 0.2980 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 0.3980 chunk 146 optimal weight: 0.3980 chunk 156 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.123089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098442 restraints weight = 32764.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101252 restraints weight = 17597.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.103110 restraints weight = 11966.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.104277 restraints weight = 9390.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105035 restraints weight = 8089.371| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17472 Z= 0.136 Angle : 0.647 10.498 24136 Z= 0.345 Chirality : 0.040 0.159 2636 Planarity : 0.005 0.071 2690 Dihedral : 21.930 167.130 3333 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.62 % Favored : 96.10 % Rotamer: Outliers : 2.65 % Allowed : 25.13 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.19), residues: 1794 helix: 1.09 (0.23), residues: 546 sheet: 0.30 (0.28), residues: 326 loop : -1.21 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 523 TYR 0.020 0.001 TYR A 500 PHE 0.017 0.001 PHE D 218 TRP 0.017 0.001 TRP A 538 HIS 0.009 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00299 (17466) covalent geometry : angle 0.64654 (24136) hydrogen bonds : bond 0.03109 ( 688) hydrogen bonds : angle 4.64829 ( 1971) metal coordination : bond 0.00118 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2760.66 seconds wall clock time: 48 minutes 43.35 seconds (2923.35 seconds total)