Starting phenix.real_space_refine on Wed Feb 4 08:35:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vkg_65136/02_2026/9vkg_65136_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vkg_65136/02_2026/9vkg_65136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vkg_65136/02_2026/9vkg_65136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vkg_65136/02_2026/9vkg_65136.map" model { file = "/net/cci-nas-00/data/ceres_data/9vkg_65136/02_2026/9vkg_65136_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vkg_65136/02_2026/9vkg_65136_trim.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 Al 1 5.89 5 P 1 5.49 5 Mg 1 5.21 5 S 45 5.16 5 C 6077 2.51 5 N 1503 2.21 5 O 1697 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9329 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6596 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 792} Chain breaks: 3 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ALF': 1, 'PCW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 2.39, per 1000 atoms: 0.26 Number of scatterers: 9329 At special positions: 0 Unit cell: (74.448, 106.032, 165.44, 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 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1697 8.00 N 1503 7.00 C 6077 6.00 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=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.04 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=1, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 482.1 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 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: 54 helices and 7 sheets defined 52.1% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 88 through 121 Proline residue: A 94 - end of helix Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.529A pdb=" N ILE A 194 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.767A pdb=" N ASP A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 204' Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 282 through 314 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 335 through 352 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 356 through 371 removed outlier: 3.991A pdb=" N TYR A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.744A pdb=" N SER A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 677 through 688 Processing helix chain 'A' and resid 707 through 721 removed outlier: 3.661A pdb=" N GLU A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 762 Processing helix chain 'A' and resid 770 through 781 removed outlier: 3.837A pdb=" N LYS A 781 " --> pdb=" O GLN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 804 removed outlier: 3.757A pdb=" N ALA A 796 " --> pdb=" O PRO A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 819 No H-bonds generated for 'chain 'A' and resid 817 through 819' Processing helix chain 'A' and resid 820 through 827 Processing helix chain 'A' and resid 839 through 845 Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 854 through 861 Processing helix chain 'A' and resid 861 through 891 Proline residue: A 887 - end of helix Processing helix chain 'A' and resid 892 through 894 No H-bonds generated for 'chain 'A' and resid 892 through 894' Processing helix chain 'A' and resid 904 through 911 Processing helix chain 'A' and resid 917 through 927 removed outlier: 3.505A pdb=" N LEU A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 938 Processing helix chain 'A' and resid 939 through 946 removed outlier: 3.596A pdb=" N ILE A 945 " --> pdb=" O TYR A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 951 Processing helix chain 'A' and resid 952 through 978 Processing helix chain 'A' and resid 991 through 1015 Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 3.758A pdb=" N LEU A1030 " --> pdb=" O ILE A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1061 Processing helix chain 'A' and resid 1063 through 1089 Proline residue: A1080 - end of helix removed outlier: 3.510A pdb=" N ASN A1089 " --> pdb=" O ILE A1085 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 52 through 74 removed outlier: 4.060A pdb=" N GLY C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.506A pdb=" N LYS C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.518A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.528A pdb=" N GLU C 158 " --> pdb=" O LYS C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.684A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 removed outlier: 3.965A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 348 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 4.295A pdb=" N ARG A 206 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137 removed outlier: 12.294A pdb=" N THR A 124 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N GLN A 150 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 126 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A 146 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS A 256 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER A 164 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR A 258 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASP A 158 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.859A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.307A pdb=" N GLY A 830 " --> pdb=" O TYR A 847 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL A 849 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY A 832 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR A 811 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE A 831 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE A 833 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY A 815 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 670 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N CYS A 787 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 672 " --> pdb=" O CYS A 787 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR A 747 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N LEU A 786 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 749 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N CYS A 788 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 751 " --> pdb=" O CYS A 788 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 81 removed outlier: 3.556A pdb=" N ARG C 307 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU C 275 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET C 120 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 110 removed outlier: 4.382A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 162 through 163 449 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1471 1.32 - 1.44: 2679 1.44 - 1.57: 5330 1.57 - 1.69: 2 1.69 - 1.81: 71 Bond restraints: 9553 Sorted by residual: bond pdb=" CA SER C 96 " pdb=" CB SER C 96 " ideal model delta sigma weight residual 1.531 1.488 0.042 1.22e-02 6.72e+03 1.21e+01 bond pdb=" CA SER C 89 " pdb=" CB SER C 89 " ideal model delta sigma weight residual 1.526 1.468 0.058 1.73e-02 3.34e+03 1.13e+01 bond pdb=" CA SER C 88 " pdb=" CB SER C 88 " ideal model delta sigma weight residual 1.531 1.479 0.052 1.62e-02 3.81e+03 1.02e+01 bond pdb=" N PRO C 28 " pdb=" CA PRO C 28 " ideal model delta sigma weight residual 1.466 1.503 -0.037 1.21e-02 6.83e+03 9.13e+00 bond pdb=" O4P PCW A1103 " pdb=" P PCW A1103 " ideal model delta sigma weight residual 1.652 1.592 0.060 2.00e-02 2.50e+03 8.92e+00 ... (remaining 9548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.82: 12947 13.82 - 27.63: 5 27.63 - 41.45: 0 41.45 - 55.27: 0 55.27 - 69.09: 2 Bond angle restraints: 12954 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 177.77 -69.09 3.00e+00 1.11e-01 5.30e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 171.88 -62.25 3.00e+00 1.11e-01 4.31e+02 angle pdb=" C CYS C 104 " pdb=" CA CYS C 104 " pdb=" CB CYS C 104 " ideal model delta sigma weight residual 109.38 93.59 15.79 2.03e+00 2.43e-01 6.05e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.69 87.60 22.09 3.00e+00 1.11e-01 5.42e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.02 87.59 21.43 3.00e+00 1.11e-01 5.10e+01 ... (remaining 12949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 5438 35.12 - 70.24: 239 70.24 - 105.35: 29 105.35 - 140.47: 1 140.47 - 175.59: 1 Dihedral angle restraints: 5708 sinusoidal: 2365 harmonic: 3343 Sorted by residual: dihedral pdb=" CB CYS C 91 " pdb=" SG CYS C 91 " pdb=" SG CYS C 104 " pdb=" CB CYS C 104 " ideal model delta sinusoidal sigma weight residual 93.00 173.80 -80.80 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" C CYS C 104 " pdb=" N CYS C 104 " pdb=" CA CYS C 104 " pdb=" CB CYS C 104 " ideal model delta harmonic sigma weight residual -122.60 -100.99 -21.61 0 2.50e+00 1.60e-01 7.47e+01 dihedral pdb=" CA ALA C 169 " pdb=" C ALA C 169 " pdb=" N PRO C 170 " pdb=" CA PRO C 170 " ideal model delta harmonic sigma weight residual 180.00 154.69 25.31 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 5705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.240: 1456 0.240 - 0.480: 2 0.480 - 0.720: 1 0.720 - 0.960: 0 0.960 - 1.200: 1 Chirality restraints: 1460 Sorted by residual: chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -1.20 -1.20 2.00e-01 2.50e+01 3.60e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.45e+01 chirality pdb=" C1 NAG C 402 " pdb=" ND2 ASN C 107 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.36e+00 ... (remaining 1457 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.343 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG C 402 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.058 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.520 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 107 " 0.155 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" CG ASN C 107 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN C 107 " 0.105 2.00e-02 2.50e+03 pdb=" ND2 ASN C 107 " -0.507 2.00e-02 2.50e+03 pdb=" C1 NAG C 402 " 0.338 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " -0.320 2.00e-02 2.50e+03 2.78e-01 9.67e+02 pdb=" C7 NAG C 401 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " 0.498 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.118 2.00e-02 2.50e+03 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 11 2.31 - 2.96: 4240 2.96 - 3.61: 13946 3.61 - 4.25: 23875 4.25 - 4.90: 38609 Nonbonded interactions: 80681 Sorted by model distance: nonbonded pdb=" O THR A 411 " pdb="MG MG A1102 " model vdw 1.669 2.170 nonbonded pdb=" OD2 ASP A 676 " pdb=" OG1 THR A 680 " model vdw 2.149 3.040 nonbonded pdb=" F4 ALF A1101 " pdb="MG MG A1102 " model vdw 2.225 2.120 nonbonded pdb=" OD1 ASP A 816 " pdb="MG MG A1102 " model vdw 2.240 2.170 nonbonded pdb=" O LEU A 162 " pdb=" OG1 THR A 193 " model vdw 2.250 3.040 ... (remaining 80676 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: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.530 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 0.312 9561 Z= 0.402 Angle : 1.139 69.087 12972 Z= 0.498 Chirality : 0.059 1.200 1460 Planarity : 0.015 0.296 1613 Dihedral : 19.282 175.591 3543 Min Nonbonded Distance : 1.669 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.65 % Allowed : 20.85 % Favored : 76.50 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.25), residues: 1129 helix: 1.11 (0.22), residues: 534 sheet: 0.44 (0.39), residues: 166 loop : -0.84 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 714 TYR 0.021 0.002 TYR A 311 PHE 0.015 0.002 PHE A 884 TRP 0.013 0.002 TRP C 260 HIS 0.003 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 9553) covalent geometry : angle 1.12741 (12954) SS BOND : bond 0.00928 ( 3) SS BOND : angle 3.25694 ( 6) hydrogen bonds : bond 0.14652 ( 449) hydrogen bonds : angle 5.95484 ( 1272) Misc. bond : bond 0.31174 ( 1) link_BETA1-4 : bond 0.04747 ( 1) link_BETA1-4 : angle 6.85004 ( 3) link_NAG-ASN : bond 0.00342 ( 3) link_NAG-ASN : angle 4.08315 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.367 Fit side-chains REVERT: A 135 ARG cc_start: 0.7362 (ttt180) cc_final: 0.6983 (tmt170) REVERT: A 224 ARG cc_start: 0.8054 (ttm110) cc_final: 0.6922 (ptp-170) REVERT: A 712 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: A 800 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.6811 (ttp-110) REVERT: A 801 MET cc_start: 0.8430 (mtp) cc_final: 0.8180 (mtm) REVERT: A 843 ARG cc_start: 0.7465 (ptt90) cc_final: 0.6827 (mtm110) REVERT: A 1081 GLU cc_start: 0.7270 (tp30) cc_final: 0.6963 (tp30) REVERT: C 27 ARG cc_start: 0.5154 (OUTLIER) cc_final: 0.4889 (mmt-90) REVERT: C 290 ARG cc_start: 0.6652 (mmt180) cc_final: 0.6331 (mmt90) REVERT: C 303 TYR cc_start: 0.7896 (m-80) cc_final: 0.7365 (m-80) outliers start: 27 outliers final: 8 residues processed: 169 average time/residue: 0.6487 time to fit residues: 116.0350 Evaluate side-chains 127 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0070 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.0470 chunk 106 optimal weight: 0.7980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.153477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.126225 restraints weight = 9784.039| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.45 r_work: 0.3375 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9561 Z= 0.120 Angle : 0.824 31.036 12972 Z= 0.354 Chirality : 0.043 0.182 1460 Planarity : 0.004 0.046 1613 Dihedral : 12.090 166.699 1378 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.05 % Allowed : 20.45 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1129 helix: 1.21 (0.23), residues: 544 sheet: 0.89 (0.38), residues: 175 loop : -0.76 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 27 TYR 0.016 0.001 TYR A 311 PHE 0.013 0.001 PHE C 179 TRP 0.011 0.001 TRP C 260 HIS 0.003 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9553) covalent geometry : angle 0.81094 (12954) SS BOND : bond 0.00475 ( 3) SS BOND : angle 1.93763 ( 6) hydrogen bonds : bond 0.04765 ( 449) hydrogen bonds : angle 4.88418 ( 1272) Misc. bond : bond 0.00048 ( 1) link_BETA1-4 : bond 0.00040 ( 1) link_BETA1-4 : angle 2.03036 ( 3) link_NAG-ASN : bond 0.00654 ( 3) link_NAG-ASN : angle 5.33015 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7746 (ttm170) cc_final: 0.6882 (mmp-170) REVERT: A 135 ARG cc_start: 0.7687 (ttt180) cc_final: 0.7081 (tmt170) REVERT: A 224 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7381 (ptp-170) REVERT: A 692 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8538 (mp10) REVERT: A 800 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.6963 (ttp-110) REVERT: A 801 MET cc_start: 0.8437 (mtp) cc_final: 0.8209 (mtm) REVERT: A 843 ARG cc_start: 0.7595 (ptt90) cc_final: 0.6970 (mtm110) REVERT: A 879 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8854 (t80) REVERT: C 37 ARG cc_start: 0.8632 (ptt180) cc_final: 0.8427 (ptt-90) REVERT: C 244 ASP cc_start: 0.8237 (t70) cc_final: 0.7947 (t0) REVERT: C 290 ARG cc_start: 0.7067 (mmt180) cc_final: 0.6764 (mmt90) REVERT: C 303 TYR cc_start: 0.8062 (m-80) cc_final: 0.7568 (m-80) outliers start: 31 outliers final: 12 residues processed: 146 average time/residue: 0.6413 time to fit residues: 99.2442 Evaluate side-chains 133 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 238 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122849 restraints weight = 9720.999| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.48 r_work: 0.3329 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9561 Z= 0.133 Angle : 0.825 30.189 12972 Z= 0.357 Chirality : 0.043 0.178 1460 Planarity : 0.004 0.042 1613 Dihedral : 11.550 167.725 1369 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.93 % Allowed : 19.57 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1129 helix: 1.21 (0.23), residues: 543 sheet: 0.93 (0.38), residues: 175 loop : -0.77 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 714 TYR 0.018 0.002 TYR A 311 PHE 0.014 0.002 PHE C 108 TRP 0.011 0.002 TRP C 260 HIS 0.004 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9553) covalent geometry : angle 0.81712 (12954) SS BOND : bond 0.00300 ( 3) SS BOND : angle 1.85110 ( 6) hydrogen bonds : bond 0.04789 ( 449) hydrogen bonds : angle 4.72869 ( 1272) Misc. bond : bond 0.00079 ( 1) link_BETA1-4 : bond 0.00147 ( 1) link_BETA1-4 : angle 2.41275 ( 3) link_NAG-ASN : bond 0.00392 ( 3) link_NAG-ASN : angle 3.81929 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7814 (ttm170) cc_final: 0.6947 (mmp-170) REVERT: A 135 ARG cc_start: 0.7745 (ttt180) cc_final: 0.7158 (tmt170) REVERT: A 142 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7340 (mtmm) REVERT: A 213 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: A 224 ARG cc_start: 0.8456 (ttm110) cc_final: 0.7411 (ptp-170) REVERT: A 330 LYS cc_start: 0.7408 (ttpt) cc_final: 0.6827 (tmtt) REVERT: A 692 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8520 (mp10) REVERT: A 712 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6404 (mm-30) REVERT: A 800 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7089 (ttp-110) REVERT: A 879 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8709 (t80) REVERT: C 136 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7826 (pptt) REVERT: C 244 ASP cc_start: 0.8256 (t70) cc_final: 0.7951 (t0) REVERT: C 290 ARG cc_start: 0.7164 (mmt180) cc_final: 0.6895 (mmt90) REVERT: C 303 TYR cc_start: 0.8134 (m-80) cc_final: 0.7666 (m-80) outliers start: 40 outliers final: 17 residues processed: 154 average time/residue: 0.6646 time to fit residues: 108.7608 Evaluate side-chains 146 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 10 optimal weight: 0.0030 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123060 restraints weight = 9767.217| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.48 r_work: 0.3343 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9561 Z= 0.127 Angle : 0.808 30.386 12972 Z= 0.347 Chirality : 0.043 0.196 1460 Planarity : 0.004 0.042 1613 Dihedral : 11.309 167.644 1368 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.44 % Allowed : 20.35 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1129 helix: 1.28 (0.23), residues: 543 sheet: 1.01 (0.38), residues: 175 loop : -0.79 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 161 TYR 0.017 0.002 TYR A 311 PHE 0.017 0.002 PHE C 108 TRP 0.012 0.001 TRP C 260 HIS 0.003 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9553) covalent geometry : angle 0.80069 (12954) SS BOND : bond 0.00418 ( 3) SS BOND : angle 1.41703 ( 6) hydrogen bonds : bond 0.04597 ( 449) hydrogen bonds : angle 4.71814 ( 1272) Misc. bond : bond 0.00061 ( 1) link_BETA1-4 : bond 0.00054 ( 1) link_BETA1-4 : angle 2.30584 ( 3) link_NAG-ASN : bond 0.00460 ( 3) link_NAG-ASN : angle 3.82291 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7816 (ttm170) cc_final: 0.6800 (mmp-170) REVERT: A 135 ARG cc_start: 0.7720 (ttt180) cc_final: 0.7018 (tmt170) REVERT: A 142 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7285 (mtmm) REVERT: A 213 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: A 224 ARG cc_start: 0.8396 (ttm110) cc_final: 0.7292 (ptp-170) REVERT: A 330 LYS cc_start: 0.7321 (ttpt) cc_final: 0.6726 (tmtt) REVERT: A 800 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.6947 (ttp-110) REVERT: A 801 MET cc_start: 0.8457 (mtp) cc_final: 0.8166 (mtm) REVERT: A 843 ARG cc_start: 0.7660 (ptt90) cc_final: 0.7010 (mtm110) REVERT: A 879 TYR cc_start: 0.9160 (OUTLIER) cc_final: 0.8706 (t80) REVERT: C 244 ASP cc_start: 0.8203 (t70) cc_final: 0.7842 (t0) REVERT: C 290 ARG cc_start: 0.7128 (mmt180) cc_final: 0.6853 (mmt90) REVERT: C 303 TYR cc_start: 0.8132 (m-80) cc_final: 0.7656 (m-80) outliers start: 35 outliers final: 16 residues processed: 142 average time/residue: 0.6279 time to fit residues: 94.6810 Evaluate side-chains 138 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 259 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 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 314 GLN C 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114092 restraints weight = 9689.354| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.60 r_work: 0.3220 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9561 Z= 0.225 Angle : 0.892 30.910 12972 Z= 0.401 Chirality : 0.049 0.191 1460 Planarity : 0.005 0.042 1613 Dihedral : 11.668 173.394 1368 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.13 % Allowed : 19.67 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.25), residues: 1129 helix: 0.99 (0.22), residues: 535 sheet: 0.96 (0.38), residues: 175 loop : -0.79 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 723 TYR 0.020 0.002 TYR A 311 PHE 0.021 0.002 PHE A1036 TRP 0.017 0.002 TRP C 236 HIS 0.004 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 9553) covalent geometry : angle 0.88335 (12954) SS BOND : bond 0.00741 ( 3) SS BOND : angle 2.11668 ( 6) hydrogen bonds : bond 0.05813 ( 449) hydrogen bonds : angle 4.97510 ( 1272) Misc. bond : bond 0.00110 ( 1) link_BETA1-4 : bond 0.00416 ( 1) link_BETA1-4 : angle 3.19270 ( 3) link_NAG-ASN : bond 0.00540 ( 3) link_NAG-ASN : angle 4.16624 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6818 (mmp-170) REVERT: A 135 ARG cc_start: 0.7816 (ttt180) cc_final: 0.7104 (tmt170) REVERT: A 142 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7379 (mtmm) REVERT: A 213 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7304 (mp10) REVERT: A 218 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7238 (mp) REVERT: A 224 ARG cc_start: 0.8457 (ttm170) cc_final: 0.7293 (ptp-170) REVERT: A 330 LYS cc_start: 0.7507 (ttpt) cc_final: 0.6961 (tmtt) REVERT: A 692 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8491 (mp10) REVERT: A 712 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6740 (mm-30) REVERT: A 800 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7073 (ttp-110) REVERT: A 801 MET cc_start: 0.8555 (mtp) cc_final: 0.8240 (mtm) REVERT: C 37 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7979 (ptt-90) REVERT: C 290 ARG cc_start: 0.7143 (mmt180) cc_final: 0.6847 (mmt90) REVERT: C 303 TYR cc_start: 0.8169 (m-80) cc_final: 0.7718 (m-80) outliers start: 42 outliers final: 21 residues processed: 152 average time/residue: 0.6941 time to fit residues: 111.8030 Evaluate side-chains 146 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 236 TRP Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 0.0770 chunk 102 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.146668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117532 restraints weight = 9677.169| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.55 r_work: 0.3292 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9561 Z= 0.119 Angle : 0.804 30.244 12972 Z= 0.345 Chirality : 0.042 0.195 1460 Planarity : 0.004 0.040 1613 Dihedral : 11.179 168.350 1368 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.65 % Allowed : 20.45 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.25), residues: 1129 helix: 1.21 (0.23), residues: 542 sheet: 0.94 (0.38), residues: 178 loop : -0.79 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.017 0.002 TYR A 311 PHE 0.019 0.001 PHE C 108 TRP 0.012 0.001 TRP C 260 HIS 0.003 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9553) covalent geometry : angle 0.79644 (12954) SS BOND : bond 0.00369 ( 3) SS BOND : angle 1.31686 ( 6) hydrogen bonds : bond 0.04523 ( 449) hydrogen bonds : angle 4.69784 ( 1272) Misc. bond : bond 0.00056 ( 1) link_BETA1-4 : bond 0.00002 ( 1) link_BETA1-4 : angle 2.27484 ( 3) link_NAG-ASN : bond 0.00430 ( 3) link_NAG-ASN : angle 3.91030 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7818 (ttm170) cc_final: 0.6688 (mmp-170) REVERT: A 135 ARG cc_start: 0.7735 (ttt180) cc_final: 0.7037 (tmt170) REVERT: A 142 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7287 (mtmm) REVERT: A 213 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: A 224 ARG cc_start: 0.8381 (ttm170) cc_final: 0.7176 (ptp-170) REVERT: A 330 LYS cc_start: 0.7357 (ttpt) cc_final: 0.6771 (tmtt) REVERT: A 712 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6499 (mm-30) REVERT: A 722 TYR cc_start: 0.5499 (OUTLIER) cc_final: 0.4764 (t80) REVERT: A 746 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.4918 (tt0) REVERT: A 789 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7817 (mmm-85) REVERT: A 800 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.6913 (ttp-110) REVERT: A 801 MET cc_start: 0.8434 (mtp) cc_final: 0.8117 (mtm) REVERT: A 879 TYR cc_start: 0.9159 (OUTLIER) cc_final: 0.8752 (t80) REVERT: A 1060 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8167 (ttt) REVERT: C 290 ARG cc_start: 0.7108 (mmt180) cc_final: 0.6799 (mmt90) REVERT: C 303 TYR cc_start: 0.8086 (m-80) cc_final: 0.7679 (m-80) outliers start: 27 outliers final: 12 residues processed: 142 average time/residue: 0.6818 time to fit residues: 102.7741 Evaluate side-chains 140 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 155 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 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 314 GLN C 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.143155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113678 restraints weight = 9732.999| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.55 r_work: 0.3242 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9561 Z= 0.225 Angle : 0.888 30.846 12972 Z= 0.399 Chirality : 0.048 0.180 1460 Planarity : 0.005 0.041 1613 Dihedral : 11.542 173.453 1368 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.74 % Allowed : 19.57 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.25), residues: 1129 helix: 0.95 (0.22), residues: 535 sheet: 0.99 (0.38), residues: 175 loop : -0.78 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 714 TYR 0.019 0.002 TYR A 311 PHE 0.022 0.002 PHE A1036 TRP 0.017 0.002 TRP C 236 HIS 0.004 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 9553) covalent geometry : angle 0.88092 (12954) SS BOND : bond 0.00807 ( 3) SS BOND : angle 1.60615 ( 6) hydrogen bonds : bond 0.05753 ( 449) hydrogen bonds : angle 4.93560 ( 1272) Misc. bond : bond 0.00124 ( 1) link_BETA1-4 : bond 0.00536 ( 1) link_BETA1-4 : angle 3.16201 ( 3) link_NAG-ASN : bond 0.00568 ( 3) link_NAG-ASN : angle 3.96948 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7850 (ttm170) cc_final: 0.6741 (mmp-170) REVERT: A 135 ARG cc_start: 0.7785 (ttt180) cc_final: 0.7055 (tmt170) REVERT: A 142 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7341 (mtmm) REVERT: A 213 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: A 218 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7261 (mp) REVERT: A 330 LYS cc_start: 0.7449 (ttpt) cc_final: 0.6827 (tmtt) REVERT: A 692 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8447 (mp10) REVERT: A 712 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6739 (mm-30) REVERT: A 760 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7798 (mp) REVERT: A 800 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.6937 (ttp-110) REVERT: A 801 MET cc_start: 0.8517 (mtp) cc_final: 0.8188 (mtm) REVERT: A 1060 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8552 (ttp) REVERT: C 37 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7893 (ptt-90) REVERT: C 136 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.7943 (pptt) REVERT: C 224 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: C 290 ARG cc_start: 0.7141 (mmt180) cc_final: 0.6813 (mmt90) REVERT: C 303 TYR cc_start: 0.8091 (m-80) cc_final: 0.7687 (m-80) outliers start: 38 outliers final: 22 residues processed: 148 average time/residue: 0.6942 time to fit residues: 109.0106 Evaluate side-chains 146 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 236 TRP Chi-restraints excluded: chain C residue 259 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116034 restraints weight = 9631.415| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.55 r_work: 0.3271 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9561 Z= 0.142 Angle : 0.827 30.429 12972 Z= 0.360 Chirality : 0.044 0.376 1460 Planarity : 0.004 0.040 1613 Dihedral : 11.041 170.125 1368 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.85 % Allowed : 20.94 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1129 helix: 1.10 (0.22), residues: 536 sheet: 0.96 (0.38), residues: 175 loop : -0.75 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 723 TYR 0.017 0.002 TYR A 311 PHE 0.016 0.002 PHE C 108 TRP 0.012 0.002 TRP C 260 HIS 0.003 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9553) covalent geometry : angle 0.82099 (12954) SS BOND : bond 0.00434 ( 3) SS BOND : angle 1.26023 ( 6) hydrogen bonds : bond 0.04874 ( 449) hydrogen bonds : angle 4.77887 ( 1272) Misc. bond : bond 0.00070 ( 1) link_BETA1-4 : bond 0.00146 ( 1) link_BETA1-4 : angle 2.53525 ( 3) link_NAG-ASN : bond 0.00423 ( 3) link_NAG-ASN : angle 3.66371 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7819 (ttm170) cc_final: 0.6673 (mmp-170) REVERT: A 135 ARG cc_start: 0.7770 (ttt180) cc_final: 0.7050 (tmt170) REVERT: A 142 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7274 (mtmm) REVERT: A 213 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7277 (mp10) REVERT: A 330 LYS cc_start: 0.7424 (ttpt) cc_final: 0.6810 (tmtt) REVERT: A 651 LYS cc_start: 0.7507 (tmtt) cc_final: 0.7286 (tmtt) REVERT: A 692 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8409 (mp10) REVERT: A 712 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.6615 (mm-30) REVERT: A 746 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.4879 (tt0) REVERT: A 800 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.6918 (ttp-110) REVERT: A 801 MET cc_start: 0.8476 (mtp) cc_final: 0.8131 (mtm) REVERT: A 1060 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8290 (ttt) REVERT: A 1081 GLU cc_start: 0.7580 (tp30) cc_final: 0.7370 (mm-30) REVERT: C 37 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7887 (ptt-90) REVERT: C 224 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: C 290 ARG cc_start: 0.7151 (mmt180) cc_final: 0.6818 (mmt90) REVERT: C 303 TYR cc_start: 0.8072 (m-80) cc_final: 0.7679 (m-80) outliers start: 29 outliers final: 17 residues processed: 139 average time/residue: 0.6975 time to fit residues: 102.8846 Evaluate side-chains 141 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114959 restraints weight = 9663.776| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.52 r_work: 0.3261 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9561 Z= 0.172 Angle : 0.856 30.590 12972 Z= 0.377 Chirality : 0.046 0.362 1460 Planarity : 0.004 0.041 1613 Dihedral : 10.855 171.101 1368 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.44 % Allowed : 20.45 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.25), residues: 1129 helix: 1.06 (0.22), residues: 536 sheet: 0.92 (0.38), residues: 175 loop : -0.74 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 723 TYR 0.019 0.002 TYR A 311 PHE 0.018 0.002 PHE A1036 TRP 0.013 0.002 TRP C 236 HIS 0.004 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9553) covalent geometry : angle 0.84402 (12954) SS BOND : bond 0.00523 ( 3) SS BOND : angle 1.40324 ( 6) hydrogen bonds : bond 0.05229 ( 449) hydrogen bonds : angle 4.83057 ( 1272) Misc. bond : bond 0.00091 ( 1) link_BETA1-4 : bond 0.00291 ( 1) link_BETA1-4 : angle 2.80008 ( 3) link_NAG-ASN : bond 0.01029 ( 3) link_NAG-ASN : angle 5.11427 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7820 (ttm170) cc_final: 0.6716 (mmp-170) REVERT: A 135 ARG cc_start: 0.7737 (ttt180) cc_final: 0.7027 (tmt170) REVERT: A 142 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7290 (mtmm) REVERT: A 213 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: A 330 LYS cc_start: 0.7469 (ttpt) cc_final: 0.6878 (tmtt) REVERT: A 692 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8416 (mp10) REVERT: A 712 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.6661 (mm-30) REVERT: A 746 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.5102 (tt0) REVERT: A 800 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.6935 (ttp-110) REVERT: A 801 MET cc_start: 0.8498 (mtp) cc_final: 0.8150 (mtm) REVERT: A 1060 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8376 (ttt) REVERT: C 37 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7878 (ptt-90) REVERT: C 224 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: C 237 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7565 (mp) REVERT: C 290 ARG cc_start: 0.7136 (mmt180) cc_final: 0.6813 (mmt90) REVERT: C 294 ASN cc_start: 0.7495 (OUTLIER) cc_final: 0.6958 (m110) REVERT: C 303 TYR cc_start: 0.8097 (m-80) cc_final: 0.7713 (m-80) outliers start: 35 outliers final: 20 residues processed: 142 average time/residue: 0.6608 time to fit residues: 99.7372 Evaluate side-chains 147 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116150 restraints weight = 9690.589| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.55 r_work: 0.3271 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9561 Z= 0.141 Angle : 0.830 30.405 12972 Z= 0.360 Chirality : 0.044 0.333 1460 Planarity : 0.004 0.041 1613 Dihedral : 10.617 169.650 1368 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.15 % Allowed : 20.65 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1129 helix: 1.15 (0.23), residues: 536 sheet: 0.94 (0.38), residues: 175 loop : -0.72 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 723 TYR 0.018 0.002 TYR A 311 PHE 0.015 0.002 PHE C 179 TRP 0.012 0.002 TRP C 260 HIS 0.003 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9553) covalent geometry : angle 0.81825 (12954) SS BOND : bond 0.00402 ( 3) SS BOND : angle 1.26199 ( 6) hydrogen bonds : bond 0.04799 ( 449) hydrogen bonds : angle 4.74268 ( 1272) Misc. bond : bond 0.00074 ( 1) link_BETA1-4 : bond 0.00116 ( 1) link_BETA1-4 : angle 2.49790 ( 3) link_NAG-ASN : bond 0.00919 ( 3) link_NAG-ASN : angle 5.00681 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7816 (ttm170) cc_final: 0.6664 (mmp-170) REVERT: A 135 ARG cc_start: 0.7740 (ttt180) cc_final: 0.7019 (tmt170) REVERT: A 142 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7292 (mtmm) REVERT: A 213 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: A 330 LYS cc_start: 0.7395 (ttpt) cc_final: 0.6795 (tmtt) REVERT: A 692 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8417 (mp10) REVERT: A 712 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6636 (mm-30) REVERT: A 746 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.4918 (tt0) REVERT: A 800 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.6914 (ttp-110) REVERT: A 801 MET cc_start: 0.8464 (mtp) cc_final: 0.8146 (mtm) REVERT: A 1060 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8277 (ttt) REVERT: A 1081 GLU cc_start: 0.7566 (tp30) cc_final: 0.7349 (mm-30) REVERT: C 37 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7884 (ptt-90) REVERT: C 224 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: C 290 ARG cc_start: 0.7143 (mmt180) cc_final: 0.6824 (mmt90) REVERT: C 294 ASN cc_start: 0.7420 (OUTLIER) cc_final: 0.6853 (m110) REVERT: C 303 TYR cc_start: 0.8079 (m-80) cc_final: 0.7702 (m-80) outliers start: 32 outliers final: 17 residues processed: 143 average time/residue: 0.6756 time to fit residues: 102.6845 Evaluate side-chains 143 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 294 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 100 optimal weight: 0.0030 chunk 95 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.144288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115049 restraints weight = 9572.621| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.53 r_work: 0.3262 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9561 Z= 0.173 Angle : 0.857 30.570 12972 Z= 0.377 Chirality : 0.046 0.333 1460 Planarity : 0.004 0.040 1613 Dihedral : 10.738 171.066 1368 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.15 % Allowed : 20.55 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1129 helix: 1.07 (0.22), residues: 536 sheet: 0.92 (0.38), residues: 175 loop : -0.71 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 723 TYR 0.018 0.002 TYR A 311 PHE 0.018 0.002 PHE A1036 TRP 0.013 0.002 TRP C 260 HIS 0.004 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9553) covalent geometry : angle 0.84515 (12954) SS BOND : bond 0.00520 ( 3) SS BOND : angle 1.33264 ( 6) hydrogen bonds : bond 0.05210 ( 449) hydrogen bonds : angle 4.81599 ( 1272) Misc. bond : bond 0.00087 ( 1) link_BETA1-4 : bond 0.00320 ( 1) link_BETA1-4 : angle 2.78142 ( 3) link_NAG-ASN : bond 0.00980 ( 3) link_NAG-ASN : angle 5.06430 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4436.80 seconds wall clock time: 76 minutes 20.95 seconds (4580.95 seconds total)