Starting phenix.real_space_refine on Fri Feb 14 04:16:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bsu_30167/02_2025/7bsu_30167_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bsu_30167/02_2025/7bsu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7bsu_30167/02_2025/7bsu_30167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bsu_30167/02_2025/7bsu_30167.map" model { file = "/net/cci-nas-00/data/ceres_data/7bsu_30167/02_2025/7bsu_30167_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bsu_30167/02_2025/7bsu_30167_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.86, per 1000 atoms: 0.63 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: 2.60 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.96 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: 2.81 Time building geometry restraints manager: 2.72 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.540 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.380 ------------------------------------------------------------------------------- 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 9555 Z= 0.374 Angle : 0.609 11.642 12957 Z= 0.326 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 : 31.07 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.001 TRP A 323 HIS 0.005 0.001 HIS A 929 PHE 0.008 0.001 PHE A 72 TYR 0.011 0.001 TYR C 134 ARG 0.001 0.000 ARG A 843 *********************** 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 : 1.144 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: 0.2511 time to fit residues: 67.3219 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 : 1.007 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.0370 overall best weight: 1.3864 ------------------------------------------------------------------------------- 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 653 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3438 r_free = 0.3438 target = 0.135081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.095539 restraints weight = 10757.956| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.79 r_work: 0.2743 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9555 Z= 0.252 Angle : 0.667 8.361 12957 Z= 0.338 Chirality : 0.046 0.245 1461 Planarity : 0.005 0.055 1609 Dihedral : 16.993 175.967 1506 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 6.21 % Allowed : 18.92 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.20), residues: 1125 helix: -3.83 (0.15), residues: 470 sheet: -2.39 (0.39), residues: 162 loop : -2.82 (0.24), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.006 0.001 HIS A 929 PHE 0.013 0.001 PHE C 108 TYR 0.012 0.002 TYR A 686 ARG 0.004 0.000 ARG A 839 *********************** 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 189 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 126 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7733 (m-80) cc_final: 0.7231 (m-80) REVERT: A 75 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8330 (tp) REVERT: A 126 TYR cc_start: 0.8803 (m-80) cc_final: 0.8488 (m-80) REVERT: A 135 ARG cc_start: 0.8184 (ptm160) cc_final: 0.7757 (tmm-80) REVERT: A 142 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7193 (mtpp) REVERT: A 224 ARG cc_start: 0.6918 (ttm170) cc_final: 0.6162 (ttm-80) REVERT: A 266 MET cc_start: 0.8126 (mmp) cc_final: 0.7107 (ttt) REVERT: A 382 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8271 (t70) REVERT: A 406 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8772 (t) REVERT: A 653 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8213 (mm-40) REVERT: A 777 GLN cc_start: 0.8380 (mt0) cc_final: 0.8070 (mt0) REVERT: A 926 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9100 (pp) REVERT: A 1089 ASN cc_start: 0.7026 (m-40) cc_final: 0.6770 (m110) REVERT: C 59 LEU cc_start: 0.8346 (tt) cc_final: 0.7774 (mt) REVERT: C 200 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8413 (tttt) REVERT: C 228 LYS cc_start: 0.8419 (mmmm) cc_final: 0.8193 (mmtp) outliers start: 63 outliers final: 41 residues processed: 178 average time/residue: 0.2472 time to fit residues: 60.2019 Evaluate side-chains 165 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 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 363 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 653 GLN 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 A residue 1065 SER 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 80 ILE Chi-restraints excluded: chain C residue 91 CYS 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 195 ILE 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 103 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN A 864 HIS A1051 GLN C 235 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.134442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.094905 restraints weight = 10969.620| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.84 r_work: 0.2731 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9555 Z= 0.281 Angle : 0.635 8.576 12957 Z= 0.320 Chirality : 0.046 0.277 1461 Planarity : 0.005 0.056 1609 Dihedral : 15.203 161.757 1439 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 7.39 % Allowed : 18.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.22), residues: 1125 helix: -2.84 (0.19), residues: 492 sheet: -1.68 (0.41), residues: 161 loop : -2.49 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.006 0.001 HIS A 929 PHE 0.011 0.001 PHE A 965 TYR 0.018 0.002 TYR A 722 ARG 0.005 0.000 ARG A 839 *********************** 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 : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7656 (m-80) cc_final: 0.7121 (m-80) REVERT: A 126 TYR cc_start: 0.8732 (m-80) cc_final: 0.8415 (m-80) REVERT: A 135 ARG cc_start: 0.8209 (ptm160) cc_final: 0.7788 (tmm-80) REVERT: A 206 ARG cc_start: 0.7927 (mmt180) cc_final: 0.7449 (mmt90) REVERT: A 224 ARG cc_start: 0.6835 (ttm170) cc_final: 0.6101 (ttm-80) REVERT: A 266 MET cc_start: 0.8142 (mmp) cc_final: 0.7102 (ttt) REVERT: A 281 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8157 (ptm-80) REVERT: A 406 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8762 (t) REVERT: A 682 LYS cc_start: 0.3931 (OUTLIER) cc_final: 0.3407 (ptmm) REVERT: A 777 GLN cc_start: 0.8404 (mt0) cc_final: 0.7970 (mt0) REVERT: A 1050 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: A 1089 ASN cc_start: 0.6911 (m-40) cc_final: 0.6711 (m110) REVERT: C 59 LEU cc_start: 0.8205 (tt) cc_final: 0.7702 (mt) REVERT: C 200 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8398 (tttm) REVERT: C 228 LYS cc_start: 0.8432 (mmmm) cc_final: 0.8175 (mmtp) outliers start: 75 outliers final: 52 residues processed: 182 average time/residue: 0.2400 time to fit residues: 59.5500 Evaluate side-chains 175 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 119 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 84 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 181 GLU 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 281 ARG 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 406 VAL 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 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 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 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 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 83 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3443 r_free = 0.3443 target = 0.135753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.096540 restraints weight = 10787.601| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.83 r_work: 0.2751 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9555 Z= 0.207 Angle : 0.578 7.766 12957 Z= 0.291 Chirality : 0.044 0.301 1461 Planarity : 0.004 0.050 1609 Dihedral : 14.138 167.030 1430 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 6.31 % Allowed : 20.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.23), residues: 1125 helix: -2.07 (0.21), residues: 485 sheet: -1.48 (0.41), residues: 168 loop : -2.12 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.006 0.001 HIS A 929 PHE 0.010 0.001 PHE A1055 TYR 0.012 0.001 TYR A 324 ARG 0.003 0.000 ARG A 839 *********************** 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 189 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 125 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7533 (m-80) cc_final: 0.6924 (m-80) REVERT: A 126 TYR cc_start: 0.8712 (m-80) cc_final: 0.8383 (m-80) REVERT: A 135 ARG cc_start: 0.8121 (ptm160) cc_final: 0.7841 (tmm-80) REVERT: A 142 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7190 (mtpp) REVERT: A 206 ARG cc_start: 0.7932 (mmt180) cc_final: 0.7554 (mmt90) REVERT: A 224 ARG cc_start: 0.6775 (ttm170) cc_final: 0.6070 (ttm-80) REVERT: A 266 MET cc_start: 0.8184 (mmp) cc_final: 0.7101 (ttt) REVERT: A 281 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8322 (ptm-80) REVERT: A 386 ASN cc_start: 0.8630 (t0) cc_final: 0.8372 (t0) REVERT: A 1050 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: C 59 LEU cc_start: 0.8202 (tt) cc_final: 0.7725 (mt) REVERT: C 188 ILE cc_start: 0.8190 (mm) cc_final: 0.7990 (mm) REVERT: C 200 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8413 (tttm) REVERT: C 228 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8139 (mmtp) outliers start: 64 outliers final: 50 residues processed: 178 average time/residue: 0.2600 time to fit residues: 62.4529 Evaluate side-chains 171 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 118 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN 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 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 181 GLU 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 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 363 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 816 ASP 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 989 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1050 GLN 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 154 SER Chi-restraints excluded: chain C residue 174 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 Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 77 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 104 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.139330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.100248 restraints weight = 10706.820| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.85 r_work: 0.2808 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9555 Z= 0.155 Angle : 0.539 7.549 12957 Z= 0.271 Chirality : 0.043 0.281 1461 Planarity : 0.004 0.046 1609 Dihedral : 13.535 171.110 1420 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.91 % Allowed : 20.20 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.24), residues: 1125 helix: -1.51 (0.22), residues: 482 sheet: -1.14 (0.42), residues: 169 loop : -1.79 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.008 0.001 HIS A 929 PHE 0.011 0.001 PHE A1055 TYR 0.013 0.001 TYR A 324 ARG 0.003 0.000 ARG A 39 *********************** 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 185 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 125 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7276 (m-80) cc_final: 0.6763 (m-80) REVERT: A 126 TYR cc_start: 0.8656 (m-80) cc_final: 0.8226 (m-80) REVERT: A 185 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8300 (mptt) REVERT: A 206 ARG cc_start: 0.7926 (mmt180) cc_final: 0.7619 (mmt90) REVERT: A 224 ARG cc_start: 0.6636 (ttm170) cc_final: 0.6007 (ttm-80) REVERT: A 266 MET cc_start: 0.8132 (mmp) cc_final: 0.7045 (ttt) REVERT: A 281 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8376 (ptm-80) REVERT: A 386 ASN cc_start: 0.8625 (t0) cc_final: 0.8331 (t0) REVERT: A 777 GLN cc_start: 0.8451 (mt0) cc_final: 0.8131 (mt0) REVERT: C 59 LEU cc_start: 0.8119 (tt) cc_final: 0.7620 (mt) REVERT: C 200 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8364 (tttm) REVERT: C 209 ASP cc_start: 0.8563 (p0) cc_final: 0.8065 (p0) REVERT: C 228 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8125 (mmtp) outliers start: 60 outliers final: 48 residues processed: 172 average time/residue: 0.2519 time to fit residues: 58.1731 Evaluate side-chains 165 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 116 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN 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 101 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 181 GLU 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 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 281 ARG 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 943 MET Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 THR 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 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 154 SER Chi-restraints excluded: chain C residue 171 CYS 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 46 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 chunk 106 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.137311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.098409 restraints weight = 10733.057| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.84 r_work: 0.2772 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9555 Z= 0.181 Angle : 0.539 7.255 12957 Z= 0.273 Chirality : 0.043 0.292 1461 Planarity : 0.004 0.047 1609 Dihedral : 13.373 171.112 1415 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.52 % Allowed : 20.59 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.24), residues: 1125 helix: -1.21 (0.23), residues: 483 sheet: -0.91 (0.42), residues: 168 loop : -1.71 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.007 0.001 HIS A 929 PHE 0.010 0.001 PHE A 965 TYR 0.012 0.001 TYR A 324 ARG 0.003 0.000 ARG A 839 *********************** 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 176 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 120 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7314 (m-80) cc_final: 0.6809 (m-80) REVERT: A 126 TYR cc_start: 0.8711 (m-80) cc_final: 0.8398 (m-80) REVERT: A 142 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7238 (mtpp) REVERT: A 185 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8309 (mptt) REVERT: A 206 ARG cc_start: 0.7953 (mmt180) cc_final: 0.7681 (mmt90) REVERT: A 266 MET cc_start: 0.8153 (mmp) cc_final: 0.7062 (ttt) REVERT: A 281 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8309 (ptm-80) REVERT: A 386 ASN cc_start: 0.8640 (t0) cc_final: 0.8346 (t0) REVERT: A 777 GLN cc_start: 0.8480 (mt0) cc_final: 0.8149 (mt0) REVERT: A 1055 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8406 (m-80) REVERT: C 27 ARG cc_start: 0.1329 (OUTLIER) cc_final: 0.0426 (tpt-90) REVERT: C 59 LEU cc_start: 0.8135 (tt) cc_final: 0.7645 (mt) REVERT: C 188 ILE cc_start: 0.8061 (mm) cc_final: 0.7852 (mm) REVERT: C 200 LYS cc_start: 0.8669 (ttmt) cc_final: 0.8359 (tttm) REVERT: C 228 LYS cc_start: 0.8401 (mmmm) cc_final: 0.8152 (mmtp) outliers start: 56 outliers final: 49 residues processed: 165 average time/residue: 0.2662 time to fit residues: 58.9126 Evaluate side-chains 170 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 101 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 181 GLU 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 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 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 755 THR 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 694 ASN A 745 GLN A1089 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.133611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.093624 restraints weight = 10883.341| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.82 r_work: 0.2708 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9555 Z= 0.365 Angle : 0.628 8.013 12957 Z= 0.317 Chirality : 0.048 0.308 1461 Planarity : 0.004 0.045 1609 Dihedral : 13.774 168.904 1414 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.24), residues: 1125 helix: -1.38 (0.22), residues: 494 sheet: -0.79 (0.44), residues: 154 loop : -1.78 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.007 0.001 HIS A 929 PHE 0.013 0.002 PHE A 884 TYR 0.014 0.002 TYR A 311 ARG 0.004 0.000 ARG A 839 *********************** 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 182 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 119 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7585 (m-80) cc_final: 0.6972 (m-80) REVERT: A 126 TYR cc_start: 0.8755 (m-80) cc_final: 0.8439 (m-80) REVERT: A 142 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7174 (mtpp) REVERT: A 206 ARG cc_start: 0.7895 (mmt180) cc_final: 0.7517 (mmt90) REVERT: A 224 ARG cc_start: 0.6712 (ttm170) cc_final: 0.6028 (ttm-80) REVERT: A 266 MET cc_start: 0.8131 (mmp) cc_final: 0.7044 (ttt) REVERT: A 745 GLN cc_start: 0.5321 (OUTLIER) cc_final: 0.5102 (tm-30) REVERT: A 1055 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: C 59 LEU cc_start: 0.8180 (tt) cc_final: 0.7666 (mt) REVERT: C 200 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8335 (tttm) REVERT: C 228 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8202 (mmmt) outliers start: 63 outliers final: 51 residues processed: 169 average time/residue: 0.2534 time to fit residues: 58.3509 Evaluate side-chains 168 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 114 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 101 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 181 GLU 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 237 ARG Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 277 LYS 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 363 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain A residue 755 THR 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 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 57 ILE Chi-restraints excluded: chain C residue 77 GLU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.136734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.097596 restraints weight = 10850.742| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.83 r_work: 0.2757 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9555 Z= 0.206 Angle : 0.557 7.727 12957 Z= 0.283 Chirality : 0.044 0.293 1461 Planarity : 0.004 0.044 1609 Dihedral : 13.421 171.066 1414 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.62 % Allowed : 20.99 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.24), residues: 1125 helix: -1.06 (0.23), residues: 488 sheet: -0.90 (0.44), residues: 156 loop : -1.61 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.008 0.001 HIS A 929 PHE 0.011 0.001 PHE A1024 TYR 0.011 0.001 TYR A 324 ARG 0.003 0.000 ARG A 839 *********************** 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 178 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 121 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7473 (m-80) cc_final: 0.6860 (m-80) REVERT: A 51 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8532 (t) REVERT: A 126 TYR cc_start: 0.8741 (m-80) cc_final: 0.8448 (m-80) REVERT: A 142 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7200 (mtpp) REVERT: A 206 ARG cc_start: 0.7877 (mmt180) cc_final: 0.7498 (mmt90) REVERT: A 224 ARG cc_start: 0.6642 (ttm170) cc_final: 0.5985 (ttm-80) REVERT: A 266 MET cc_start: 0.8146 (mmp) cc_final: 0.7071 (ttt) REVERT: A 281 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8104 (ptm-80) REVERT: A 386 ASN cc_start: 0.8676 (t0) cc_final: 0.8468 (t0) REVERT: A 1055 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: C 59 LEU cc_start: 0.8168 (tt) cc_final: 0.7647 (mt) REVERT: C 200 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8357 (tttm) REVERT: C 228 LYS cc_start: 0.8379 (mmmm) cc_final: 0.8078 (mmtp) outliers start: 57 outliers final: 48 residues processed: 165 average time/residue: 0.2486 time to fit residues: 55.3571 Evaluate side-chains 170 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 186 THR 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 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 363 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 755 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 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 78 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.2980 chunk 11 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 65 optimal weight: 0.0570 chunk 111 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.4300 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.140740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.101645 restraints weight = 10559.334| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.72 r_work: 0.2853 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9555 Z= 0.138 Angle : 0.512 7.846 12957 Z= 0.262 Chirality : 0.042 0.274 1461 Planarity : 0.004 0.045 1609 Dihedral : 12.823 173.826 1414 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.04 % Allowed : 22.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.25), residues: 1125 helix: -0.62 (0.24), residues: 482 sheet: -0.61 (0.44), residues: 162 loop : -1.46 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 323 HIS 0.009 0.001 HIS A 929 PHE 0.009 0.001 PHE A 72 TYR 0.014 0.001 TYR A 324 ARG 0.003 0.000 ARG A 133 *********************** 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 168 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7228 (m-80) cc_final: 0.6769 (m-80) REVERT: A 185 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8229 (mptt) REVERT: A 266 MET cc_start: 0.8078 (mmp) cc_final: 0.6947 (ttt) REVERT: A 281 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8300 (ptm-80) REVERT: A 777 GLN cc_start: 0.8431 (mt0) cc_final: 0.8069 (mt0) REVERT: A 1055 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: C 42 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7644 (mm-40) REVERT: C 59 LEU cc_start: 0.8119 (tt) cc_final: 0.7613 (mt) REVERT: C 200 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8329 (tttm) REVERT: C 228 LYS cc_start: 0.8382 (mmmm) cc_final: 0.8181 (mmmm) outliers start: 41 outliers final: 33 residues processed: 159 average time/residue: 0.2897 time to fit residues: 62.0603 Evaluate side-chains 151 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 101 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 181 GLU 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 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 363 VAL 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 989 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 44 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 154 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0870 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.140280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.101978 restraints weight = 10750.731| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.77 r_work: 0.2836 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9555 Z= 0.151 Angle : 0.534 11.112 12957 Z= 0.270 Chirality : 0.043 0.268 1461 Planarity : 0.004 0.044 1609 Dihedral : 12.451 170.314 1412 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.14 % Allowed : 23.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.25), residues: 1125 helix: -0.44 (0.24), residues: 479 sheet: -0.50 (0.44), residues: 162 loop : -1.39 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 323 HIS 0.008 0.001 HIS A 929 PHE 0.009 0.001 PHE A 72 TYR 0.012 0.001 TYR A 324 ARG 0.007 0.000 ARG A 133 ********************** 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 161 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7136 (m-80) cc_final: 0.6695 (m-80) REVERT: A 266 MET cc_start: 0.8095 (mmp) cc_final: 0.6947 (ttt) REVERT: A 281 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8276 (ptm-80) REVERT: A 1055 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: C 59 LEU cc_start: 0.8113 (tt) cc_final: 0.7601 (mt) REVERT: C 200 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8305 (tttm) REVERT: C 228 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8174 (mmmm) outliers start: 42 outliers final: 37 residues processed: 151 average time/residue: 0.2559 time to fit residues: 52.1187 Evaluate side-chains 155 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 101 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 181 GLU 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 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 363 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 833 ILE 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 C residue 27 ARG Chi-restraints excluded: chain C residue 44 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.0370 chunk 21 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.141836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.103023 restraints weight = 10611.076| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.75 r_work: 0.2855 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9555 Z= 0.138 Angle : 0.521 11.062 12957 Z= 0.263 Chirality : 0.042 0.254 1461 Planarity : 0.003 0.043 1609 Dihedral : 12.125 169.284 1412 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.04 % Allowed : 23.15 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.25), residues: 1125 helix: -0.15 (0.25), residues: 472 sheet: -0.40 (0.44), residues: 168 loop : -1.31 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.009 0.001 HIS A 929 PHE 0.009 0.001 PHE A 72 TYR 0.013 0.001 TYR A 324 ARG 0.006 0.000 ARG A 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5216.06 seconds wall clock time: 93 minutes 15.27 seconds (5595.27 seconds total)