Starting phenix.real_space_refine on Wed Mar 4 01:08:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bsu_30167/03_2026/7bsu_30167_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bsu_30167/03_2026/7bsu_30167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bsu_30167/03_2026/7bsu_30167_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bsu_30167/03_2026/7bsu_30167_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bsu_30167/03_2026/7bsu_30167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bsu_30167/03_2026/7bsu_30167.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 45 5.16 5 Be 1 3.05 5 C 6076 2.51 5 N 1503 2.21 5 O 1695 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9325 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6591 Classifications: {'peptide': 814} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 791} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {'AH2': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.24, per 1000 atoms: 0.24 Number of scatterers: 9325 At special positions: 0 Unit cell: (114.54, 83.83, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 45 16.00 P 1 15.00 Mg 1 11.99 F 3 9.00 O 1695 8.00 N 1503 7.00 C 6076 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 404 " - " ASN C 294 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 475.0 milliseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 40.1% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.987A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 79 removed outlier: 3.583A pdb=" N PHE A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 102 removed outlier: 3.508A pdb=" N LEU A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Proline residue: A 94 - end of helix removed outlier: 4.241A pdb=" N THR A 100 " --> pdb=" O PHE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 111 through 117 removed outlier: 3.777A pdb=" N ASP A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.543A pdb=" N ILE A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.563A pdb=" N ALA A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.550A pdb=" N THR A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 352 removed outlier: 4.312A pdb=" N PHE A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.546A pdb=" N MET A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.875A pdb=" N SER A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.785A pdb=" N PHE A 380 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 381 " --> pdb=" O LYS A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 381' Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.679A pdb=" N LEU A 400 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 666 Processing helix chain 'A' and resid 677 through 688 Processing helix chain 'A' and resid 711 through 716 removed outlier: 3.740A pdb=" N HIS A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 761 removed outlier: 3.612A pdb=" N LEU A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 779 removed outlier: 3.542A pdb=" N ILE A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 805 removed outlier: 3.511A pdb=" N VAL A 799 " --> pdb=" O LYS A 795 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 804 " --> pdb=" O ARG A 800 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 805 " --> pdb=" O MET A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 860 Processing helix chain 'A' and resid 862 through 890 removed outlier: 3.549A pdb=" N ILE A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 872 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 878 " --> pdb=" O VAL A 874 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Proline residue: A 887 - end of helix Processing helix chain 'A' and resid 891 through 894 Processing helix chain 'A' and resid 904 through 914 removed outlier: 3.550A pdb=" N LEU A 908 " --> pdb=" O ASP A 904 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 910 " --> pdb=" O ALA A 906 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 removed outlier: 3.530A pdb=" N LEU A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 927 removed outlier: 3.674A pdb=" N LEU A 926 " --> pdb=" O ALA A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 944 removed outlier: 3.529A pdb=" N MET A 943 " --> pdb=" O ARG A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 975 removed outlier: 3.571A pdb=" N TYR A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 980 removed outlier: 3.818A pdb=" N GLN A 979 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR A 980 " --> pdb=" O LEU A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 976 through 980' Processing helix chain 'A' and resid 992 through 997 Processing helix chain 'A' and resid 997 through 1009 Processing helix chain 'A' and resid 1021 through 1027 removed outlier: 3.763A pdb=" N TRP A1027 " --> pdb=" O HIS A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1041 removed outlier: 3.614A pdb=" N TYR A1033 " --> pdb=" O SER A1029 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1061 Processing helix chain 'A' and resid 1062 through 1067 removed outlier: 6.938A pdb=" N SER A1065 " --> pdb=" O SER A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 3.743A pdb=" N ILE A1085 " --> pdb=" O GLU A1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 61 removed outlier: 3.548A pdb=" N PHE C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 60 " --> pdb=" O ILE C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 66 through 75 removed outlier: 3.548A pdb=" N VAL C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN C 73 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 4.062A pdb=" N LYS C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.632A pdb=" N LYS C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.010A pdb=" N ARG C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.796A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 Processing helix chain 'C' and resid 323 through 346 removed outlier: 3.592A pdb=" N ILE C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 331 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.963A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 390 through 391 removed outlier: 3.545A pdb=" N SER A 848 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY A 830 " --> pdb=" O TYR A 847 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N VAL A 849 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY A 832 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR A 811 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE A 831 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N SER A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE A 833 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLY A 815 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 814 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL A 406 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A 673 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N THR A 408 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 785 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.947A pdb=" N VAL C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU C 275 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET C 120 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 104 through 110 removed outlier: 3.517A pdb=" N PHE C 108 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 162 through 163 248 hydrogen bonds defined for protein. 693 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: 1.48 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2858 1.34 - 1.46: 2021 1.46 - 1.58: 4602 1.58 - 1.70: 3 1.70 - 1.82: 71 Bond restraints: 9555 Sorted by residual: bond pdb=" F3 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 1.529 1.763 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" F2 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 1.535 1.766 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" F1 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 1.542 1.767 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" CG BFD A 409 " pdb=" OD1 BFD A 409 " ideal model delta sigma weight residual 1.269 1.447 -0.178 2.00e-02 2.50e+03 7.93e+01 bond pdb=" O15 P5S A1101 " pdb=" P12 P5S A1101 " ideal model delta sigma weight residual 1.493 1.608 -0.115 2.00e-02 2.50e+03 3.28e+01 ... (remaining 9550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 12816 2.33 - 4.66: 123 4.66 - 6.98: 8 6.98 - 9.31: 9 9.31 - 11.64: 1 Bond angle restraints: 12957 Sorted by residual: angle pdb=" N ILE A 385 " pdb=" CA ILE A 385 " pdb=" C ILE A 385 " ideal model delta sigma weight residual 113.71 107.71 6.00 9.50e-01 1.11e+00 3.99e+01 angle pdb=" N ILE A 293 " pdb=" CA ILE A 293 " pdb=" C ILE A 293 " ideal model delta sigma weight residual 113.42 108.88 4.54 1.17e+00 7.31e-01 1.51e+01 angle pdb=" O13 P5S A1101 " pdb=" P12 P5S A1101 " pdb=" O15 P5S A1101 " ideal model delta sigma weight residual 121.25 109.61 11.64 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C THR A 408 " pdb=" N BFD A 409 " pdb=" CA BFD A 409 " ideal model delta sigma weight residual 121.70 127.50 -5.80 1.80e+00 3.09e-01 1.04e+01 angle pdb=" C39 P5S A1101 " pdb=" C38 P5S A1101 " pdb=" O37 P5S A1101 " ideal model delta sigma weight residual 110.52 119.70 -9.18 3.00e+00 1.11e-01 9.36e+00 ... (remaining 12952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 5485 35.10 - 70.21: 207 70.21 - 105.31: 27 105.31 - 140.42: 13 140.42 - 175.52: 5 Dihedral angle restraints: 5737 sinusoidal: 2395 harmonic: 3342 Sorted by residual: dihedral pdb=" C3 P5S A1101 " pdb=" C1 P5S A1101 " pdb=" C2 P5S A1101 " pdb=" O19 P5S A1101 " ideal model delta sinusoidal sigma weight residual 179.75 -4.73 -175.52 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C41 P5S A1101 " pdb=" C42 P5S A1101 " pdb=" C43 P5S A1101 " pdb=" C44 P5S A1101 " ideal model delta sinusoidal sigma weight residual 92.81 -102.19 -165.00 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CB P5S A1101 " pdb=" OG P5S A1101 " pdb=" P12 P5S A1101 " pdb=" O13 P5S A1101 " ideal model delta sinusoidal sigma weight residual 47.21 -151.34 -161.45 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 5734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1283 0.060 - 0.120: 171 0.120 - 0.180: 5 0.180 - 0.240: 1 0.240 - 0.299: 1 Chirality restraints: 1461 Sorted by residual: chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA BFD A 409 " pdb=" N BFD A 409 " pdb=" C BFD A 409 " pdb=" CB BFD A 409 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA TRP A 323 " pdb=" N TRP A 323 " pdb=" C TRP A 323 " pdb=" CB TRP A 323 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 1458 not shown) Planarity restraints: 1610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.349 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG C 402 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 405 " 0.188 2.00e-02 2.50e+03 1.59e-01 3.16e+02 pdb=" C7 NAG C 405 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG C 405 " -0.039 2.00e-02 2.50e+03 pdb=" N2 NAG C 405 " -0.257 2.00e-02 2.50e+03 pdb=" O7 NAG C 405 " 0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.181 2.00e-02 2.50e+03 1.53e-01 2.92e+02 pdb=" C7 NAG C 401 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.245 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " 0.144 2.00e-02 2.50e+03 ... (remaining 1607 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 29 2.28 - 2.94: 4660 2.94 - 3.59: 12115 3.59 - 4.25: 22674 4.25 - 4.90: 38587 Nonbonded interactions: 78065 Sorted by model distance: nonbonded pdb=" F2 BFD A 409 " pdb=" ND2 ASN A 819 " model vdw 1.626 3.070 nonbonded pdb=" O4 NAG C 401 " pdb=" O5 NAG C 402 " model vdw 1.876 3.040 nonbonded pdb=" F1 BFD A 409 " pdb="MG MG A1100 " model vdw 1.976 2.120 nonbonded pdb=" O LEU A 162 " pdb=" OG1 THR A 193 " model vdw 2.003 3.040 nonbonded pdb=" OG SER A 282 " pdb=" OE2 GLU A 398 " model vdw 2.008 3.040 ... (remaining 78060 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.150 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.234 9559 Z= 0.296 Angle : 0.616 11.642 12966 Z= 0.327 Chirality : 0.041 0.299 1461 Planarity : 0.010 0.297 1609 Dihedral : 20.437 175.521 3572 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 30.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 7.59 % Allowed : 20.79 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -6.52 (0.16), residues: 1125 helix: -5.01 (0.09), residues: 482 sheet: -3.22 (0.37), residues: 149 loop : -3.81 (0.21), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 843 TYR 0.011 0.001 TYR C 134 PHE 0.008 0.001 PHE A 72 TRP 0.016 0.001 TRP A 323 HIS 0.005 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 9555) covalent geometry : angle 0.60903 (12957) SS BOND : bond 0.00261 ( 3) SS BOND : angle 0.71378 ( 6) hydrogen bonds : bond 0.32365 ( 248) hydrogen bonds : angle 13.63072 ( 693) link_NAG-ASN : bond 0.01151 ( 1) link_NAG-ASN : angle 6.06006 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 130 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8365 (tttm) cc_final: 0.8111 (ttmt) REVERT: A 126 TYR cc_start: 0.8551 (m-80) cc_final: 0.8272 (m-80) REVERT: A 206 ARG cc_start: 0.7925 (mmt180) cc_final: 0.7367 (mmt90) REVERT: A 213 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8592 (mm110) REVERT: A 224 ARG cc_start: 0.6796 (ttm170) cc_final: 0.6065 (ttm-80) REVERT: A 266 MET cc_start: 0.7087 (mmp) cc_final: 0.6711 (ttt) REVERT: A 382 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8019 (t70) REVERT: C 200 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8248 (tttt) REVERT: C 279 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7409 (mttt) outliers start: 77 outliers final: 64 residues processed: 197 average time/residue: 0.1165 time to fit residues: 31.1971 Evaluate side-chains 188 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 122 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.0060 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 38 GLN A 43 ASN A 59 ASN A 275 GLN A 386 ASN A 397 ASN ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN A 794 GLN A 828 HIS A 862 HIS ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 HIS A 875 GLN A 928 GLN A1051 GLN A1089 ASN C 216 ASN C 298 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.137249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.097983 restraints weight = 10850.029| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.77 r_work: 0.2785 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9559 Z= 0.129 Angle : 0.664 14.604 12966 Z= 0.332 Chirality : 0.045 0.236 1461 Planarity : 0.005 0.054 1609 Dihedral : 16.689 172.914 1506 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.52 % Allowed : 18.92 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -4.81 (0.20), residues: 1125 helix: -3.73 (0.15), residues: 469 sheet: -2.47 (0.38), residues: 167 loop : -2.70 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.013 0.001 TYR A 686 PHE 0.013 0.001 PHE C 108 TRP 0.019 0.001 TRP A 323 HIS 0.006 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9555) covalent geometry : angle 0.64715 (12957) SS BOND : bond 0.00385 ( 3) SS BOND : angle 0.91976 ( 6) hydrogen bonds : bond 0.03934 ( 248) hydrogen bonds : angle 6.05846 ( 693) link_NAG-ASN : bond 0.01903 ( 1) link_NAG-ASN : angle 9.62858 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 128 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7659 (m-80) cc_final: 0.7131 (m-80) REVERT: A 75 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8237 (tp) REVERT: A 126 TYR cc_start: 0.8723 (m-80) cc_final: 0.8405 (m-80) REVERT: A 135 ARG cc_start: 0.8168 (ptm160) cc_final: 0.7774 (tmm-80) REVERT: A 142 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7107 (mtpp) REVERT: A 224 ARG cc_start: 0.6823 (ttm170) cc_final: 0.6052 (ttm-80) REVERT: A 266 MET cc_start: 0.8095 (mmp) cc_final: 0.7062 (ttt) REVERT: A 716 HIS cc_start: 0.7470 (p90) cc_final: 0.7160 (p90) REVERT: A 777 GLN cc_start: 0.8381 (mt0) cc_final: 0.8054 (mt0) REVERT: A 926 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9053 (pp) REVERT: A 1089 ASN cc_start: 0.7064 (m-40) cc_final: 0.6807 (m110) REVERT: C 59 LEU cc_start: 0.8256 (tt) cc_final: 0.7692 (mt) REVERT: C 200 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8345 (tttm) REVERT: C 228 LYS cc_start: 0.8413 (mmmm) cc_final: 0.8185 (mmtp) outliers start: 56 outliers final: 35 residues processed: 174 average time/residue: 0.1035 time to fit residues: 25.0805 Evaluate side-chains 154 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 114 HIS A 653 GLN ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN A 864 HIS C 152 ASN C 235 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.132184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.092209 restraints weight = 10914.949| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.79 r_work: 0.2697 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9559 Z= 0.259 Angle : 0.710 15.252 12966 Z= 0.352 Chirality : 0.048 0.287 1461 Planarity : 0.005 0.057 1609 Dihedral : 15.511 161.714 1431 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 7.39 % Allowed : 18.33 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -3.96 (0.21), residues: 1125 helix: -2.87 (0.19), residues: 486 sheet: -1.69 (0.41), residues: 161 loop : -2.53 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 839 TYR 0.016 0.002 TYR A 722 PHE 0.012 0.002 PHE A 72 TRP 0.016 0.002 TRP A 323 HIS 0.005 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00635 ( 9555) covalent geometry : angle 0.69311 (12957) SS BOND : bond 0.00577 ( 3) SS BOND : angle 1.23340 ( 6) hydrogen bonds : bond 0.04454 ( 248) hydrogen bonds : angle 5.48559 ( 693) link_NAG-ASN : bond 0.01751 ( 1) link_NAG-ASN : angle 9.98257 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 121 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7747 (m-80) cc_final: 0.7224 (m-80) REVERT: A 75 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8261 (tp) REVERT: A 126 TYR cc_start: 0.8771 (m-80) cc_final: 0.8416 (m-80) REVERT: A 135 ARG cc_start: 0.8205 (ptm160) cc_final: 0.7660 (tmm-80) REVERT: A 142 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7219 (mtpp) REVERT: A 206 ARG cc_start: 0.7940 (mmt180) cc_final: 0.7410 (mmt90) REVERT: A 224 ARG cc_start: 0.6871 (ttm170) cc_final: 0.6092 (ttm-80) REVERT: A 266 MET cc_start: 0.8186 (mmp) cc_final: 0.7135 (ttt) REVERT: A 386 ASN cc_start: 0.8710 (t0) cc_final: 0.8467 (t0) REVERT: A 682 LYS cc_start: 0.4084 (OUTLIER) cc_final: 0.3490 (ptmm) REVERT: A 777 GLN cc_start: 0.8452 (mt0) cc_final: 0.8041 (mt0) REVERT: A 1055 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: C 59 LEU cc_start: 0.8229 (tt) cc_final: 0.7719 (mt) REVERT: C 200 LYS cc_start: 0.8676 (ttmt) cc_final: 0.8347 (tttt) REVERT: C 228 LYS cc_start: 0.8432 (mmmm) cc_final: 0.8172 (mmtp) outliers start: 75 outliers final: 56 residues processed: 183 average time/residue: 0.1089 time to fit residues: 27.4160 Evaluate side-chains 174 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 114 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 114 HIS A 694 ASN A 745 GLN A1089 ASN C 152 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.136006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.096941 restraints weight = 10987.431| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.85 r_work: 0.2748 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9559 Z= 0.145 Angle : 0.608 14.883 12966 Z= 0.301 Chirality : 0.044 0.282 1461 Planarity : 0.004 0.053 1609 Dihedral : 14.300 167.027 1429 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.81 % Allowed : 20.00 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -3.17 (0.23), residues: 1125 helix: -2.14 (0.21), residues: 483 sheet: -1.30 (0.42), residues: 161 loop : -2.19 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 39 TYR 0.012 0.001 TYR A 911 PHE 0.011 0.001 PHE A1024 TRP 0.018 0.001 TRP A 323 HIS 0.006 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9555) covalent geometry : angle 0.58960 (12957) SS BOND : bond 0.00329 ( 3) SS BOND : angle 0.97204 ( 6) hydrogen bonds : bond 0.03322 ( 248) hydrogen bonds : angle 4.97304 ( 693) link_NAG-ASN : bond 0.01661 ( 1) link_NAG-ASN : angle 9.60973 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 122 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7489 (m-80) cc_final: 0.6882 (m-80) REVERT: A 126 TYR cc_start: 0.8695 (m-80) cc_final: 0.8336 (m-80) REVERT: A 135 ARG cc_start: 0.8129 (ptm160) cc_final: 0.7834 (tmm-80) REVERT: A 206 ARG cc_start: 0.7907 (mmt180) cc_final: 0.7531 (mmt90) REVERT: A 224 ARG cc_start: 0.6766 (ttm170) cc_final: 0.6059 (ttm-80) REVERT: A 281 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8133 (ptm-80) REVERT: A 386 ASN cc_start: 0.8636 (t0) cc_final: 0.8329 (t0) REVERT: A 404 ASP cc_start: 0.8543 (m-30) cc_final: 0.8308 (m-30) REVERT: A 745 GLN cc_start: 0.5440 (OUTLIER) cc_final: 0.5218 (tm-30) REVERT: A 771 TYR cc_start: 0.6639 (OUTLIER) cc_final: 0.6318 (m-10) REVERT: A 777 GLN cc_start: 0.8417 (mt0) cc_final: 0.8028 (mt0) REVERT: A 1050 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7166 (pm20) REVERT: A 1055 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: C 59 LEU cc_start: 0.8184 (tt) cc_final: 0.7708 (mt) REVERT: C 188 ILE cc_start: 0.8213 (mm) cc_final: 0.8011 (mm) REVERT: C 200 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8376 (tttm) REVERT: C 228 LYS cc_start: 0.8430 (mmmm) cc_final: 0.8174 (mmtp) outliers start: 59 outliers final: 45 residues processed: 168 average time/residue: 0.1150 time to fit residues: 26.3816 Evaluate side-chains 167 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 117 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN C 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.136601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.097438 restraints weight = 10876.204| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.84 r_work: 0.2765 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9559 Z= 0.127 Angle : 0.588 14.636 12966 Z= 0.291 Chirality : 0.044 0.293 1461 Planarity : 0.004 0.049 1609 Dihedral : 13.926 169.403 1420 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 6.31 % Allowed : 19.70 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.73 (0.24), residues: 1125 helix: -1.73 (0.22), residues: 486 sheet: -1.30 (0.42), residues: 163 loop : -1.93 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 839 TYR 0.012 0.001 TYR A 324 PHE 0.010 0.001 PHE A 965 TRP 0.017 0.001 TRP A 323 HIS 0.006 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9555) covalent geometry : angle 0.57012 (12957) SS BOND : bond 0.00446 ( 3) SS BOND : angle 0.95945 ( 6) hydrogen bonds : bond 0.03142 ( 248) hydrogen bonds : angle 4.77676 ( 693) link_NAG-ASN : bond 0.02084 ( 1) link_NAG-ASN : angle 9.38319 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 122 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7443 (m-80) cc_final: 0.6818 (m-80) REVERT: A 58 LYS cc_start: 0.8186 (ttmm) cc_final: 0.7833 (ttmm) REVERT: A 126 TYR cc_start: 0.8693 (m-80) cc_final: 0.8370 (m-80) REVERT: A 135 ARG cc_start: 0.8100 (ptm160) cc_final: 0.7861 (tmm-80) REVERT: A 142 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7101 (mtpp) REVERT: A 206 ARG cc_start: 0.7905 (mmt180) cc_final: 0.7548 (mmt90) REVERT: A 224 ARG cc_start: 0.6745 (ttm170) cc_final: 0.6057 (ttm-80) REVERT: A 281 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8104 (ptm-80) REVERT: A 404 ASP cc_start: 0.8521 (m-30) cc_final: 0.8293 (m-30) REVERT: A 1055 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: C 59 LEU cc_start: 0.8176 (tt) cc_final: 0.7676 (mt) REVERT: C 200 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8403 (tttm) REVERT: C 228 LYS cc_start: 0.8401 (mmmm) cc_final: 0.8133 (mmtp) outliers start: 64 outliers final: 50 residues processed: 171 average time/residue: 0.1130 time to fit residues: 26.5435 Evaluate side-chains 173 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 120 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 109 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.135308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.096205 restraints weight = 10814.866| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.86 r_work: 0.2742 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9559 Z= 0.140 Angle : 0.582 14.599 12966 Z= 0.290 Chirality : 0.044 0.304 1461 Planarity : 0.004 0.047 1609 Dihedral : 13.620 170.808 1415 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 6.21 % Allowed : 20.30 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.45 (0.24), residues: 1125 helix: -1.45 (0.22), residues: 487 sheet: -1.18 (0.42), residues: 162 loop : -1.82 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 839 TYR 0.012 0.001 TYR A 911 PHE 0.010 0.001 PHE A 965 TRP 0.016 0.001 TRP A 323 HIS 0.005 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9555) covalent geometry : angle 0.56486 (12957) SS BOND : bond 0.00453 ( 3) SS BOND : angle 0.97609 ( 6) hydrogen bonds : bond 0.03198 ( 248) hydrogen bonds : angle 4.66717 ( 693) link_NAG-ASN : bond 0.02049 ( 1) link_NAG-ASN : angle 9.22841 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 124 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7435 (m-80) cc_final: 0.6830 (m-80) REVERT: A 126 TYR cc_start: 0.8704 (m-80) cc_final: 0.8433 (m-80) REVERT: A 135 ARG cc_start: 0.8125 (ptm160) cc_final: 0.7902 (tmm-80) REVERT: A 142 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7210 (mtpp) REVERT: A 206 ARG cc_start: 0.7902 (mmt180) cc_final: 0.7580 (mmt90) REVERT: A 224 ARG cc_start: 0.6707 (ttm170) cc_final: 0.6042 (ttm-80) REVERT: A 266 MET cc_start: 0.8190 (mmp) cc_final: 0.7139 (ttt) REVERT: A 281 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8119 (ptm-80) REVERT: A 777 GLN cc_start: 0.8514 (mt0) cc_final: 0.8219 (mt0) REVERT: A 1055 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: C 59 LEU cc_start: 0.8216 (tt) cc_final: 0.7699 (mt) REVERT: C 200 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8364 (tttt) REVERT: C 228 LYS cc_start: 0.8421 (mmmm) cc_final: 0.8138 (mmtp) outliers start: 63 outliers final: 51 residues processed: 173 average time/residue: 0.1091 time to fit residues: 25.9096 Evaluate side-chains 170 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 116 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.135637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.096535 restraints weight = 10830.745| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.85 r_work: 0.2741 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9559 Z= 0.142 Angle : 0.577 14.448 12966 Z= 0.287 Chirality : 0.044 0.303 1461 Planarity : 0.004 0.047 1609 Dihedral : 13.494 171.973 1415 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 6.40 % Allowed : 20.30 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.17 (0.24), residues: 1125 helix: -1.21 (0.23), residues: 486 sheet: -1.02 (0.42), residues: 162 loop : -1.69 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 839 TYR 0.012 0.001 TYR A 311 PHE 0.010 0.001 PHE A 72 TRP 0.016 0.001 TRP A 323 HIS 0.005 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9555) covalent geometry : angle 0.55918 (12957) SS BOND : bond 0.00451 ( 3) SS BOND : angle 0.95335 ( 6) hydrogen bonds : bond 0.03162 ( 248) hydrogen bonds : angle 4.57644 ( 693) link_NAG-ASN : bond 0.02198 ( 1) link_NAG-ASN : angle 9.17423 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 123 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7439 (m-80) cc_final: 0.6849 (m-80) REVERT: A 58 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7937 (ttmm) REVERT: A 126 TYR cc_start: 0.8709 (m-80) cc_final: 0.8430 (m-80) REVERT: A 135 ARG cc_start: 0.8173 (ptm160) cc_final: 0.7962 (tmm-80) REVERT: A 142 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7205 (mtpp) REVERT: A 206 ARG cc_start: 0.7888 (mmt180) cc_final: 0.7526 (mmt90) REVERT: A 224 ARG cc_start: 0.6646 (ttm170) cc_final: 0.6003 (ttm-80) REVERT: A 266 MET cc_start: 0.8182 (mmp) cc_final: 0.7095 (ttt) REVERT: A 281 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8150 (ptm-80) REVERT: A 1050 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: A 1055 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: C 59 LEU cc_start: 0.8181 (tt) cc_final: 0.7667 (mt) REVERT: C 200 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8408 (tttm) REVERT: C 228 LYS cc_start: 0.8433 (mmmm) cc_final: 0.8136 (mmtp) outliers start: 65 outliers final: 54 residues processed: 173 average time/residue: 0.1079 time to fit residues: 25.7178 Evaluate side-chains 178 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 120 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.136759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.097503 restraints weight = 10747.209| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.86 r_work: 0.2756 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9559 Z= 0.116 Angle : 0.559 14.243 12966 Z= 0.279 Chirality : 0.043 0.293 1461 Planarity : 0.004 0.046 1609 Dihedral : 13.209 172.870 1414 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.01 % Allowed : 21.28 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.81 (0.25), residues: 1125 helix: -0.91 (0.23), residues: 480 sheet: -0.82 (0.44), residues: 154 loop : -1.49 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 839 TYR 0.012 0.001 TYR A 324 PHE 0.010 0.001 PHE A 72 TRP 0.017 0.001 TRP A 323 HIS 0.005 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9555) covalent geometry : angle 0.54194 (12957) SS BOND : bond 0.00412 ( 3) SS BOND : angle 0.80890 ( 6) hydrogen bonds : bond 0.02938 ( 248) hydrogen bonds : angle 4.47781 ( 693) link_NAG-ASN : bond 0.02249 ( 1) link_NAG-ASN : angle 9.02855 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 122 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7385 (m-80) cc_final: 0.6884 (m-80) REVERT: A 58 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7912 (ttmm) REVERT: A 126 TYR cc_start: 0.8687 (m-80) cc_final: 0.8410 (m-80) REVERT: A 142 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7211 (mtpp) REVERT: A 206 ARG cc_start: 0.7882 (mmt180) cc_final: 0.7617 (mmt90) REVERT: A 224 ARG cc_start: 0.6506 (ttm170) cc_final: 0.5827 (ttm110) REVERT: A 266 MET cc_start: 0.8178 (mmp) cc_final: 0.7060 (ttt) REVERT: A 281 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8296 (ptm-80) REVERT: A 297 PHE cc_start: 0.8740 (m-80) cc_final: 0.8524 (m-80) REVERT: A 979 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.7677 (mm110) REVERT: A 1050 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7225 (pm20) REVERT: A 1055 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: C 59 LEU cc_start: 0.8169 (tt) cc_final: 0.7658 (mt) REVERT: C 200 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8376 (tttm) REVERT: C 228 LYS cc_start: 0.8401 (mmmm) cc_final: 0.8120 (mmtp) outliers start: 61 outliers final: 50 residues processed: 168 average time/residue: 0.1110 time to fit residues: 25.6781 Evaluate side-chains 171 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 116 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 82 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.136215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.096969 restraints weight = 10769.675| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.86 r_work: 0.2745 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9559 Z= 0.134 Angle : 0.577 14.330 12966 Z= 0.286 Chirality : 0.044 0.292 1461 Planarity : 0.004 0.046 1609 Dihedral : 12.986 172.327 1413 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.91 % Allowed : 21.38 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.69 (0.25), residues: 1125 helix: -0.78 (0.23), residues: 480 sheet: -0.77 (0.44), residues: 160 loop : -1.47 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 133 TYR 0.012 0.001 TYR A 311 PHE 0.011 0.001 PHE A 72 TRP 0.016 0.001 TRP A 323 HIS 0.005 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9555) covalent geometry : angle 0.56027 (12957) SS BOND : bond 0.00421 ( 3) SS BOND : angle 0.90087 ( 6) hydrogen bonds : bond 0.03058 ( 248) hydrogen bonds : angle 4.47985 ( 693) link_NAG-ASN : bond 0.02263 ( 1) link_NAG-ASN : angle 9.05348 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 119 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7401 (m-80) cc_final: 0.6857 (m-80) REVERT: A 142 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7199 (mtpp) REVERT: A 206 ARG cc_start: 0.7904 (mmt180) cc_final: 0.7651 (mmt90) REVERT: A 224 ARG cc_start: 0.6519 (ttm170) cc_final: 0.5818 (ttm110) REVERT: A 266 MET cc_start: 0.8188 (mmp) cc_final: 0.7108 (ttt) REVERT: A 281 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8168 (ptm-80) REVERT: A 979 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.7700 (mm110) REVERT: A 1050 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: A 1055 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8265 (m-80) REVERT: C 59 LEU cc_start: 0.8169 (tt) cc_final: 0.7654 (mt) REVERT: C 200 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8392 (tttm) REVERT: C 228 LYS cc_start: 0.8399 (mmmm) cc_final: 0.8113 (mmtp) outliers start: 60 outliers final: 51 residues processed: 166 average time/residue: 0.1122 time to fit residues: 25.5498 Evaluate side-chains 173 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 107 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.139048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.100439 restraints weight = 10645.237| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.79 r_work: 0.2806 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9559 Z= 0.108 Angle : 0.554 14.051 12966 Z= 0.275 Chirality : 0.043 0.280 1461 Planarity : 0.004 0.046 1609 Dihedral : 12.665 173.500 1413 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.73 % Allowed : 22.66 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.44 (0.25), residues: 1125 helix: -0.55 (0.24), residues: 482 sheet: -0.60 (0.44), residues: 160 loop : -1.38 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 839 TYR 0.013 0.001 TYR A 324 PHE 0.010 0.001 PHE A 72 TRP 0.017 0.001 TRP A 323 HIS 0.010 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9555) covalent geometry : angle 0.53737 (12957) SS BOND : bond 0.00409 ( 3) SS BOND : angle 0.75045 ( 6) hydrogen bonds : bond 0.02818 ( 248) hydrogen bonds : angle 4.37662 ( 693) link_NAG-ASN : bond 0.02335 ( 1) link_NAG-ASN : angle 8.85938 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7344 (m-80) cc_final: 0.6864 (m-80) REVERT: A 96 PHE cc_start: 0.7992 (m-10) cc_final: 0.6965 (t80) REVERT: A 126 TYR cc_start: 0.8771 (m-80) cc_final: 0.8513 (m-80) REVERT: A 142 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7027 (mtpp) REVERT: A 185 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8236 (mptt) REVERT: A 206 ARG cc_start: 0.7866 (mmt180) cc_final: 0.7631 (mmt90) REVERT: A 224 ARG cc_start: 0.6409 (ttm170) cc_final: 0.5750 (ttm110) REVERT: A 266 MET cc_start: 0.8085 (mmp) cc_final: 0.6973 (ttt) REVERT: A 359 MET cc_start: 0.9342 (ttp) cc_final: 0.9094 (ttm) REVERT: A 979 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.7586 (mm110) REVERT: A 1055 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: C 59 LEU cc_start: 0.8137 (tt) cc_final: 0.7623 (mt) REVERT: C 200 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8369 (tttm) REVERT: C 228 LYS cc_start: 0.8427 (mmmm) cc_final: 0.8211 (mmmm) outliers start: 48 outliers final: 43 residues processed: 161 average time/residue: 0.1103 time to fit residues: 24.5526 Evaluate side-chains 163 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 979 GLN Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 100 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS A 397 ASN ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.140682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.102865 restraints weight = 10558.565| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.71 r_work: 0.2830 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9559 Z= 0.103 Angle : 0.547 13.899 12966 Z= 0.272 Chirality : 0.043 0.270 1461 Planarity : 0.004 0.045 1609 Dihedral : 12.460 173.843 1412 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.83 % Allowed : 21.97 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.23 (0.25), residues: 1125 helix: -0.33 (0.24), residues: 482 sheet: -0.47 (0.45), residues: 160 loop : -1.33 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.013 0.001 TYR A 324 PHE 0.010 0.001 PHE A 72 TRP 0.017 0.001 TRP A 323 HIS 0.010 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9555) covalent geometry : angle 0.53093 (12957) SS BOND : bond 0.00398 ( 3) SS BOND : angle 0.73163 ( 6) hydrogen bonds : bond 0.02783 ( 248) hydrogen bonds : angle 4.30660 ( 693) link_NAG-ASN : bond 0.02382 ( 1) link_NAG-ASN : angle 8.73936 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2756.80 seconds wall clock time: 47 minutes 56.59 seconds (2876.59 seconds total)