Starting phenix.real_space_refine on Mon Sep 14 11:48:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jby_6488/09_2026/3jby_6488.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jby_6488/09_2026/3jby_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/3jby_6488/09_2026/3jby_6488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jby_6488/09_2026/3jby_6488.map" restraint_files = "/net/cci-nas-00/data/ceres_data/3jby_6488/09_2026/3jby_6488.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jby_6488/09_2026/3jby_6488.cif" model { file = "/net/cci-nas-00/data/ceres_data/3jby_6488/09_2026/3jby_6488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jby_6488/09_2026/3jby_6488.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.46, per 1000 atoms: 0.21 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: 1.48 Conformation dependent library (CDL) restraints added in 642.6 milliseconds 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: 2.00 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: 3.49 Time building geometry restraints manager: 1.95 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=" C1' DG F 15 " pdb=" N9 DG F 15 " ideal model delta sigma weight residual 1.468 1.342 0.126 1.40e-02 5.10e+03 8.07e+01 bond pdb=" C3' DC G 11 " pdb=" O3' DC G 11 " ideal model delta sigma weight residual 1.435 1.323 0.112 1.30e-02 5.92e+03 7.38e+01 bond pdb=" C3' DG H 7 " pdb=" O3' DG H 7 " ideal model delta sigma weight residual 1.435 1.326 0.109 1.30e-02 5.92e+03 7.01e+01 bond pdb=" C3' DT E 6 " pdb=" O3' DT E 6 " ideal model delta sigma weight residual 1.435 1.329 0.106 1.30e-02 5.92e+03 6.59e+01 bond pdb=" C1' DT H 6 " pdb=" N1 DT H 6 " ideal model delta sigma weight residual 1.468 1.361 0.107 1.40e-02 5.10e+03 5.80e+01 ... (remaining 17461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 22368 2.74 - 5.48: 1448 5.48 - 8.23: 239 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=" C8 DG F 15 " pdb=" N9 DG F 15 " pdb=" C4 DG F 15 " ideal model delta sigma weight residual 106.40 109.92 -3.52 4.00e-01 6.25e+00 7.74e+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 ... (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 - 0.073: 1904 0.073 - 0.146: 598 0.146 - 0.219: 114 0.219 - 0.292: 13 0.292 - 0.365: 7 Chirality restraints: 2636 Sorted by residual: 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 -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.33e+00 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=" C3' DG E 7 " pdb=" C4' DG E 7 " pdb=" O3' DG E 7 " pdb=" C2' DG E 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.41 -0.32 2.00e-01 2.50e+01 2.58e+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: 0.500 Set stop_for_unknowns flag: 0.010 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: 19.390 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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= 0.939 Angle : 1.591 13.709 24136 Z= 0.951 Chirality : 0.073 0.365 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 are 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/Z covalent geometry : bond 0.01528 / 0.93 (17466) covalent geometry : angle 1.59081 / 0.95 (24136) hydrogen bonds : bond 0.15553 / 10.56 ( 688) hydrogen bonds : angle 9.77255 / 6.95 ( 1971) metal coordination : bond 0.18046 / 11.29 ( 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 : 0.607 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: 0.8806 (mt) REVERT: A 858 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: A 905 MET cc_start: 0.9283 (tpp) cc_final: 0.8850 (tpp) REVERT: B 186 ASP cc_start: 0.7657 (t0) cc_final: 0.7447 (t0) REVERT: B 189 PHE cc_start: 0.7109 (m-80) cc_final: 0.6521 (m-80) REVERT: B 192 CYS cc_start: 0.7887 (m) cc_final: 0.7516 (t) REVERT: B 300 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6772 (tt0) REVERT: C 515 ILE cc_start: 0.8169 (mp) cc_final: 0.7920 (mp) REVERT: C 641 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7764 (mtp180) REVERT: C 674 CYS cc_start: 0.7769 (t) cc_final: 0.7286 (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: 0.7548 (p90) REVERT: D 186 ASP cc_start: 0.7474 (t0) cc_final: 0.6830 (m-30) REVERT: D 192 CYS cc_start: 0.7917 (m) cc_final: 0.7622 (t) outliers start: 91 outliers final: 22 residues processed: 510 average time/residue: 0.1448 time to fit residues: 106.8643 Evaluate side-chains 273 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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: 6.9990 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... ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 HIS C 822 ASN C 831 GLN C 910 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.118901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094504 restraints weight = 32350.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097085 restraints weight = 17866.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098805 restraints weight = 12331.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099916 restraints weight = 9739.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100383 restraints weight = 8393.230| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17472 Z= 0.218 Angle : 0.851 8.631 24136 Z= 0.469 Chirality : 0.050 0.321 2636 Planarity : 0.007 0.071 2690 Dihedral : 22.985 149.950 3377 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.79 % Favored : 97.10 % Rotamer: Outliers : 5.24 % Allowed : 18.94 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.17), residues: 1794 helix: -1.18 (0.20), residues: 538 sheet: -0.48 (0.26), residues: 326 loop : -1.67 (0.17), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 797 TYR 0.026 0.003 TYR C 500 PHE 0.021 0.002 PHE D 274 TRP 0.022 0.001 TRP A 538 HIS 0.007 0.002 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 (17466) covalent geometry : angle 0.85069 / 0.47 (24136) hydrogen bonds : bond 0.05538 / 3.77 ( 688) hydrogen bonds : angle 6.28692 / 4.42 ( 1971) metal coordination : bond 0.01574 / 1.02 ( 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 387 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 304 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8380 (tt) REVERT: A 850 ARG cc_start: 0.7817 (ttm110) cc_final: 0.7585 (ttm-80) REVERT: A 871 MET cc_start: 0.9056 (mmm) cc_final: 0.8836 (tpt) REVERT: A 947 LYS cc_start: 0.7894 (tppt) cc_final: 0.7689 (tppt) REVERT: B 66 SER cc_start: 0.8893 (p) cc_final: 0.8681 (t) REVERT: B 128 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7986 (tm-30) REVERT: B 189 PHE cc_start: 0.6699 (m-80) cc_final: 0.6319 (m-80) REVERT: B 210 LEU cc_start: 0.8865 (mt) cc_final: 0.8353 (mp) REVERT: B 245 PRO cc_start: 0.7498 (Cg_endo) cc_final: 0.7243 (Cg_exo) REVERT: B 300 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6917 (tm-30) REVERT: C 526 GLU cc_start: 0.7601 (pm20) cc_final: 0.7131 (pt0) REVERT: C 705 MET cc_start: 0.8036 (mmm) cc_final: 0.7509 (mmm) REVERT: C 806 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7672 (p90) REVERT: C 905 MET cc_start: 0.8788 (tpp) cc_final: 0.8566 (tpp) REVERT: D 33 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8003 (pt0) REVERT: D 171 ASN cc_start: 0.8558 (t0) cc_final: 0.8260 (t0) REVERT: D 258 ILE cc_start: 0.8954 (tp) cc_final: 0.8701 (pt) REVERT: D 260 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8737 (p) REVERT: D 317 TRP cc_start: 0.8628 (p-90) cc_final: 0.8380 (p-90) outliers start: 83 outliers final: 35 residues processed: 361 average time/residue: 0.1240 time to fit residues: 68.4018 Evaluate side-chains 271 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 677 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 846 GLU 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 97 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 300 GLU 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 975 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 130 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: 0.9990 chunk 148 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN C 524 ASN C 629 HIS C 669 ASN C 822 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 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 = 0.3580 r_free = 0.3580 target = 0.116184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.091379 restraints weight = 32697.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.093950 restraints weight = 18081.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095652 restraints weight = 12456.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096761 restraints weight = 9865.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097402 restraints weight = 8507.213| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 17472 Z= 0.271 Angle : 0.811 10.006 24136 Z= 0.436 Chirality : 0.049 0.308 2636 Planarity : 0.006 0.064 2690 Dihedral : 22.958 155.125 3347 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.40 % Favored : 96.43 % Rotamer: Outliers : 5.43 % Allowed : 20.45 % Favored : 74.12 % 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 are not related in a simple way. whole: -1.46 (0.18), residues: 1794 helix: -0.38 (0.22), residues: 540 sheet: -0.46 (0.26), residues: 338 loop : -1.51 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 523 TYR 0.023 0.003 TYR A 933 PHE 0.021 0.002 PHE D 350 TRP 0.015 0.002 TRP B 317 HIS 0.009 0.002 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.27 (17466) covalent geometry : angle 0.81052 / 0.44 (24136) hydrogen bonds : bond 0.05014 / 3.38 ( 688) hydrogen bonds : angle 5.80255 / 4.05 ( 1971) metal coordination : bond 0.00840 / 0.61 ( 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 320 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 234 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 733 MET cc_start: 0.8452 (tpp) cc_final: 0.8008 (tpp) REVERT: A 799 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8653 (mtpt) REVERT: A 863 MET cc_start: 0.8263 (mmm) cc_final: 0.8056 (mmm) REVERT: B 1 MET cc_start: 0.6417 (mpp) cc_final: 0.5754 (mpp) REVERT: B 186 ASP cc_start: 0.7154 (t0) cc_final: 0.6829 (t0) REVERT: B 189 PHE cc_start: 0.6793 (m-80) cc_final: 0.6519 (m-80) REVERT: B 328 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8973 (tp) REVERT: C 526 GLU cc_start: 0.8129 (pm20) cc_final: 0.7601 (pm20) REVERT: C 594 MET cc_start: 0.8917 (mmp) cc_final: 0.8717 (mmt) REVERT: C 806 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.7942 (p90) REVERT: C 905 MET cc_start: 0.8950 (tpp) cc_final: 0.8730 (tpp) REVERT: D 258 ILE cc_start: 0.9052 (tp) cc_final: 0.8736 (pt) REVERT: D 317 TRP cc_start: 0.8609 (p-90) cc_final: 0.8373 (p-90) outliers start: 86 outliers final: 47 residues processed: 294 average time/residue: 0.1285 time to fit residues: 57.9650 Evaluate side-chains 253 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 203 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 622 MET Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 97 THR 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 182 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 260 SER 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 491 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 734 VAL 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 C residue 985 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 130 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 182 VAL 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: 4.9990 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 669 ASN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN B 65 ASN B 181 GLN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN D 33 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.120788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096113 restraints weight = 32320.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098882 restraints weight = 17515.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.100677 restraints weight = 11964.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.101821 restraints weight = 9432.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.102450 restraints weight = 8148.985| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17472 Z= 0.175 Angle : 0.727 8.689 24136 Z= 0.397 Chirality : 0.046 0.319 2636 Planarity : 0.005 0.068 2690 Dihedral : 22.835 157.344 3342 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.68 % Favored : 96.10 % Rotamer: Outliers : 4.48 % Allowed : 22.16 % Favored : 73.36 % 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 are not related in a simple way. whole: -1.06 (0.18), residues: 1794 helix: 0.24 (0.22), residues: 528 sheet: -0.35 (0.27), residues: 338 loop : -1.40 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 897 TYR 0.021 0.002 TYR A 578 PHE 0.024 0.002 PHE D 80 TRP 0.012 0.001 TRP D 317 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (17466) covalent geometry : angle 0.72659 / 0.40 (24136) hydrogen bonds : bond 0.04368 / 2.96 ( 688) hydrogen bonds : angle 5.44370 / 3.80 ( 1971) metal coordination : bond 0.00341 / 0.25 ( 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 311 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 240 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.8270 (mmm) cc_final: 0.7507 (mmm) REVERT: A 799 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8630 (mtpt) REVERT: A 905 MET cc_start: 0.8800 (tpp) cc_final: 0.8517 (tpp) REVERT: A 909 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8946 (mt) REVERT: A 981 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8344 (mm-30) REVERT: A 984 GLU cc_start: 0.8550 (tp30) cc_final: 0.8203 (mm-30) REVERT: B 1 MET cc_start: 0.6573 (mpp) cc_final: 0.5940 (mpp) REVERT: B 80 PHE cc_start: 0.7871 (t80) cc_final: 0.7606 (t80) REVERT: B 186 ASP cc_start: 0.7246 (t0) cc_final: 0.6869 (t0) REVERT: B 189 PHE cc_start: 0.6789 (m-80) cc_final: 0.6518 (m-80) REVERT: B 260 SER cc_start: 0.9360 (OUTLIER) cc_final: 0.9116 (p) REVERT: B 292 LEU cc_start: 0.7418 (pt) cc_final: 0.6926 (pp) REVERT: B 328 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8883 (tp) REVERT: C 526 GLU cc_start: 0.7823 (pm20) cc_final: 0.7142 (pt0) REVERT: C 839 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7191 (mt0) REVERT: C 905 MET cc_start: 0.8853 (tpp) cc_final: 0.8643 (tpp) REVERT: D 224 LEU cc_start: 0.7629 (mt) cc_final: 0.7414 (mt) REVERT: D 328 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8780 (tp) outliers start: 71 outliers final: 49 residues processed: 285 average time/residue: 0.1275 time to fit residues: 56.3586 Evaluate side-chains 257 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 622 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 793 GLU Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 97 THR 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 240 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER 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 491 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 519 LEU 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 604 ASP Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 975 ILE 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 182 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 252 LEU 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 Chi-restraints excluded: chain D residue 328 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 67 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 176 optimal weight: 4.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 687 HIS ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN D 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.120520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096057 restraints weight = 32158.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098694 restraints weight = 17829.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100465 restraints weight = 12398.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.101592 restraints weight = 9831.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.102235 restraints weight = 8505.807| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17472 Z= 0.190 Angle : 0.714 8.848 24136 Z= 0.389 Chirality : 0.045 0.300 2636 Planarity : 0.005 0.066 2690 Dihedral : 22.790 158.614 3340 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.07 % Favored : 95.65 % Rotamer: Outliers : 4.55 % Allowed : 22.10 % Favored : 73.36 % 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 are not related in a simple way. whole: -0.86 (0.19), residues: 1794 helix: 0.52 (0.22), residues: 526 sheet: -0.29 (0.27), residues: 340 loop : -1.33 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 73 TYR 0.021 0.002 TYR A 500 PHE 0.022 0.002 PHE D 80 TRP 0.023 0.001 TRP A 538 HIS 0.005 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (17466) covalent geometry : angle 0.71387 / 0.39 (24136) hydrogen bonds : bond 0.04202 / 2.84 ( 688) hydrogen bonds : angle 5.32187 / 3.72 ( 1971) metal coordination : bond 0.00445 / 0.34 ( 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 295 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 223 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.8292 (mmm) cc_final: 0.7661 (mmm) REVERT: A 733 MET cc_start: 0.8282 (tpp) cc_final: 0.8045 (tpp) REVERT: A 799 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8644 (mtpt) REVERT: A 905 MET cc_start: 0.8893 (tpp) cc_final: 0.8617 (tpp) REVERT: A 984 GLU cc_start: 0.8541 (tp30) cc_final: 0.8182 (mm-30) REVERT: B 80 PHE cc_start: 0.7770 (t80) cc_final: 0.7512 (t80) REVERT: B 292 LEU cc_start: 0.7309 (pt) cc_final: 0.6833 (pp) REVERT: B 328 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8871 (tp) REVERT: C 526 GLU cc_start: 0.7877 (pm20) cc_final: 0.7353 (pm20) REVERT: C 594 MET cc_start: 0.8841 (mmp) cc_final: 0.8632 (mmt) REVERT: C 839 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7207 (mt0) REVERT: D 224 LEU cc_start: 0.7705 (mt) cc_final: 0.7335 (mt) REVERT: D 328 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8806 (tp) outliers start: 72 outliers final: 51 residues processed: 270 average time/residue: 0.1317 time to fit residues: 54.9037 Evaluate side-chains 254 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 622 MET Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 698 VAL 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 807 MET Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 97 THR 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 240 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 328 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 130 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 182 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 168 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 161 optimal weight: 0.0770 chunk 44 optimal weight: 4.9990 chunk 164 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.120959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096491 restraints weight = 32077.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099177 restraints weight = 17712.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100950 restraints weight = 12235.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.102048 restraints weight = 9714.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.102786 restraints weight = 8435.566| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17472 Z= 0.168 Angle : 0.693 11.185 24136 Z= 0.378 Chirality : 0.044 0.303 2636 Planarity : 0.005 0.068 2690 Dihedral : 22.714 159.711 3339 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.18 % Favored : 95.54 % Rotamer: Outliers : 4.99 % Allowed : 21.59 % 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 are not related in a simple way. whole: -0.72 (0.19), residues: 1794 helix: 0.69 (0.23), residues: 528 sheet: -0.20 (0.27), residues: 340 loop : -1.29 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 598 TYR 0.021 0.002 TYR A 500 PHE 0.021 0.001 PHE D 80 TRP 0.019 0.001 TRP C 978 HIS 0.005 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (17466) covalent geometry : angle 0.69293 / 0.38 (24136) hydrogen bonds : bond 0.03955 / 2.67 ( 688) hydrogen bonds : angle 5.17033 / 3.61 ( 1971) metal coordination : bond 0.00377 / 0.29 ( 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 300 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 221 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.8220 (mmm) cc_final: 0.7681 (mmm) REVERT: A 737 MET cc_start: 0.7888 (mmt) cc_final: 0.7593 (mmm) REVERT: A 799 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8609 (mtpt) REVERT: A 905 MET cc_start: 0.8847 (tpp) cc_final: 0.8570 (tpp) REVERT: A 909 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8951 (mt) REVERT: A 933 TYR cc_start: 0.7646 (t80) cc_final: 0.7199 (t80) REVERT: B 150 LYS cc_start: 0.8257 (tttp) cc_final: 0.7984 (tttp) REVERT: B 260 SER cc_start: 0.9362 (OUTLIER) cc_final: 0.9136 (p) REVERT: B 328 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8813 (tp) REVERT: C 526 GLU cc_start: 0.7850 (pm20) cc_final: 0.7240 (pm20) REVERT: C 710 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8213 (pt) REVERT: D 210 LEU cc_start: 0.8750 (mt) cc_final: 0.8444 (mp) REVERT: D 280 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7317 (tm-30) REVERT: D 328 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8818 (tp) outliers start: 79 outliers final: 53 residues processed: 274 average time/residue: 0.1284 time to fit residues: 54.8075 Evaluate side-chains 267 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 622 MET 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 846 GLU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 97 THR 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 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 528 GLU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain D residue 22 LEU 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 182 VAL 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: 0.9990 chunk 84 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 187 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 ASN A 687 HIS ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.121954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097925 restraints weight = 32141.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100626 restraints weight = 17664.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102462 restraints weight = 12102.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.103599 restraints weight = 9513.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.104323 restraints weight = 8214.436| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17472 Z= 0.148 Angle : 0.693 8.920 24136 Z= 0.375 Chirality : 0.044 0.298 2636 Planarity : 0.005 0.065 2690 Dihedral : 22.639 160.532 3337 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.24 % Favored : 95.48 % Rotamer: Outliers : 4.29 % Allowed : 22.03 % Favored : 73.67 % 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 are not related in a simple way. whole: -0.62 (0.19), residues: 1794 helix: 0.84 (0.23), residues: 528 sheet: -0.08 (0.28), residues: 330 loop : -1.29 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 852 TYR 0.018 0.002 TYR A 500 PHE 0.026 0.001 PHE B 80 TRP 0.012 0.001 TRP A 538 HIS 0.004 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (17466) covalent geometry : angle 0.69272 / 0.38 (24136) hydrogen bonds : bond 0.03818 / 2.55 ( 688) hydrogen bonds : angle 5.06562 / 3.54 ( 1971) metal coordination : bond 0.00240 / 0.19 ( 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 288 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 220 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.8139 (mmm) cc_final: 0.7614 (mmm) REVERT: A 799 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8562 (mtpt) REVERT: A 905 MET cc_start: 0.8807 (tpp) cc_final: 0.8534 (tpp) REVERT: A 909 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8955 (mt) REVERT: A 933 TYR cc_start: 0.7583 (t80) cc_final: 0.7197 (t80) REVERT: B 260 SER cc_start: 0.9355 (OUTLIER) cc_final: 0.9138 (p) REVERT: B 328 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8836 (tp) REVERT: C 500 TYR cc_start: 0.8906 (t80) cc_final: 0.8557 (t80) REVERT: C 526 GLU cc_start: 0.7732 (pm20) cc_final: 0.6955 (pt0) REVERT: C 710 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8308 (pt) REVERT: C 839 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7263 (mt0) REVERT: D 210 LEU cc_start: 0.8726 (mt) cc_final: 0.8446 (mp) REVERT: D 280 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7273 (tm-30) REVERT: D 328 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8793 (tp) outliers start: 68 outliers final: 48 residues processed: 265 average time/residue: 0.1252 time to fit residues: 52.1932 Evaluate side-chains 257 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 622 MET Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 48 VAL 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 240 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 292 LEU 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 528 GLU 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 710 ILE Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain D residue 22 LEU 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 182 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 153 optimal weight: 10.0000 chunk 99 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 687 HIS ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS C 492 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.121728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097547 restraints weight = 32381.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.100256 restraints weight = 17720.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102010 restraints weight = 12173.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103157 restraints weight = 9676.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.103756 restraints weight = 8363.205| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4616 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= 0.169 Angle : 0.694 9.060 24136 Z= 0.376 Chirality : 0.044 0.287 2636 Planarity : 0.005 0.068 2690 Dihedral : 22.622 161.443 3337 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.18 % Favored : 95.54 % Rotamer: Outliers : 4.80 % Allowed : 21.65 % Favored : 73.55 % 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 are not related in a simple way. whole: -0.55 (0.19), residues: 1794 helix: 0.91 (0.23), residues: 534 sheet: -0.08 (0.27), residues: 346 loop : -1.26 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 778 TYR 0.018 0.002 TYR A 933 PHE 0.020 0.002 PHE B 80 TRP 0.014 0.001 TRP A 538 HIS 0.005 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (17466) covalent geometry : angle 0.69398 / 0.38 (24136) hydrogen bonds : bond 0.03742 / 2.48 ( 688) hydrogen bonds : angle 4.99452 / 3.49 ( 1971) metal coordination : bond 0.00384 / 0.30 ( 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 295 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 219 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.8098 (mmm) cc_final: 0.7595 (mmm) REVERT: A 733 MET cc_start: 0.8568 (tpp) cc_final: 0.8365 (tpp) REVERT: A 799 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8593 (mtpt) REVERT: A 905 MET cc_start: 0.8810 (tpp) cc_final: 0.8559 (tpp) REVERT: A 909 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8990 (mt) REVERT: A 933 TYR cc_start: 0.7623 (t80) cc_final: 0.7151 (t80) REVERT: A 999 ARG cc_start: 0.8318 (tpp-160) cc_final: 0.8106 (tpp-160) REVERT: B 56 LYS cc_start: 0.8724 (mttp) cc_final: 0.8419 (mtpp) REVERT: B 260 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.9137 (p) REVERT: B 328 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8826 (tp) REVERT: C 526 GLU cc_start: 0.7856 (pm20) cc_final: 0.7224 (pm20) REVERT: C 710 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8220 (pt) REVERT: C 842 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7640 (p0) REVERT: D 210 LEU cc_start: 0.8728 (mt) cc_final: 0.8509 (mt) REVERT: D 280 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7275 (tm-30) REVERT: D 328 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8795 (tp) outliers start: 76 outliers final: 55 residues processed: 270 average time/residue: 0.1254 time to fit residues: 52.8642 Evaluate side-chains 267 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 205 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 716 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 909 LEU Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 97 THR 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 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 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 515 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 734 VAL 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 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 130 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 182 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 252 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 78 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 687 HIS ** A 964 HIS ** 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 = 0.3646 r_free = 0.3646 target = 0.120287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.095915 restraints weight = 32221.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098571 restraints weight = 17775.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.100327 restraints weight = 12299.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101433 restraints weight = 9780.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102131 restraints weight = 8504.993| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4684 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= 0.207 Angle : 0.711 9.027 24136 Z= 0.385 Chirality : 0.044 0.272 2636 Planarity : 0.005 0.068 2690 Dihedral : 22.643 162.254 3334 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.35 % Favored : 95.37 % Rotamer: Outliers : 4.48 % Allowed : 22.29 % Favored : 73.23 % 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 are not related in a simple way. whole: -0.62 (0.19), residues: 1794 helix: 0.86 (0.23), residues: 536 sheet: -0.21 (0.27), residues: 340 loop : -1.27 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 73 TYR 0.020 0.002 TYR C 933 PHE 0.019 0.002 PHE B 80 TRP 0.015 0.001 TRP A 538 HIS 0.007 0.001 HIS C 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (17466) covalent geometry : angle 0.71135 / 0.38 (24136) hydrogen bonds : bond 0.03872 / 2.57 ( 688) hydrogen bonds : angle 4.97115 / 3.47 ( 1971) metal coordination : bond 0.00570 / 0.43 ( 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 286 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 215 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.8112 (mmm) cc_final: 0.7597 (mmm) REVERT: A 799 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8621 (mtpt) REVERT: A 905 MET cc_start: 0.8793 (tpp) cc_final: 0.8544 (tpp) REVERT: A 909 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9057 (mt) REVERT: A 933 TYR cc_start: 0.7663 (t80) cc_final: 0.7153 (t80) REVERT: A 999 ARG cc_start: 0.8222 (tpp-160) cc_final: 0.7998 (tpp-160) REVERT: B 328 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8826 (tp) REVERT: C 526 GLU cc_start: 0.7991 (pm20) cc_final: 0.7474 (pm20) REVERT: C 594 MET cc_start: 0.8889 (mmp) cc_final: 0.8684 (mmt) REVERT: C 842 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7668 (p0) REVERT: D 280 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7309 (tm-30) REVERT: D 298 HIS cc_start: 0.7622 (m90) cc_final: 0.7374 (t70) REVERT: D 328 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8776 (tp) outliers start: 71 outliers final: 61 residues processed: 259 average time/residue: 0.1237 time to fit residues: 50.3729 Evaluate side-chains 272 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 206 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 716 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 885 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 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 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 292 LEU 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 515 ILE Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 734 VAL 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 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain C residue 1025 MET Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 130 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 182 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 252 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 184 optimal weight: 30.0000 chunk 74 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 189 optimal weight: 40.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 687 HIS ** A 964 HIS ** 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 = 0.3675 r_free = 0.3675 target = 0.122104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097905 restraints weight = 32035.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.100586 restraints weight = 17553.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102378 restraints weight = 12119.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.103525 restraints weight = 9596.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.104173 restraints weight = 8294.069| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17472 Z= 0.156 Angle : 0.697 9.767 24136 Z= 0.375 Chirality : 0.043 0.265 2636 Planarity : 0.005 0.070 2690 Dihedral : 22.531 163.258 3334 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.29 % Favored : 95.43 % Rotamer: Outliers : 4.10 % Allowed : 23.36 % Favored : 72.54 % 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 are not related in a simple way. whole: -0.54 (0.19), residues: 1794 helix: 0.96 (0.23), residues: 536 sheet: -0.05 (0.28), residues: 326 loop : -1.28 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 73 TYR 0.021 0.002 TYR C 500 PHE 0.020 0.001 PHE B 80 TRP 0.017 0.001 TRP A 538 HIS 0.004 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (17466) covalent geometry : angle 0.69723 / 0.38 (24136) hydrogen bonds : bond 0.03667 / 2.43 ( 688) hydrogen bonds : angle 4.89841 / 3.42 ( 1971) metal coordination : bond 0.00358 / 0.26 ( 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 287 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 222 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.8064 (mmm) cc_final: 0.7778 (mmm) REVERT: A 799 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8596 (mtpt) REVERT: A 905 MET cc_start: 0.8724 (tpp) cc_final: 0.8482 (tpp) REVERT: A 933 TYR cc_start: 0.7574 (t80) cc_final: 0.7111 (t80) REVERT: B 146 ASN cc_start: 0.8401 (t0) cc_final: 0.8128 (m-40) REVERT: B 328 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8835 (tp) REVERT: C 526 GLU cc_start: 0.7765 (pm20) cc_final: 0.7338 (pm20) REVERT: C 701 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8770 (mtm110) REVERT: C 842 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7649 (p0) REVERT: D 204 GLN cc_start: 0.7893 (pt0) cc_final: 0.7599 (pt0) REVERT: D 210 LEU cc_start: 0.8741 (mt) cc_final: 0.8456 (mt) REVERT: D 233 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7774 (tp) REVERT: D 280 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7298 (tm-30) REVERT: D 298 HIS cc_start: 0.7572 (m90) cc_final: 0.7370 (t70) REVERT: D 328 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8763 (tp) outliers start: 65 outliers final: 51 residues processed: 261 average time/residue: 0.1227 time to fit residues: 50.3104 Evaluate side-chains 264 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 716 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 807 MET Chi-restraints excluded: chain A residue 847 GLU 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 97 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 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 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 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 734 VAL 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 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 1025 MET Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 130 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 182 VAL Chi-restraints excluded: chain D residue 233 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 40 optimal weight: 0.0020 chunk 126 optimal weight: 0.5980 chunk 177 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 146 optimal weight: 0.2980 chunk 156 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS D 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.121718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097653 restraints weight = 32231.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.100360 restraints weight = 17694.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102135 restraints weight = 12165.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103246 restraints weight = 9654.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.103951 restraints weight = 8355.582| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17472 Z= 0.162 Angle : 0.694 11.675 24136 Z= 0.374 Chirality : 0.043 0.257 2636 Planarity : 0.005 0.070 2690 Dihedral : 22.509 163.760 3334 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.24 % Favored : 95.48 % Rotamer: Outliers : 3.72 % Allowed : 24.43 % Favored : 71.84 % 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 are not related in a simple way. whole: -0.52 (0.19), residues: 1794 helix: 0.95 (0.23), residues: 538 sheet: -0.00 (0.28), residues: 340 loop : -1.28 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 232 TYR 0.021 0.002 TYR C 933 PHE 0.021 0.001 PHE D 80 TRP 0.017 0.001 TRP A 538 HIS 0.004 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (17466) covalent geometry : angle 0.69379 / 0.37 (24136) hydrogen bonds : bond 0.03641 / 2.41 ( 688) hydrogen bonds : angle 4.86679 / 3.40 ( 1971) metal coordination : bond 0.00424 / 0.31 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2663.72 seconds wall clock time: 47 minutes 21.53 seconds (2841.53 seconds total)