Starting phenix.real_space_refine on Thu Aug 6 06:11:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iff_35415/08_2026/8iff_35415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iff_35415/08_2026/8iff_35415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iff_35415/08_2026/8iff_35415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iff_35415/08_2026/8iff_35415.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8iff_35415/08_2026/8iff_35415.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iff_35415/08_2026/8iff_35415.cif" model { file = "/net/cci-nas-00/data/ceres_data/8iff_35415/08_2026/8iff_35415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iff_35415/08_2026/8iff_35415.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 8705 2.51 5 N 2366 2.21 5 O 2523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13698 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6800 Classifications: {'peptide': 868} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 834} Chain breaks: 5 Chain: "B" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6812 Classifications: {'peptide': 868} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 834} Chain breaks: 5 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.85, per 1000 atoms: 0.21 Number of scatterers: 13698 At special positions: 0 Unit cell: (113.05, 122.4, 139.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 2523 8.00 N 2366 7.00 C 8705 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 417.1 milliseconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3264 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 17 sheets defined 39.2% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 134 through 146 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 196 through 202 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 218 through 235 removed outlier: 3.668A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 380 through 426 removed outlier: 3.970A pdb=" N LYS A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.870A pdb=" N GLN A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 Processing helix chain 'A' and resid 464 through 467 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.554A pdb=" N ALA A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 494' Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.540A pdb=" N LEU A 501 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 502 " --> pdb=" O LEU A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 502' Processing helix chain 'A' and resid 570 through 588 removed outlier: 4.088A pdb=" N ILE A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 789 through 794 removed outlier: 4.159A pdb=" N ILE A 794 " --> pdb=" O GLU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 828 Processing helix chain 'A' and resid 876 through 922 removed outlier: 3.780A pdb=" N ARG A 896 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 899 " --> pdb=" O LYS A 895 " (cutoff:3.500A) Proline residue: A 910 - end of helix Processing helix chain 'A' and resid 927 through 948 Processing helix chain 'A' and resid 969 through 980 removed outlier: 4.364A pdb=" N VAL A 973 " --> pdb=" O THR A 969 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 988 removed outlier: 3.528A pdb=" N SER A 985 " --> pdb=" O VAL A 981 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1015 removed outlier: 4.133A pdb=" N VAL A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1026 removed outlier: 3.634A pdb=" N PHE A1019 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET A1020 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET A1022 " --> pdb=" O PHE A1019 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A1024 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A1026 " --> pdb=" O ALA A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1070 Processing helix chain 'A' and resid 1080 through 1082 No H-bonds generated for 'chain 'A' and resid 1080 through 1082' Processing helix chain 'A' and resid 1083 through 1095 removed outlier: 3.825A pdb=" N MET A1087 " --> pdb=" O GLY A1083 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.806A pdb=" N LYS B 76 " --> pdb=" O HIS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 removed outlier: 4.143A pdb=" N GLU B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.641A pdb=" N SER B 131 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 132 " --> pdb=" O ILE B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 134 through 146 Processing helix chain 'B' and resid 149 through 153 removed outlier: 4.081A pdb=" N LEU B 152 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 219 through 235 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 321 through 331 removed outlier: 3.767A pdb=" N MET B 331 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 401 Processing helix chain 'B' and resid 402 through 414 removed outlier: 3.600A pdb=" N ASN B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.657A pdb=" N VAL B 433 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 442 Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'B' and resid 489 through 494 removed outlier: 3.710A pdb=" N ALA B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 removed outlier: 4.428A pdb=" N LEU B 501 " --> pdb=" O ARG B 497 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 497 through 502' Processing helix chain 'B' and resid 570 through 588 removed outlier: 3.939A pdb=" N ILE B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 787 Processing helix chain 'B' and resid 820 through 832 removed outlier: 3.601A pdb=" N VAL B 824 " --> pdb=" O ASN B 820 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 826 " --> pdb=" O GLY B 822 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 922 removed outlier: 3.619A pdb=" N ALA B 889 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR B 892 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 899 " --> pdb=" O LYS B 895 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS B 904 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) Proline residue: B 910 - end of helix Processing helix chain 'B' and resid 927 through 948 removed outlier: 3.900A pdb=" N GLN B 943 " --> pdb=" O LEU B 939 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU B 944 " --> pdb=" O CYS B 940 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 945 " --> pdb=" O GLN B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 980 removed outlier: 3.839A pdb=" N THR B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1002 removed outlier: 4.002A pdb=" N MET B1001 " --> pdb=" O GLY B 997 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B1002 " --> pdb=" O GLU B 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 997 through 1002' Processing helix chain 'B' and resid 1011 through 1017 Processing helix chain 'B' and resid 1018 through 1020 No H-bonds generated for 'chain 'B' and resid 1018 through 1020' Processing helix chain 'B' and resid 1021 through 1026 removed outlier: 3.688A pdb=" N ASN B1025 " --> pdb=" O LEU B1021 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B1026 " --> pdb=" O MET B1022 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1021 through 1026' Processing helix chain 'B' and resid 1065 through 1073 removed outlier: 3.547A pdb=" N GLN B1071 " --> pdb=" O PHE B1067 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET B1072 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B1073 " --> pdb=" O LEU B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1095 removed outlier: 3.740A pdb=" N LEU B1095 " --> pdb=" O LYS B1091 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 98 removed outlier: 6.658A pdb=" N ALA A 88 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 269 removed outlier: 3.541A pdb=" N GLY A 250 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA A 241 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU A 255 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A 239 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TRP A 366 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 341 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 368 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N MET A 339 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL A 370 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 337 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N HIS A 372 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA A 335 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 455 through 460 Processing sheet with id=AA4, first strand: chain 'A' and resid 775 through 778 removed outlier: 6.306A pdb=" N GLY A 768 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP A 778 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 766 " --> pdb=" O TRP A 778 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 867 " --> pdb=" O LYS A 858 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 803 through 804 removed outlier: 3.759A pdb=" N GLY A 804 " --> pdb=" O CYS A 810 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1035 through 1037 removed outlier: 4.259A pdb=" N SER A1110 " --> pdb=" O LEU A1103 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A1103 " --> pdb=" O SER A1110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1040 through 1042 removed outlier: 4.040A pdb=" N HIS A1049 " --> pdb=" O ALA A1119 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A1117 " --> pdb=" O ALA A1051 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 80 removed outlier: 6.497A pdb=" N ALA B 88 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR B 99 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 86 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 182 " --> pdb=" O CYS B 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 256 through 257 removed outlier: 3.676A pdb=" N GLY B 250 " --> pdb=" O TYR B 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 256 through 257 removed outlier: 6.831A pdb=" N TRP B 366 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 341 " --> pdb=" O TRP B 366 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU B 368 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET B 339 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL B 370 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 337 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N HIS B 372 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA B 335 " --> pdb=" O HIS B 372 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 459 through 460 removed outlier: 3.502A pdb=" N ALA B 448 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY B 484 " --> pdb=" O LYS B 744 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 529 through 531 removed outlier: 3.913A pdb=" N VAL B 530 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 559 " --> pdb=" O VAL B 530 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 775 through 778 removed outlier: 6.509A pdb=" N GLY B 768 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP B 778 " --> pdb=" O ILE B 766 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE B 766 " --> pdb=" O TRP B 778 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 867 " --> pdb=" O LYS B 858 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 858 " --> pdb=" O GLY B 867 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 967 through 969 Processing sheet with id=AB6, first strand: chain 'B' and resid 991 through 992 removed outlier: 7.408A pdb=" N ARG B 991 " --> pdb=" O LEU B1033 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 1035 through 1042 removed outlier: 3.592A pdb=" N LEU B1057 " --> pdb=" O PHE B1111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1035 through 1042 removed outlier: 4.166A pdb=" N HIS B1049 " --> pdb=" O ALA B1119 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1629 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3046 1.33 - 1.45: 2848 1.45 - 1.57: 7890 1.57 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 13952 Sorted by residual: bond pdb=" CAP O6E B1201 " pdb=" CBL O6E B1201 " ideal model delta sigma weight residual 1.448 1.363 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" CAP O6E A1201 " pdb=" CBL O6E A1201 " ideal model delta sigma weight residual 1.448 1.363 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CAB O6E B1201 " pdb=" CBI O6E B1201 " ideal model delta sigma weight residual 1.449 1.372 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" CAB O6E A1201 " pdb=" CBI O6E A1201 " ideal model delta sigma weight residual 1.449 1.383 0.066 2.00e-02 2.50e+03 1.07e+01 bond pdb=" CBC O6E A1201 " pdb=" CBI O6E A1201 " ideal model delta sigma weight residual 1.357 1.410 -0.053 2.00e-02 2.50e+03 7.02e+00 ... (remaining 13947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 18520 2.10 - 4.20: 275 4.20 - 6.30: 35 6.30 - 8.40: 6 8.40 - 10.50: 3 Bond angle restraints: 18839 Sorted by residual: angle pdb=" CA LYS A 807 " pdb=" CB LYS A 807 " pdb=" CG LYS A 807 " ideal model delta sigma weight residual 114.10 120.57 -6.47 2.00e+00 2.50e-01 1.05e+01 angle pdb=" N ASN A 758 " pdb=" CA ASN A 758 " pdb=" C ASN A 758 " ideal model delta sigma weight residual 109.81 102.75 7.06 2.21e+00 2.05e-01 1.02e+01 angle pdb=" C ALA A 938 " pdb=" N LEU A 939 " pdb=" CA LEU A 939 " ideal model delta sigma weight residual 121.14 115.76 5.38 1.75e+00 3.27e-01 9.45e+00 angle pdb=" CA LEU A 939 " pdb=" CB LEU A 939 " pdb=" CG LEU A 939 " ideal model delta sigma weight residual 116.30 126.80 -10.50 3.50e+00 8.16e-02 9.00e+00 angle pdb=" CA LYS A 807 " pdb=" C LYS A 807 " pdb=" N SER A 808 " ideal model delta sigma weight residual 118.30 114.64 3.66 1.26e+00 6.30e-01 8.44e+00 ... (remaining 18834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7133 18.00 - 36.01: 985 36.01 - 54.01: 284 54.01 - 72.01: 47 72.01 - 90.02: 22 Dihedral angle restraints: 8471 sinusoidal: 3447 harmonic: 5024 Sorted by residual: dihedral pdb=" CA THR A 969 " pdb=" C THR A 969 " pdb=" N LEU A 970 " pdb=" CA LEU A 970 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PHE A 871 " pdb=" C PHE A 871 " pdb=" N LEU A 872 " pdb=" CA LEU A 872 " ideal model delta harmonic sigma weight residual -180.00 -161.30 -18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASP A 441 " pdb=" CB ASP A 441 " pdb=" CG ASP A 441 " pdb=" OD1 ASP A 441 " ideal model delta sinusoidal sigma weight residual -30.00 -89.26 59.26 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 8468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1522 0.039 - 0.078: 463 0.078 - 0.117: 121 0.117 - 0.156: 38 0.156 - 0.195: 3 Chirality restraints: 2147 Sorted by residual: chirality pdb=" CBD O6E B1201 " pdb=" CAT O6E B1201 " pdb=" CAX O6E B1201 " pdb=" CBJ O6E B1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.50 -0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CBD O6E A1201 " pdb=" CAT O6E A1201 " pdb=" CAX O6E A1201 " pdb=" CBJ O6E A1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.52 -0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CG LEU B 267 " pdb=" CB LEU B 267 " pdb=" CD1 LEU B 267 " pdb=" CD2 LEU B 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 2144 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " 0.329 2.00e-02 2.50e+03 2.42e-01 1.47e+03 pdb=" CAP O6E B1201 " -0.118 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " -0.131 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " -0.191 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " -0.087 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " 0.080 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " 0.491 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " -0.063 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " -0.383 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " -0.337 2.00e-02 2.50e+03 2.00e-01 1.00e+03 pdb=" CAP O6E A1201 " 0.178 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " 0.172 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " 0.136 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " 0.080 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " -0.088 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " -0.409 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " 0.051 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " 0.128 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E A1201 " -0.051 2.00e-02 2.50e+03 1.72e-01 7.42e+02 pdb=" CAO O6E A1201 " -0.167 2.00e-02 2.50e+03 pdb=" CAP O6E A1201 " -0.295 2.00e-02 2.50e+03 pdb=" CAR O6E A1201 " 0.019 2.00e-02 2.50e+03 pdb=" CAV O6E A1201 " 0.079 2.00e-02 2.50e+03 pdb=" CBB O6E A1201 " 0.010 2.00e-02 2.50e+03 pdb=" CBH O6E A1201 " 0.024 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.043 2.00e-02 2.50e+03 pdb=" CBO O6E A1201 " -0.070 2.00e-02 2.50e+03 pdb=" NAE O6E A1201 " 0.407 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 359 2.70 - 3.25: 13044 3.25 - 3.80: 20343 3.80 - 4.35: 25515 4.35 - 4.90: 44201 Nonbonded interactions: 103462 Sorted by model distance: nonbonded pdb=" OG SER A 100 " pdb=" OD1 ASN A 102 " model vdw 2.153 3.040 nonbonded pdb=" O ASN A 909 " pdb=" OG SER A 912 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP A 90 " pdb=" OG1 THR A 93 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASN B 330 " pdb=" NE2 HIS B 549 " model vdw 2.256 3.120 nonbonded pdb=" N GLU A 262 " pdb=" OE1 GLU A 262 " model vdw 2.300 3.120 ... (remaining 103457 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 71 through 187 or resid 194 or resid 196 through 1201)) selection = (chain 'B' and (resid 71 through 187 or resid 195 through 1201)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.030 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.007 0.442 13954 Z= 0.554 Angle : 0.634 10.498 18839 Z= 0.322 Chirality : 0.042 0.195 2147 Planarity : 0.010 0.242 2400 Dihedral : 18.239 90.017 5207 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.27 % Allowed : 29.18 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.20), residues: 1712 helix: 1.28 (0.23), residues: 544 sheet: -0.05 (0.30), residues: 303 loop : -1.43 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 497 TYR 0.016 0.001 TYR A 242 PHE 0.019 0.002 PHE A 871 TRP 0.017 0.002 TRP B 366 HIS 0.006 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (13952) covalent geometry : angle 0.63369 / 0.32 (18839) hydrogen bonds : bond 0.12922 / 8.65 ( 582) hydrogen bonds : angle 6.24402 / 4.45 ( 1629) Misc. bond : bond 0.43781 / 21.95 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8051 (t) cc_final: 0.7653 (p) outliers start: 4 outliers final: 2 residues processed: 136 average time/residue: 0.0978 time to fit residues: 19.9975 Evaluate side-chains 132 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 532 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.3331 > 50:) chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.239611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148781 restraints weight = 15555.719| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 4.41 r_work: 0.3385 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 13954 Z= 0.272 Angle : 0.724 12.094 18839 Z= 0.362 Chirality : 0.047 0.270 2147 Planarity : 0.005 0.047 2400 Dihedral : 6.014 62.350 1878 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 6.26 % Allowed : 24.45 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1712 helix: 0.66 (0.22), residues: 566 sheet: -0.36 (0.29), residues: 332 loop : -1.47 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1090 TYR 0.020 0.002 TYR A 242 PHE 0.024 0.002 PHE A 520 TRP 0.023 0.003 TRP B 366 HIS 0.008 0.002 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.27 (13952) covalent geometry : angle 0.72403 / 0.36 (18839) hydrogen bonds : bond 0.06234 / 4.20 ( 582) hydrogen bonds : angle 5.46558 / 3.87 ( 1629) Misc. bond : bond 0.00150 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 145 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7825 (mmt180) cc_final: 0.7548 (mmt180) REVERT: A 224 ASP cc_start: 0.8157 (m-30) cc_final: 0.7739 (m-30) REVERT: A 265 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8020 (tt) REVERT: A 385 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8138 (t80) REVERT: A 497 ARG cc_start: 0.6979 (mtm110) cc_final: 0.6643 (mtm110) REVERT: A 508 MET cc_start: 0.8397 (ttm) cc_final: 0.8036 (ttm) REVERT: B 214 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7678 (mp) REVERT: B 912 SER cc_start: 0.6028 (OUTLIER) cc_final: 0.5755 (t) REVERT: B 915 MET cc_start: 0.3196 (mtm) cc_final: 0.2944 (tpp) REVERT: B 920 MET cc_start: 0.1814 (ptm) cc_final: 0.1443 (mtp) outliers start: 94 outliers final: 61 residues processed: 221 average time/residue: 0.0929 time to fit residues: 31.7142 Evaluate side-chains 203 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 138 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 912 SER Chi-restraints excluded: chain B residue 982 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 156 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 166 optimal weight: 50.0000 chunk 44 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS A 971 ASN B 245 HIS B 884 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.243841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.153828 restraints weight = 15590.756| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 4.09 r_work: 0.3509 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13954 Z= 0.125 Angle : 0.573 9.474 18839 Z= 0.285 Chirality : 0.041 0.144 2147 Planarity : 0.004 0.041 2400 Dihedral : 5.335 59.086 1878 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.26 % Allowed : 26.65 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.20), residues: 1712 helix: 1.08 (0.22), residues: 570 sheet: -0.03 (0.30), residues: 309 loop : -1.42 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1090 TYR 0.016 0.001 TYR B 752 PHE 0.017 0.001 PHE A 871 TRP 0.016 0.001 TRP B 366 HIS 0.004 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (13952) covalent geometry : angle 0.57344 / 0.29 (18839) hydrogen bonds : bond 0.04434 / 2.99 ( 582) hydrogen bonds : angle 4.92748 / 3.48 ( 1629) Misc. bond : bond 0.00154 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 140 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6092 (OUTLIER) cc_final: 0.5682 (m170) REVERT: A 128 ASP cc_start: 0.7786 (t0) cc_final: 0.7484 (t0) REVERT: A 130 ARG cc_start: 0.7750 (mmt180) cc_final: 0.7502 (mmt180) REVERT: A 224 ASP cc_start: 0.8142 (m-30) cc_final: 0.7717 (m-30) REVERT: A 385 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.8132 (t80) REVERT: A 742 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6589 (ttt) REVERT: A 887 ARG cc_start: 0.7808 (ttp-110) cc_final: 0.7456 (ttm110) REVERT: B 325 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7172 (mm) REVERT: B 338 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8379 (t) REVERT: B 920 MET cc_start: 0.1976 (ptm) cc_final: 0.1575 (mtp) REVERT: B 1049 HIS cc_start: 0.0062 (OUTLIER) cc_final: -0.0708 (m170) outliers start: 64 outliers final: 43 residues processed: 187 average time/residue: 0.0967 time to fit residues: 27.5018 Evaluate side-chains 182 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1049 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 40 optimal weight: 0.0010 chunk 30 optimal weight: 0.4980 chunk 164 optimal weight: 0.0040 chunk 142 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 134 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 884 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.246422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.156110 restraints weight = 15641.112| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 4.17 r_work: 0.3527 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13954 Z= 0.101 Angle : 0.531 9.189 18839 Z= 0.264 Chirality : 0.040 0.136 2147 Planarity : 0.004 0.040 2400 Dihedral : 4.899 57.945 1876 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.46 % Allowed : 25.92 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1712 helix: 1.32 (0.23), residues: 580 sheet: -0.07 (0.29), residues: 319 loop : -1.26 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1090 TYR 0.014 0.001 TYR B 752 PHE 0.015 0.001 PHE A 871 TRP 0.012 0.001 TRP B 366 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (13952) covalent geometry : angle 0.53091 / 0.26 (18839) hydrogen bonds : bond 0.03746 / 2.54 ( 582) hydrogen bonds : angle 4.60103 / 3.25 ( 1629) Misc. bond : bond 0.00148 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 133 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6023 (OUTLIER) cc_final: 0.5672 (m170) REVERT: A 128 ASP cc_start: 0.7860 (t0) cc_final: 0.7609 (t0) REVERT: A 130 ARG cc_start: 0.7638 (mmt180) cc_final: 0.7416 (mmt180) REVERT: A 224 ASP cc_start: 0.8158 (m-30) cc_final: 0.7724 (m-30) REVERT: A 385 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.8155 (t80) REVERT: A 450 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7661 (tt) REVERT: A 742 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.6366 (ttt) REVERT: A 887 ARG cc_start: 0.7740 (ttp-110) cc_final: 0.7406 (ttm110) REVERT: A 983 MET cc_start: 0.1358 (mmm) cc_final: 0.1076 (mtp) REVERT: B 251 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: B 325 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7377 (mm) REVERT: B 338 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8415 (t) REVERT: B 456 ILE cc_start: 0.9184 (mm) cc_final: 0.8952 (mm) REVERT: B 912 SER cc_start: 0.6288 (OUTLIER) cc_final: 0.5537 (t) REVERT: B 915 MET cc_start: 0.2829 (mtm) cc_final: 0.2534 (tpp) REVERT: B 920 MET cc_start: 0.2270 (ptm) cc_final: 0.0758 (mmt) REVERT: B 1001 MET cc_start: 0.1428 (mpp) cc_final: -0.0525 (ttp) REVERT: B 1049 HIS cc_start: 0.0088 (OUTLIER) cc_final: -0.0675 (m170) outliers start: 67 outliers final: 42 residues processed: 187 average time/residue: 0.0866 time to fit residues: 24.7506 Evaluate side-chains 179 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 912 SER Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1049 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 147 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 971 ASN B 884 HIS B 943 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.243172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146284 restraints weight = 15510.105| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.86 r_work: 0.3498 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13954 Z= 0.158 Angle : 0.588 12.627 18839 Z= 0.291 Chirality : 0.042 0.167 2147 Planarity : 0.004 0.044 2400 Dihedral : 5.151 56.863 1876 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.73 % Allowed : 24.85 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.21), residues: 1712 helix: 1.18 (0.22), residues: 575 sheet: -0.03 (0.29), residues: 319 loop : -1.26 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 551 TYR 0.017 0.001 TYR A 242 PHE 0.026 0.002 PHE A 916 TRP 0.015 0.002 TRP B 366 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (13952) covalent geometry : angle 0.58807 / 0.29 (18839) hydrogen bonds : bond 0.04727 / 3.23 ( 582) hydrogen bonds : angle 4.77437 / 3.37 ( 1629) Misc. bond : bond 0.00153 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 130 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6148 (OUTLIER) cc_final: 0.5804 (m170) REVERT: A 128 ASP cc_start: 0.7840 (t0) cc_final: 0.7563 (t0) REVERT: A 130 ARG cc_start: 0.7648 (mmt180) cc_final: 0.7419 (mmt180) REVERT: A 224 ASP cc_start: 0.8178 (m-30) cc_final: 0.7764 (m-30) REVERT: A 385 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8114 (t80) REVERT: A 480 MET cc_start: 0.8286 (mtm) cc_final: 0.7722 (mpp) REVERT: A 742 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6345 (ttt) REVERT: A 887 ARG cc_start: 0.7721 (ttp-110) cc_final: 0.7403 (ttm110) REVERT: A 983 MET cc_start: 0.1402 (mmm) cc_final: 0.1187 (mtp) REVERT: B 325 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7246 (mm) REVERT: B 444 LYS cc_start: 0.8416 (tmtt) cc_final: 0.8215 (tptp) REVERT: B 558 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6830 (tp) REVERT: B 912 SER cc_start: 0.6309 (OUTLIER) cc_final: 0.5557 (t) REVERT: B 915 MET cc_start: 0.2670 (mtm) cc_final: 0.2343 (tpp) REVERT: B 920 MET cc_start: 0.2327 (ptm) cc_final: 0.0782 (mmt) REVERT: B 922 GLU cc_start: 0.1136 (OUTLIER) cc_final: -0.0313 (tm-30) REVERT: B 1001 MET cc_start: 0.1655 (mpp) cc_final: -0.0353 (ttp) REVERT: B 1049 HIS cc_start: 0.0083 (OUTLIER) cc_final: -0.0675 (m170) outliers start: 86 outliers final: 65 residues processed: 200 average time/residue: 0.0877 time to fit residues: 26.8830 Evaluate side-chains 198 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 125 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 912 SER Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1049 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 152 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 171 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 971 ASN B 884 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.246365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.160039 restraints weight = 15483.414| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 3.97 r_work: 0.3540 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13954 Z= 0.100 Angle : 0.533 10.531 18839 Z= 0.263 Chirality : 0.040 0.147 2147 Planarity : 0.004 0.049 2400 Dihedral : 4.866 57.074 1876 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.86 % Allowed : 26.25 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1712 helix: 1.41 (0.23), residues: 582 sheet: -0.03 (0.30), residues: 307 loop : -1.25 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1090 TYR 0.013 0.001 TYR A 242 PHE 0.023 0.001 PHE A 916 TRP 0.012 0.001 TRP B 366 HIS 0.003 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (13952) covalent geometry : angle 0.53266 / 0.26 (18839) hydrogen bonds : bond 0.03698 / 2.51 ( 582) hydrogen bonds : angle 4.51299 / 3.19 ( 1629) Misc. bond : bond 0.00140 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 132 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6073 (OUTLIER) cc_final: 0.5745 (m170) REVERT: A 128 ASP cc_start: 0.7884 (t0) cc_final: 0.7623 (t0) REVERT: A 224 ASP cc_start: 0.8122 (m-30) cc_final: 0.7692 (m-30) REVERT: A 385 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.8154 (t80) REVERT: A 450 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7705 (tt) REVERT: A 480 MET cc_start: 0.8268 (mtm) cc_final: 0.7781 (mpp) REVERT: A 497 ARG cc_start: 0.7003 (mtm180) cc_final: 0.6730 (mtm110) REVERT: A 742 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6406 (ttt) REVERT: A 887 ARG cc_start: 0.7708 (ttp-110) cc_final: 0.7380 (ttm110) REVERT: A 915 MET cc_start: 0.3711 (mmm) cc_final: 0.3175 (tpp) REVERT: A 983 MET cc_start: 0.1837 (mmm) cc_final: 0.1623 (mtp) REVERT: B 251 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7832 (pt0) REVERT: B 299 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6128 (ptm160) REVERT: B 325 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7128 (mm) REVERT: B 338 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8398 (t) REVERT: B 744 LYS cc_start: 0.8291 (mmtm) cc_final: 0.7966 (mptt) REVERT: B 912 SER cc_start: 0.6178 (OUTLIER) cc_final: 0.5298 (t) REVERT: B 915 MET cc_start: 0.2566 (mtm) cc_final: 0.2257 (tpp) REVERT: B 920 MET cc_start: 0.2363 (ptm) cc_final: 0.0881 (mmt) REVERT: B 922 GLU cc_start: 0.1115 (OUTLIER) cc_final: -0.0335 (tm-30) REVERT: B 1001 MET cc_start: 0.1775 (mpp) cc_final: -0.0306 (ttp) REVERT: B 1049 HIS cc_start: 0.0076 (OUTLIER) cc_final: -0.0628 (m170) outliers start: 73 outliers final: 51 residues processed: 192 average time/residue: 0.1057 time to fit residues: 30.5627 Evaluate side-chains 191 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 129 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 912 SER Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1049 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 971 ASN B 884 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.245608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.153810 restraints weight = 15550.614| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 4.23 r_work: 0.3513 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13954 Z= 0.170 Angle : 0.601 10.750 18839 Z= 0.298 Chirality : 0.042 0.169 2147 Planarity : 0.004 0.054 2400 Dihedral : 5.185 56.496 1876 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.53 % Allowed : 25.52 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.20), residues: 1712 helix: 1.19 (0.22), residues: 579 sheet: -0.06 (0.29), residues: 312 loop : -1.26 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 426 TYR 0.018 0.001 TYR A 242 PHE 0.019 0.002 PHE A 871 TRP 0.015 0.002 TRP B 366 HIS 0.005 0.001 HIS B 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (13952) covalent geometry : angle 0.60107 / 0.30 (18839) hydrogen bonds : bond 0.04832 / 3.30 ( 582) hydrogen bonds : angle 4.75759 / 3.36 ( 1629) Misc. bond : bond 0.00150 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 128 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6002 (OUTLIER) cc_final: 0.5725 (m170) REVERT: A 128 ASP cc_start: 0.7855 (t0) cc_final: 0.7510 (t0) REVERT: A 224 ASP cc_start: 0.8203 (m-30) cc_final: 0.7799 (m-30) REVERT: A 385 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8171 (t80) REVERT: A 450 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7823 (tt) REVERT: A 480 MET cc_start: 0.8313 (mtm) cc_final: 0.7810 (mpp) REVERT: A 742 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6441 (ttt) REVERT: A 887 ARG cc_start: 0.7689 (ttp-110) cc_final: 0.7366 (ttm110) REVERT: A 915 MET cc_start: 0.4226 (mmm) cc_final: 0.3840 (tpp) REVERT: A 948 LEU cc_start: 0.4561 (OUTLIER) cc_final: 0.4212 (tt) REVERT: A 983 MET cc_start: 0.1881 (mmm) cc_final: 0.1666 (mtp) REVERT: B 299 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.6189 (ptm160) REVERT: B 325 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7288 (mm) REVERT: B 444 LYS cc_start: 0.8460 (tmtt) cc_final: 0.8253 (tptp) REVERT: B 558 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6764 (tp) REVERT: B 744 LYS cc_start: 0.8370 (mmtm) cc_final: 0.8161 (mptt) REVERT: B 912 SER cc_start: 0.6252 (OUTLIER) cc_final: 0.5980 (t) REVERT: B 920 MET cc_start: 0.2650 (ptm) cc_final: 0.1125 (mmt) REVERT: B 922 GLU cc_start: 0.1051 (OUTLIER) cc_final: -0.0442 (tm-30) REVERT: B 1001 MET cc_start: 0.2020 (mpp) cc_final: 0.0009 (ttp) REVERT: B 1049 HIS cc_start: 0.0148 (OUTLIER) cc_final: -0.0576 (m170) outliers start: 83 outliers final: 65 residues processed: 196 average time/residue: 0.1068 time to fit residues: 31.6904 Evaluate side-chains 203 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 127 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 912 SER Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1049 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 137 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 17 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 163 optimal weight: 30.0000 chunk 155 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 971 ASN B 884 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.248646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.159252 restraints weight = 15444.839| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.82 r_work: 0.3582 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13954 Z= 0.102 Angle : 0.542 9.219 18839 Z= 0.268 Chirality : 0.040 0.145 2147 Planarity : 0.004 0.054 2400 Dihedral : 4.901 57.015 1876 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.13 % Allowed : 26.32 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.21), residues: 1712 helix: 1.45 (0.23), residues: 581 sheet: -0.04 (0.30), residues: 309 loop : -1.23 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 426 TYR 0.013 0.001 TYR A 242 PHE 0.017 0.001 PHE A 916 TRP 0.012 0.001 TRP B 366 HIS 0.003 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (13952) covalent geometry : angle 0.54161 / 0.27 (18839) hydrogen bonds : bond 0.03726 / 2.54 ( 582) hydrogen bonds : angle 4.50243 / 3.18 ( 1629) Misc. bond : bond 0.00135 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 132 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6016 (OUTLIER) cc_final: 0.5756 (m170) REVERT: A 128 ASP cc_start: 0.7882 (t0) cc_final: 0.7551 (t0) REVERT: A 224 ASP cc_start: 0.8182 (m-30) cc_final: 0.7815 (m-30) REVERT: A 385 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8209 (t80) REVERT: A 450 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7866 (tt) REVERT: A 480 MET cc_start: 0.8257 (mtm) cc_final: 0.7759 (mpp) REVERT: A 742 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6487 (ttt) REVERT: A 887 ARG cc_start: 0.7756 (ttp-110) cc_final: 0.7430 (ttm110) REVERT: A 915 MET cc_start: 0.4337 (mmm) cc_final: 0.3993 (tpp) REVERT: A 948 LEU cc_start: 0.4556 (OUTLIER) cc_final: 0.4190 (tt) REVERT: A 983 MET cc_start: 0.2109 (mmm) cc_final: 0.1905 (mtp) REVERT: B 299 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.6176 (ptm160) REVERT: B 325 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7206 (mm) REVERT: B 338 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8348 (t) REVERT: B 744 LYS cc_start: 0.8329 (mmtm) cc_final: 0.8104 (mptt) REVERT: B 912 SER cc_start: 0.6433 (OUTLIER) cc_final: 0.5734 (t) REVERT: B 915 MET cc_start: 0.2704 (mtm) cc_final: 0.2287 (tpp) REVERT: B 920 MET cc_start: 0.2614 (ptm) cc_final: 0.1019 (mmt) REVERT: B 922 GLU cc_start: 0.1092 (OUTLIER) cc_final: -0.0422 (tm-30) REVERT: B 1001 MET cc_start: 0.1809 (mpp) cc_final: -0.0104 (ttp) REVERT: B 1049 HIS cc_start: 0.0042 (OUTLIER) cc_final: -0.0727 (m170) outliers start: 77 outliers final: 59 residues processed: 197 average time/residue: 0.0928 time to fit residues: 27.2247 Evaluate side-chains 200 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 130 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 912 SER Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1049 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 63 optimal weight: 7.9990 chunk 19 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 HIS A 971 ASN B 884 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.242645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148027 restraints weight = 15476.497| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.92 r_work: 0.3501 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13954 Z= 0.167 Angle : 0.603 9.708 18839 Z= 0.299 Chirality : 0.042 0.167 2147 Planarity : 0.004 0.054 2400 Dihedral : 5.187 59.456 1876 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.33 % Allowed : 26.45 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.21), residues: 1712 helix: 1.22 (0.22), residues: 579 sheet: -0.05 (0.30), residues: 312 loop : -1.24 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 551 TYR 0.017 0.001 TYR A 242 PHE 0.019 0.002 PHE A 871 TRP 0.015 0.002 TRP B 366 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (13952) covalent geometry : angle 0.60305 / 0.30 (18839) hydrogen bonds : bond 0.04785 / 3.27 ( 582) hydrogen bonds : angle 4.73871 / 3.35 ( 1629) Misc. bond : bond 0.00151 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 132 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6012 (OUTLIER) cc_final: 0.5743 (m170) REVERT: A 128 ASP cc_start: 0.7842 (t0) cc_final: 0.7534 (t0) REVERT: A 224 ASP cc_start: 0.8200 (m-30) cc_final: 0.7826 (m-30) REVERT: A 385 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8150 (t80) REVERT: A 450 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7861 (tt) REVERT: A 480 MET cc_start: 0.8313 (mtm) cc_final: 0.7724 (mpp) REVERT: A 742 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6388 (ttt) REVERT: A 887 ARG cc_start: 0.7704 (ttp-110) cc_final: 0.7382 (ttm110) REVERT: A 915 MET cc_start: 0.4734 (mmm) cc_final: 0.4392 (tpp) REVERT: A 948 LEU cc_start: 0.4571 (OUTLIER) cc_final: 0.4201 (tt) REVERT: A 983 MET cc_start: 0.2324 (mmm) cc_final: 0.2089 (mtp) REVERT: B 299 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6161 (ptm160) REVERT: B 325 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7186 (mm) REVERT: B 744 LYS cc_start: 0.8359 (mmtm) cc_final: 0.8080 (mptt) REVERT: B 887 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6626 (tmm-80) REVERT: B 912 SER cc_start: 0.6411 (OUTLIER) cc_final: 0.5740 (t) REVERT: B 915 MET cc_start: 0.2678 (mtm) cc_final: 0.2189 (tpp) REVERT: B 920 MET cc_start: 0.2814 (ptm) cc_final: 0.1302 (mmp) REVERT: B 922 GLU cc_start: 0.1106 (OUTLIER) cc_final: -0.0388 (tm-30) REVERT: B 1001 MET cc_start: 0.1712 (mpp) cc_final: -0.0158 (ttp) REVERT: B 1049 HIS cc_start: 0.0115 (OUTLIER) cc_final: -0.0660 (m170) outliers start: 80 outliers final: 65 residues processed: 197 average time/residue: 0.1099 time to fit residues: 32.0503 Evaluate side-chains 207 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 131 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 887 ARG Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 912 SER Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1049 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 13 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 0.0020 chunk 119 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 156 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 971 ASN B 884 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.246765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151973 restraints weight = 15493.297| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.80 r_work: 0.3571 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13954 Z= 0.099 Angle : 0.542 9.290 18839 Z= 0.270 Chirality : 0.040 0.143 2147 Planarity : 0.004 0.054 2400 Dihedral : 4.890 59.370 1876 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.66 % Allowed : 27.12 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.21), residues: 1712 helix: 1.48 (0.23), residues: 582 sheet: -0.02 (0.30), residues: 309 loop : -1.22 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 497 TYR 0.012 0.001 TYR B 752 PHE 0.019 0.001 PHE A 466 TRP 0.012 0.001 TRP B 366 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (13952) covalent geometry : angle 0.54180 / 0.27 (18839) hydrogen bonds : bond 0.03597 / 2.44 ( 582) hydrogen bonds : angle 4.46511 / 3.15 ( 1629) Misc. bond : bond 0.00131 / 0.06 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 130 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6000 (OUTLIER) cc_final: 0.5763 (m170) REVERT: A 128 ASP cc_start: 0.7832 (t0) cc_final: 0.7506 (t0) REVERT: A 338 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8682 (t) REVERT: A 385 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.8145 (t80) REVERT: A 450 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7839 (tt) REVERT: A 480 MET cc_start: 0.8302 (mtm) cc_final: 0.7695 (mpp) REVERT: A 497 ARG cc_start: 0.7091 (mtm180) cc_final: 0.6789 (mtm110) REVERT: A 742 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6446 (ttt) REVERT: A 887 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7400 (ttm110) REVERT: A 915 MET cc_start: 0.4706 (mmm) cc_final: 0.4425 (tpp) REVERT: A 948 LEU cc_start: 0.4506 (OUTLIER) cc_final: 0.4131 (tt) REVERT: B 299 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.6111 (ptm160) REVERT: B 325 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7101 (mm) REVERT: B 744 LYS cc_start: 0.8243 (mmtm) cc_final: 0.8022 (mptt) REVERT: B 887 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6616 (tmm-80) REVERT: B 912 SER cc_start: 0.6360 (OUTLIER) cc_final: 0.5694 (t) REVERT: B 915 MET cc_start: 0.2670 (mtm) cc_final: 0.2252 (tpp) REVERT: B 920 MET cc_start: 0.2784 (ptm) cc_final: 0.1467 (mmm) REVERT: B 922 GLU cc_start: 0.1341 (OUTLIER) cc_final: -0.0157 (tm-30) REVERT: B 1001 MET cc_start: 0.1745 (mpp) cc_final: -0.0015 (ttp) outliers start: 70 outliers final: 56 residues processed: 188 average time/residue: 0.1181 time to fit residues: 33.1568 Evaluate side-chains 195 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 128 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 887 ARG Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 912 SER Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1049 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 52 optimal weight: 2.9990 chunk 19 optimal weight: 0.0570 chunk 83 optimal weight: 20.0000 chunk 149 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 971 ASN B 884 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.244465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149406 restraints weight = 15505.363| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.75 r_work: 0.3523 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13954 Z= 0.128 Angle : 0.569 9.194 18839 Z= 0.282 Chirality : 0.041 0.155 2147 Planarity : 0.004 0.054 2400 Dihedral : 4.970 57.653 1876 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 5.00 % Allowed : 26.72 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1712 helix: 1.41 (0.22), residues: 587 sheet: -0.01 (0.30), residues: 309 loop : -1.20 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 288 TYR 0.015 0.001 TYR A 242 PHE 0.018 0.001 PHE A 871 TRP 0.013 0.001 TRP B 366 HIS 0.004 0.001 HIS B 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (13952) covalent geometry : angle 0.56874 / 0.28 (18839) hydrogen bonds : bond 0.04180 / 2.86 ( 582) hydrogen bonds : angle 4.56282 / 3.22 ( 1629) Misc. bond : bond 0.00146 / 0.07 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3955.44 seconds wall clock time: 68 minutes 6.65 seconds (4086.65 seconds total)