Starting phenix.real_space_refine on Thu Jun 26 04:26:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jby_6488/06_2025/3jby_6488.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jby_6488/06_2025/3jby_6488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jby_6488/06_2025/3jby_6488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jby_6488/06_2025/3jby_6488.map" model { file = "/net/cci-nas-00/data/ceres_data/3jby_6488/06_2025/3jby_6488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jby_6488/06_2025/3jby_6488.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.64, per 1000 atoms: 0.57 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: 4.51 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 5.72 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: 7.11 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2888 1.32 - 1.45: 6125 1.45 - 1.59: 8094 1.59 - 1.72: 201 1.72 - 1.86: 158 Bond restraints: 17466 Sorted by residual: bond pdb=" CA PRO D 339 " pdb=" C PRO D 339 " ideal model delta sigma weight residual 1.517 1.576 -0.059 9.30e-03 1.16e+04 4.03e+01 bond pdb=" C1' DG F 15 " pdb=" N9 DG F 15 " ideal model delta sigma weight residual 1.460 1.342 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" CA PRO B 339 " pdb=" C PRO B 339 " ideal model delta sigma weight residual 1.517 1.568 -0.051 9.30e-03 1.16e+04 2.97e+01 bond pdb=" C SER A 985 " pdb=" N GLY A 986 " ideal model delta sigma weight residual 1.333 1.402 -0.070 1.31e-02 5.83e+03 2.83e+01 bond pdb=" CA ASN C 983 " pdb=" C ASN C 983 " ideal model delta sigma weight residual 1.525 1.479 0.046 1.02e-02 9.61e+03 2.02e+01 ... (remaining 17461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 22428 2.74 - 5.48: 1386 5.48 - 8.23: 241 8.23 - 10.97: 65 10.97 - 13.71: 16 Bond angle restraints: 24136 Sorted by residual: angle pdb=" N PRO D 339 " pdb=" CA PRO D 339 " pdb=" C PRO D 339 " ideal model delta sigma weight residual 110.70 121.88 -11.18 1.22e+00 6.72e-01 8.40e+01 angle pdb=" N ARG A 999 " pdb=" CA ARG A 999 " pdb=" C ARG A 999 " ideal model delta sigma weight residual 111.14 120.34 -9.20 1.08e+00 8.57e-01 7.26e+01 angle pdb=" C THR D 338 " pdb=" N PRO D 339 " pdb=" CA PRO D 339 " ideal model delta sigma weight residual 120.38 128.86 -8.48 1.03e+00 9.43e-01 6.77e+01 angle pdb=" N PRO B 339 " pdb=" CA PRO B 339 " pdb=" C PRO B 339 " ideal model delta sigma weight residual 110.70 120.21 -9.51 1.22e+00 6.72e-01 6.07e+01 angle pdb=" N ARG C 999 " pdb=" CA ARG C 999 " pdb=" C ARG C 999 " ideal model delta sigma weight residual 111.40 119.25 -7.85 1.22e+00 6.72e-01 4.15e+01 ... (remaining 24131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.34: 9194 29.34 - 58.68: 948 58.68 - 88.02: 46 88.02 - 117.35: 6 117.35 - 146.69: 4 Dihedral angle restraints: 10198 sinusoidal: 4986 harmonic: 5212 Sorted by residual: dihedral pdb=" CA ASP A 658 " pdb=" C ASP A 658 " pdb=" N GLY A 659 " pdb=" CA GLY A 659 " ideal model delta harmonic sigma weight residual 180.00 137.23 42.77 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA ASP C 658 " pdb=" C ASP C 658 " pdb=" N GLY C 659 " pdb=" CA GLY C 659 " ideal model delta harmonic sigma weight residual 180.00 142.38 37.62 0 5.00e+00 4.00e-02 5.66e+01 dihedral pdb=" CA PHE A1004 " pdb=" C PHE A1004 " pdb=" N GLU A1005 " pdb=" CA GLU A1005 " ideal model delta harmonic sigma weight residual -180.00 -145.84 -34.16 0 5.00e+00 4.00e-02 4.67e+01 ... (remaining 10195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1802 0.065 - 0.129: 655 0.129 - 0.193: 152 0.193 - 0.258: 20 0.258 - 0.322: 7 Chirality restraints: 2636 Sorted by residual: chirality pdb=" CB ILE D 272 " pdb=" CA ILE D 272 " pdb=" CG1 ILE D 272 " pdb=" CG2 ILE D 272 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA THR C 493 " pdb=" N THR C 493 " pdb=" C THR C 493 " pdb=" CB THR C 493 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' DG H 7 " pdb=" C4' DG H 7 " pdb=" O3' DG H 7 " pdb=" C2' DG H 7 " both_signs ideal model delta sigma weight residual False -2.66 -2.37 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2633 not shown) Planarity restraints: 2690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG F 1 " 0.033 2.00e-02 2.50e+03 2.58e-02 1.99e+01 pdb=" N9 DG F 1 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DG F 1 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG F 1 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG F 1 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG F 1 " -0.046 2.00e-02 2.50e+03 pdb=" O6 DG F 1 " 0.047 2.00e-02 2.50e+03 pdb=" N1 DG F 1 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DG F 1 " -0.039 2.00e-02 2.50e+03 pdb=" N2 DG F 1 " 0.026 2.00e-02 2.50e+03 pdb=" N3 DG F 1 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG F 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG G 1 " 0.047 2.00e-02 2.50e+03 2.53e-02 1.92e+01 pdb=" N9 DG G 1 " -0.032 2.00e-02 2.50e+03 pdb=" C8 DG G 1 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG G 1 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG G 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG G 1 " -0.033 2.00e-02 2.50e+03 pdb=" O6 DG G 1 " 0.047 2.00e-02 2.50e+03 pdb=" N1 DG G 1 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG G 1 " -0.024 2.00e-02 2.50e+03 pdb=" N2 DG G 1 " 0.020 2.00e-02 2.50e+03 pdb=" N3 DG G 1 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DG G 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG G 15 " -0.057 2.00e-02 2.50e+03 2.23e-02 1.49e+01 pdb=" N9 DG G 15 " 0.037 2.00e-02 2.50e+03 pdb=" C8 DG G 15 " 0.020 2.00e-02 2.50e+03 pdb=" N7 DG G 15 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG G 15 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG G 15 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG G 15 " -0.026 2.00e-02 2.50e+03 pdb=" N1 DG G 15 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG G 15 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG G 15 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG G 15 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DG G 15 " 0.005 2.00e-02 2.50e+03 ... (remaining 2687 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 276 2.59 - 3.17: 15173 3.17 - 3.75: 27503 3.75 - 4.32: 37786 4.32 - 4.90: 59813 Nonbonded interactions: 140551 Sorted by model distance: nonbonded pdb=" NE2 GLN A 858 " pdb=" O ALA A 887 " model vdw 2.015 3.120 nonbonded pdb=" OE2 GLU C 981 " pdb=" N2 DG F 15 " model vdw 2.100 3.120 nonbonded pdb=" OG SER C 760 " pdb=" O ASP C 951 " model vdw 2.116 3.040 nonbonded pdb=" NZ LYS A 508 " pdb=" OP1 DG F 5 " model vdw 2.133 3.120 nonbonded pdb=" O3' DA J 16 " pdb="CA CA C1103 " model vdw 2.175 2.510 ... (remaining 140546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 46.080 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.313 17472 Z= 0.713 Angle : 1.574 13.709 24136 Z= 0.849 Chirality : 0.070 0.322 2636 Planarity : 0.009 0.090 2690 Dihedral : 20.891 146.691 6846 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 24.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.004 TRP B 172 HIS 0.019 0.004 HIS A1028 PHE 0.029 0.005 PHE C 576 TYR 0.037 0.005 TYR A 875 ARG 0.011 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.15553 ( 688) hydrogen bonds : angle 9.77255 ( 1971) metal coordination : bond 0.18046 ( 6) covalent geometry : bond 0.01518 (17466) covalent geometry : angle 1.57416 (24136) *********************** 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 : 1.551 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: 0.8849 (tpp) REVERT: B 186 ASP cc_start: 0.7657 (t0) cc_final: 0.7446 (t0) REVERT: B 189 PHE cc_start: 0.7109 (m-80) cc_final: 0.6524 (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: 0.6773 (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: 0.7758 (mtp180) REVERT: C 674 CYS cc_start: 0.7769 (t) cc_final: 0.7279 (p) REVERT: C 737 MET cc_start: 0.7764 (mtm) cc_final: 0.7481 (ptp) REVERT: C 778 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8401 (mtt180) REVERT: C 806 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7549 (p90) REVERT: D 186 ASP cc_start: 0.7474 (t0) cc_final: 0.6828 (m-30) REVERT: D 192 CYS cc_start: 0.7917 (m) cc_final: 0.7619 (t) outliers start: 91 outliers final: 22 residues processed: 510 average time/residue: 0.3301 time to fit residues: 240.5638 Evaluate side-chains 277 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 250 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 160 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 HIS A 766 HIS A 910 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 278 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 HIS ** C 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 687 HIS C 766 HIS C 831 GLN C 910 GLN C 937 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.118803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.094054 restraints weight = 32176.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096742 restraints weight = 17508.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098488 restraints weight = 11953.883| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17472 Z= 0.222 Angle : 0.779 8.581 24136 Z= 0.426 Chirality : 0.046 0.264 2636 Planarity : 0.006 0.078 2690 Dihedral : 22.982 155.243 3377 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.95 % Favored : 96.93 % Rotamer: Outliers : 5.11 % Allowed : 19.19 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.17), residues: 1794 helix: -1.00 (0.20), residues: 540 sheet: -0.42 (0.26), residues: 326 loop : -1.67 (0.16), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 538 HIS 0.006 0.001 HIS A1013 PHE 0.014 0.002 PHE D 274 TYR 0.025 0.002 TYR A 933 ARG 0.007 0.001 ARG A 850 Details of bonding type rmsd hydrogen bonds : bond 0.04891 ( 688) hydrogen bonds : angle 5.88113 ( 1971) metal coordination : bond 0.01375 ( 6) covalent geometry : bond 0.00492 (17466) covalent geometry : angle 0.77933 (24136) *********************** 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 385 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 304 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 799 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8685 (mtpt) REVERT: A 974 SER cc_start: 0.7300 (OUTLIER) cc_final: 0.6973 (m) REVERT: B 66 SER cc_start: 0.8899 (p) cc_final: 0.8663 (t) REVERT: B 177 ASP cc_start: 0.8614 (m-30) cc_final: 0.8412 (m-30) REVERT: B 186 ASP cc_start: 0.7239 (t0) cc_final: 0.7028 (t0) REVERT: B 189 PHE cc_start: 0.6740 (m-80) cc_final: 0.6356 (m-80) REVERT: B 210 LEU cc_start: 0.8978 (mt) cc_final: 0.8489 (mp) REVERT: C 705 MET cc_start: 0.8118 (mmm) cc_final: 0.7791 (mmm) REVERT: C 793 GLU cc_start: 0.7790 (mp0) cc_final: 0.7544 (mp0) REVERT: C 806 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7721 (p90) REVERT: C 863 MET cc_start: 0.7345 (mmm) cc_final: 0.6919 (mmp) REVERT: D 33 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8059 (pt0) REVERT: D 258 ILE cc_start: 0.9021 (tp) cc_final: 0.8703 (pt) REVERT: D 317 TRP cc_start: 0.8537 (p-90) cc_final: 0.8276 (p-90) outliers start: 81 outliers final: 32 residues processed: 357 average time/residue: 0.2942 time to fit residues: 155.1269 Evaluate side-chains 258 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 1.583 ------------------------------------------------------------------------------- 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 648 SER Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 166 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 185 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN B 65 ASN C 524 ASN C 669 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.121900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097229 restraints weight = 31872.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.099919 restraints weight = 17778.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.101656 restraints weight = 12319.043| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 0.042 17472 Z= 0.184 Angle : 0.695 8.674 24136 Z= 0.380 Chirality : 0.043 0.282 2636 Planarity : 0.005 0.070 2690 Dihedral : 22.645 159.058 3344 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.62 % Favored : 96.15 % Rotamer: Outliers : 4.61 % Allowed : 20.83 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 1794 helix: 0.26 (0.22), residues: 524 sheet: -0.02 (0.27), residues: 316 loop : -1.42 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 538 HIS 0.008 0.001 HIS D 253 PHE 0.023 0.002 PHE B 62 TYR 0.022 0.002 TYR C 933 ARG 0.005 0.001 ARG A 701 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 688) hydrogen bonds : angle 5.38049 ( 1971) metal coordination : bond 0.00348 ( 6) covalent geometry : bond 0.00411 (17466) covalent geometry : angle 0.69522 (24136) *********************** 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 331 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 258 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 MET cc_start: 0.8546 (tpp) cc_final: 0.8195 (tpp) REVERT: A 736 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7886 (tt0) REVERT: A 799 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8590 (mtpt) REVERT: A 974 SER cc_start: 0.7418 (OUTLIER) cc_final: 0.7139 (m) REVERT: B 38 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7612 (mmtm) REVERT: B 119 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7612 (ttmm) REVERT: B 177 ASP cc_start: 0.8525 (m-30) cc_final: 0.8248 (m-30) REVERT: B 224 LEU cc_start: 0.8031 (mt) cc_final: 0.7827 (mt) REVERT: B 260 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.9089 (p) REVERT: B 292 LEU cc_start: 0.7338 (pt) cc_final: 0.6854 (pp) REVERT: B 328 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8901 (tp) REVERT: C 516 PHE cc_start: 0.8875 (m-80) cc_final: 0.8595 (m-80) REVERT: C 526 GLU cc_start: 0.7784 (pm20) cc_final: 0.7139 (pt0) REVERT: C 594 MET cc_start: 0.8872 (mmp) cc_final: 0.8641 (mmt) REVERT: C 641 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7874 (mtp180) REVERT: C 839 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7169 (mt0) REVERT: C 863 MET cc_start: 0.7168 (mmm) cc_final: 0.6898 (mmp) REVERT: C 889 CYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8685 (p) REVERT: C 947 LYS cc_start: 0.7988 (tppt) cc_final: 0.7731 (tppt) REVERT: D 21 LEU cc_start: 0.9165 (mt) cc_final: 0.8274 (tp) REVERT: D 119 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7944 (mmtm) REVERT: D 258 ILE cc_start: 0.8908 (tp) cc_final: 0.8683 (pt) REVERT: D 285 MET cc_start: 0.7960 (mmm) cc_final: 0.7757 (mmm) REVERT: D 317 TRP cc_start: 0.8445 (p-90) cc_final: 0.8227 (p-90) outliers start: 73 outliers final: 39 residues processed: 302 average time/residue: 0.2992 time to fit residues: 134.7239 Evaluate side-chains 256 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 572 ILE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 799 LYS 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 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 260 SER 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 716 LEU 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 869 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 889 CYS Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 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 111 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 ASN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.122753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098351 restraints weight = 32211.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101062 restraints weight = 17738.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.102844 restraints weight = 12215.986| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17472 Z= 0.161 Angle : 0.659 9.000 24136 Z= 0.358 Chirality : 0.041 0.281 2636 Planarity : 0.005 0.077 2690 Dihedral : 22.544 160.433 3339 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.29 % Favored : 96.49 % Rotamer: Outliers : 4.80 % Allowed : 21.02 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.19), residues: 1794 helix: 0.71 (0.22), residues: 530 sheet: 0.10 (0.28), residues: 314 loop : -1.35 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 538 HIS 0.011 0.001 HIS D 253 PHE 0.019 0.001 PHE D 80 TYR 0.019 0.002 TYR A 933 ARG 0.004 0.000 ARG A 701 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 688) hydrogen bonds : angle 5.08720 ( 1971) metal coordination : bond 0.00309 ( 6) covalent geometry : bond 0.00358 (17466) covalent geometry : angle 0.65894 (24136) *********************** 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 326 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 250 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7816 (ptm) REVERT: A 705 MET cc_start: 0.8127 (mmm) cc_final: 0.7511 (mmm) REVERT: A 905 MET cc_start: 0.8809 (tpp) cc_final: 0.8503 (tpp) REVERT: A 933 TYR cc_start: 0.7592 (t80) cc_final: 0.7244 (t80) REVERT: A 947 LYS cc_start: 0.8060 (tppt) cc_final: 0.7816 (tppt) REVERT: A 974 SER cc_start: 0.7303 (OUTLIER) cc_final: 0.7081 (m) REVERT: B 200 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8175 (pp) REVERT: B 260 SER cc_start: 0.9336 (OUTLIER) cc_final: 0.9105 (p) REVERT: B 292 LEU cc_start: 0.7270 (pt) cc_final: 0.6849 (pp) REVERT: B 328 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8808 (tp) REVERT: C 526 GLU cc_start: 0.7630 (pm20) cc_final: 0.6985 (pt0) REVERT: C 839 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7237 (mt0) REVERT: C 902 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8264 (mt) REVERT: D 328 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8847 (tp) outliers start: 76 outliers final: 46 residues processed: 292 average time/residue: 0.3989 time to fit residues: 177.7808 Evaluate side-chains 256 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 572 ILE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 3 LEU 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 200 LEU 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 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 590 GLU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 238 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 131 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** 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 = 0.3681 r_free = 0.3681 target = 0.122610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.098387 restraints weight = 32442.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.101138 restraints weight = 17704.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.102947 restraints weight = 12105.005| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17472 Z= 0.164 Angle : 0.650 8.898 24136 Z= 0.352 Chirality : 0.041 0.287 2636 Planarity : 0.005 0.072 2690 Dihedral : 22.470 162.018 3336 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.62 % Favored : 96.15 % Rotamer: Outliers : 5.30 % Allowed : 21.09 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 1794 helix: 0.97 (0.23), residues: 532 sheet: 0.09 (0.27), residues: 328 loop : -1.27 (0.18), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 538 HIS 0.008 0.001 HIS B 269 PHE 0.018 0.001 PHE D 80 TYR 0.023 0.002 TYR A 500 ARG 0.006 0.000 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 688) hydrogen bonds : angle 4.91139 ( 1971) metal coordination : bond 0.00388 ( 6) covalent geometry : bond 0.00366 (17466) covalent geometry : angle 0.64996 (24136) *********************** 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 309 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 225 time to evaluate : 4.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.8084 (mmm) cc_final: 0.7495 (mmm) REVERT: A 792 ASP cc_start: 0.7789 (t0) cc_final: 0.7582 (t0) REVERT: A 799 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8504 (mtpt) REVERT: A 902 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8774 (mt) REVERT: A 905 MET cc_start: 0.8808 (tpp) cc_final: 0.8513 (tpp) REVERT: A 933 TYR cc_start: 0.7634 (t80) cc_final: 0.7165 (t80) REVERT: B 80 PHE cc_start: 0.7939 (t80) cc_final: 0.7606 (t80) REVERT: B 167 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7985 (mmm160) REVERT: B 210 LEU cc_start: 0.8817 (mt) cc_final: 0.8595 (mp) REVERT: B 260 SER cc_start: 0.9337 (OUTLIER) cc_final: 0.9137 (p) REVERT: B 328 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8846 (tp) REVERT: C 526 GLU cc_start: 0.7765 (pm20) cc_final: 0.7100 (pm20) REVERT: C 537 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7126 (tm-30) REVERT: C 650 SER cc_start: 0.9378 (p) cc_final: 0.9062 (t) REVERT: C 705 MET cc_start: 0.8110 (mmm) cc_final: 0.7697 (mmm) REVERT: C 737 MET cc_start: 0.7201 (mtp) cc_final: 0.6721 (mtp) REVERT: C 824 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8974 (t) REVERT: D 210 LEU cc_start: 0.8760 (mt) cc_final: 0.8485 (mt) REVERT: D 280 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7328 (tm-30) REVERT: D 328 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8840 (tp) outliers start: 84 outliers final: 53 residues processed: 273 average time/residue: 0.3784 time to fit residues: 161.4954 Evaluate side-chains 265 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 205 time to evaluate : 3.746 ------------------------------------------------------------------------------- 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 497 CYS Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 328 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 134 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.119398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094949 restraints weight = 32475.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097644 restraints weight = 18037.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099404 restraints weight = 12419.768| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17472 Z= 0.239 Angle : 0.697 9.036 24136 Z= 0.376 Chirality : 0.043 0.293 2636 Planarity : 0.005 0.075 2690 Dihedral : 22.610 163.269 3334 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.01 % Favored : 95.71 % Rotamer: Outliers : 5.49 % Allowed : 20.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 1794 helix: 0.77 (0.22), residues: 548 sheet: -0.13 (0.28), residues: 322 loop : -1.26 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 538 HIS 0.007 0.001 HIS A1013 PHE 0.017 0.002 PHE D 80 TYR 0.020 0.002 TYR C 504 ARG 0.004 0.001 ARG A 991 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 688) hydrogen bonds : angle 4.95210 ( 1971) metal coordination : bond 0.00727 ( 6) covalent geometry : bond 0.00542 (17466) covalent geometry : angle 0.69686 (24136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 212 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.8032 (mmm) cc_final: 0.7479 (mmm) REVERT: A 799 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8458 (mtpt) REVERT: A 902 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8805 (mt) REVERT: A 905 MET cc_start: 0.8836 (tpp) cc_final: 0.8606 (tpp) REVERT: A 933 TYR cc_start: 0.7716 (t80) cc_final: 0.7195 (t80) REVERT: B 80 PHE cc_start: 0.8017 (t80) cc_final: 0.7735 (t80) REVERT: B 90 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: B 119 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7718 (ttmt) REVERT: B 167 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8239 (tpt-90) REVERT: B 328 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8802 (tp) REVERT: C 705 MET cc_start: 0.8116 (mmm) cc_final: 0.7715 (mmm) REVERT: C 842 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7672 (p0) REVERT: C 902 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8353 (mt) REVERT: D 280 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7434 (tm-30) REVERT: D 285 MET cc_start: 0.7703 (mmm) cc_final: 0.7394 (mmm) REVERT: D 328 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8779 (tp) outliers start: 87 outliers final: 58 residues processed: 269 average time/residue: 0.2810 time to fit residues: 116.2278 Evaluate side-chains 269 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 203 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 731 GLU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 842 ASN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 883 GLU Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 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 94 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.122030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097727 restraints weight = 32169.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100459 restraints weight = 17730.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102243 restraints weight = 12185.816| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17472 Z= 0.160 Angle : 0.657 8.587 24136 Z= 0.354 Chirality : 0.041 0.295 2636 Planarity : 0.005 0.072 2690 Dihedral : 22.354 164.202 3334 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.96 % Favored : 95.76 % Rotamer: Outliers : 4.29 % Allowed : 23.04 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.19), residues: 1794 helix: 0.92 (0.23), residues: 548 sheet: 0.10 (0.28), residues: 314 loop : -1.28 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 538 HIS 0.006 0.001 HIS D 253 PHE 0.017 0.001 PHE D 80 TYR 0.020 0.002 TYR A 500 ARG 0.005 0.000 ARG A 991 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 688) hydrogen bonds : angle 4.81957 ( 1971) metal coordination : bond 0.00324 ( 6) covalent geometry : bond 0.00357 (17466) covalent geometry : angle 0.65684 (24136) *********************** 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 290 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.8016 (mmm) cc_final: 0.7510 (mmm) REVERT: A 799 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8456 (mtpt) REVERT: A 902 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8719 (mt) REVERT: A 905 MET cc_start: 0.8743 (tpp) cc_final: 0.8515 (tpp) REVERT: A 933 TYR cc_start: 0.7672 (t80) cc_final: 0.7183 (t80) REVERT: B 80 PHE cc_start: 0.8027 (t80) cc_final: 0.7704 (t80) REVERT: B 119 LYS cc_start: 0.7839 (ttpt) cc_final: 0.7565 (ttmt) REVERT: B 260 SER cc_start: 0.9372 (OUTLIER) cc_final: 0.9157 (p) REVERT: B 328 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8830 (tp) REVERT: C 824 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8957 (t) REVERT: C 842 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7653 (p0) REVERT: C 902 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8308 (mt) REVERT: D 280 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7448 (tm-30) REVERT: D 328 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8844 (tp) outliers start: 68 outliers final: 48 residues processed: 260 average time/residue: 0.3427 time to fit residues: 138.5584 Evaluate side-chains 263 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 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 885 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 842 ASN Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 328 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 1 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 111 optimal weight: 6.9990 chunk 86 optimal weight: 0.0970 chunk 150 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN D 99 ASN D 237 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.120684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.095739 restraints weight = 32740.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098600 restraints weight = 17175.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100496 restraints weight = 11536.081| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17472 Z= 0.141 Angle : 0.643 9.340 24136 Z= 0.346 Chirality : 0.040 0.296 2636 Planarity : 0.005 0.072 2690 Dihedral : 22.157 165.509 3333 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.01 % Favored : 95.71 % Rotamer: Outliers : 3.98 % Allowed : 23.55 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 1794 helix: 1.03 (0.23), residues: 546 sheet: 0.13 (0.28), residues: 340 loop : -1.22 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 538 HIS 0.005 0.001 HIS D 253 PHE 0.015 0.001 PHE D 80 TYR 0.024 0.002 TYR C 933 ARG 0.005 0.000 ARG A 991 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 688) hydrogen bonds : angle 4.70083 ( 1971) metal coordination : bond 0.00206 ( 6) covalent geometry : bond 0.00311 (17466) covalent geometry : angle 0.64288 (24136) *********************** 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 293 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 230 time to evaluate : 3.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 ASP cc_start: 0.7926 (m-30) cc_final: 0.7708 (t0) REVERT: A 705 MET cc_start: 0.8219 (mmm) cc_final: 0.7817 (mmm) REVERT: A 799 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8388 (mtpt) REVERT: A 905 MET cc_start: 0.8696 (tpp) cc_final: 0.8429 (tpp) REVERT: B 80 PHE cc_start: 0.8160 (t80) cc_final: 0.7613 (t80) REVERT: B 90 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: B 119 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7551 (ttmt) REVERT: B 210 LEU cc_start: 0.9027 (mt) cc_final: 0.8750 (mp) REVERT: B 328 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8881 (tp) REVERT: C 622 MET cc_start: 0.8609 (ptm) cc_final: 0.8349 (ptp) REVERT: C 705 MET cc_start: 0.8155 (mmm) cc_final: 0.7852 (mmm) REVERT: C 842 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7661 (p0) REVERT: D 204 GLN cc_start: 0.7972 (pt0) cc_final: 0.7678 (pt0) REVERT: D 210 LEU cc_start: 0.8851 (mt) cc_final: 0.8475 (mt) REVERT: D 260 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8809 (p) REVERT: D 280 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7493 (tm-30) REVERT: D 285 MET cc_start: 0.7703 (mmm) cc_final: 0.7385 (mmm) outliers start: 63 outliers final: 37 residues processed: 270 average time/residue: 0.4721 time to fit residues: 200.5738 Evaluate side-chains 249 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 97 THR 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 189 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 842 ASN Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 140 optimal weight: 7.9990 chunk 58 optimal weight: 0.0980 chunk 79 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 172 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN ** D 99 ASN ** 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 = 0.3618 r_free = 0.3618 target = 0.119508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.094538 restraints weight = 33193.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097364 restraints weight = 17471.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099219 restraints weight = 11739.380| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17472 Z= 0.162 Angle : 0.652 9.228 24136 Z= 0.350 Chirality : 0.041 0.285 2636 Planarity : 0.005 0.071 2690 Dihedral : 22.154 165.795 3333 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.96 % Favored : 95.76 % Rotamer: Outliers : 3.41 % Allowed : 24.24 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1794 helix: 1.03 (0.23), residues: 548 sheet: 0.19 (0.28), residues: 326 loop : -1.21 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 538 HIS 0.008 0.001 HIS D 253 PHE 0.018 0.001 PHE D 46 TYR 0.022 0.002 TYR C 933 ARG 0.005 0.000 ARG A 991 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 688) hydrogen bonds : angle 4.67183 ( 1971) metal coordination : bond 0.00412 ( 6) covalent geometry : bond 0.00365 (17466) covalent geometry : angle 0.65179 (24136) *********************** 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 272 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 3.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 ASP cc_start: 0.8022 (m-30) cc_final: 0.7807 (t0) REVERT: A 680 MET cc_start: 0.8110 (ptp) cc_final: 0.7898 (mtm) REVERT: A 705 MET cc_start: 0.8236 (mmm) cc_final: 0.7793 (mmm) REVERT: A 799 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8433 (mtpt) REVERT: A 905 MET cc_start: 0.8687 (tpp) cc_final: 0.8432 (tpp) REVERT: B 80 PHE cc_start: 0.8182 (t80) cc_final: 0.7643 (t80) REVERT: B 90 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7150 (m-80) REVERT: B 171 ASN cc_start: 0.8661 (t0) cc_final: 0.8456 (t0) REVERT: B 186 ASP cc_start: 0.6845 (t0) cc_final: 0.6408 (t0) REVERT: B 210 LEU cc_start: 0.9037 (mt) cc_final: 0.8765 (mp) REVERT: B 232 ARG cc_start: 0.8549 (tmm-80) cc_final: 0.8322 (tmm-80) REVERT: B 328 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8869 (tp) REVERT: C 622 MET cc_start: 0.8642 (ptm) cc_final: 0.8372 (ptp) REVERT: C 705 MET cc_start: 0.8198 (mmm) cc_final: 0.7914 (mmm) REVERT: C 737 MET cc_start: 0.7702 (mtp) cc_final: 0.7327 (ttm) REVERT: C 842 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7715 (p0) REVERT: D 204 GLN cc_start: 0.7911 (pt0) cc_final: 0.7609 (pt0) REVERT: D 210 LEU cc_start: 0.8898 (mt) cc_final: 0.8570 (mt) REVERT: D 260 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8766 (p) REVERT: D 280 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7493 (tm-30) REVERT: D 285 MET cc_start: 0.7750 (mmm) cc_final: 0.7498 (mmm) outliers start: 54 outliers final: 41 residues processed: 247 average time/residue: 0.3231 time to fit residues: 124.4296 Evaluate side-chains 260 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 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 955 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 666 GLN 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 974 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 91 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 102 optimal weight: 0.0770 chunk 132 optimal weight: 6.9990 chunk 58 optimal weight: 0.0570 chunk 106 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN D 83 GLN ** D 99 ASN ** 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 = 0.123225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.098535 restraints weight = 32921.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.101384 restraints weight = 17589.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103249 restraints weight = 11885.755| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17472 Z= 0.135 Angle : 0.646 10.697 24136 Z= 0.346 Chirality : 0.040 0.270 2636 Planarity : 0.005 0.071 2690 Dihedral : 21.927 167.034 3333 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.01 % Favored : 95.71 % Rotamer: Outliers : 2.53 % Allowed : 25.44 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1794 helix: 1.08 (0.23), residues: 546 sheet: 0.29 (0.28), residues: 336 loop : -1.18 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 538 HIS 0.005 0.001 HIS D 253 PHE 0.015 0.001 PHE D 80 TYR 0.023 0.001 TYR C 933 ARG 0.005 0.000 ARG B 232 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 688) hydrogen bonds : angle 4.63208 ( 1971) metal coordination : bond 0.00124 ( 6) covalent geometry : bond 0.00294 (17466) covalent geometry : angle 0.64557 (24136) ********************** 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 286 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 SER cc_start: 0.8935 (t) cc_final: 0.8731 (m) REVERT: A 680 MET cc_start: 0.8131 (ptp) cc_final: 0.7880 (mtm) REVERT: A 705 MET cc_start: 0.8188 (mmm) cc_final: 0.7775 (mmm) REVERT: A 799 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8368 (mtpt) REVERT: B 54 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7781 (mt-10) REVERT: B 80 PHE cc_start: 0.8051 (t80) cc_final: 0.7646 (t80) REVERT: B 90 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: B 119 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7491 (ttmt) REVERT: B 140 HIS cc_start: 0.8206 (p90) cc_final: 0.7863 (p-80) REVERT: B 197 LEU cc_start: 0.8402 (mp) cc_final: 0.8043 (tt) REVERT: B 210 LEU cc_start: 0.8933 (mt) cc_final: 0.8462 (mp) REVERT: B 292 LEU cc_start: 0.7635 (pt) cc_final: 0.7406 (mp) REVERT: C 622 MET cc_start: 0.8666 (ptm) cc_final: 0.8399 (ptp) REVERT: C 705 MET cc_start: 0.8154 (mmm) cc_final: 0.7838 (mmm) REVERT: C 842 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7618 (p0) REVERT: D 204 GLN cc_start: 0.7956 (pt0) cc_final: 0.7695 (pt0) REVERT: D 210 LEU cc_start: 0.8788 (mt) cc_final: 0.8435 (mt) REVERT: D 280 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7375 (tm-30) REVERT: D 285 MET cc_start: 0.7606 (mmm) cc_final: 0.7314 (mmm) outliers start: 40 outliers final: 33 residues processed: 264 average time/residue: 0.3799 time to fit residues: 152.5031 Evaluate side-chains 256 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 326 THR 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 565 ASP Chi-restraints excluded: chain C residue 666 GLN 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 985 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 271 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 90 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.121323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.096389 restraints weight = 32877.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.099239 restraints weight = 17365.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.101122 restraints weight = 11661.768| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.5482 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= 0.154 Angle : 0.659 9.654 24136 Z= 0.351 Chirality : 0.040 0.167 2636 Planarity : 0.005 0.071 2690 Dihedral : 21.953 166.935 3333 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.07 % Favored : 95.65 % Rotamer: Outliers : 2.46 % Allowed : 25.95 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1794 helix: 1.11 (0.23), residues: 546 sheet: 0.23 (0.28), residues: 326 loop : -1.17 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 538 HIS 0.004 0.001 HIS D 253 PHE 0.019 0.001 PHE D 80 TYR 0.027 0.002 TYR A 933 ARG 0.006 0.000 ARG C 897 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 688) hydrogen bonds : angle 4.62364 ( 1971) metal coordination : bond 0.00342 ( 6) covalent geometry : bond 0.00346 (17466) covalent geometry : angle 0.65912 (24136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6543.66 seconds wall clock time: 120 minutes 24.66 seconds (7224.66 seconds total)