Starting phenix.real_space_refine on Thu Jul 2 20:48:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2k_44111/07_2026/9b2k_44111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2k_44111/07_2026/9b2k_44111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b2k_44111/07_2026/9b2k_44111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2k_44111/07_2026/9b2k_44111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b2k_44111/07_2026/9b2k_44111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2k_44111/07_2026/9b2k_44111.map" } resolution = 3.67 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= 0.014 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: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 16 5.16 5 C 6213 2.51 5 N 1802 2.21 5 O 2137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10242 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 381 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "B" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1206 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 31, 'rna3p_pyr': 18} Link IDs: {'rna2p': 7, 'rna3p': 48} Chain breaks: 1 Chain: "P" Number of atoms: 8655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8655 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 27, 'TRANS': 1034} Chain breaks: 2 Time building chain proxies: 2.11, per 1000 atoms: 0.21 Number of scatterers: 10242 At special positions: 0 Unit cell: (85.4, 118.3, 139.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 74 15.00 O 2137 8.00 N 1802 7.00 C 6213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 304.8 milliseconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 7 sheets defined 52.6% alpha, 7.3% beta 18 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'P' and resid 58 through 64 Processing helix chain 'P' and resid 68 through 91 removed outlier: 4.180A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 3.851A pdb=" N ARG P 100 " --> pdb=" O SER P 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU P 101 " --> pdb=" O PHE P 97 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU P 103 " --> pdb=" O HIS P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 132 removed outlier: 4.291A pdb=" N GLU P 125 " --> pdb=" O ASN P 121 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL P 126 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA P 127 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N HIS P 129 " --> pdb=" O GLU P 125 " (cutoff:3.500A) Processing helix chain 'P' and resid 134 through 144 removed outlier: 4.001A pdb=" N LEU P 138 " --> pdb=" O THR P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 164 Processing helix chain 'P' and resid 175 through 179 Processing helix chain 'P' and resid 181 through 196 Processing helix chain 'P' and resid 207 through 213 removed outlier: 3.554A pdb=" N ILE P 211 " --> pdb=" O ASP P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 227 removed outlier: 4.044A pdb=" N LEU P 225 " --> pdb=" O ARG P 221 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE P 226 " --> pdb=" O LEU P 222 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 245 Processing helix chain 'P' and resid 271 through 283 Processing helix chain 'P' and resid 284 through 287 Processing helix chain 'P' and resid 293 through 306 removed outlier: 3.813A pdb=" N ASP P 298 " --> pdb=" O LYS P 294 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA P 299 " --> pdb=" O ASN P 295 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 342 Processing helix chain 'P' and resid 346 through 352 Processing helix chain 'P' and resid 358 through 365 Processing helix chain 'P' and resid 368 through 383 Proline residue: P 378 - end of helix Processing helix chain 'P' and resid 389 through 395 removed outlier: 3.511A pdb=" N ASN P 394 " --> pdb=" O LEU P 390 " (cutoff:3.500A) Processing helix chain 'P' and resid 411 through 426 removed outlier: 4.492A pdb=" N HIS P 415 " --> pdb=" O PRO P 411 " (cutoff:3.500A) Processing helix chain 'P' and resid 430 through 446 removed outlier: 4.227A pdb=" N LYS P 434 " --> pdb=" O TYR P 430 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP P 435 " --> pdb=" O PRO P 431 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLU P 438 " --> pdb=" O LYS P 434 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS P 439 " --> pdb=" O ASP P 435 " (cutoff:3.500A) Processing helix chain 'P' and resid 719 through 727 removed outlier: 3.853A pdb=" N LEU P 727 " --> pdb=" O HIS P 723 " (cutoff:3.500A) Processing helix chain 'P' and resid 730 through 751 removed outlier: 3.652A pdb=" N LYS P 734 " --> pdb=" O SER P 730 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET P 751 " --> pdb=" O LEU P 747 " (cutoff:3.500A) Processing helix chain 'P' and resid 771 through 792 removed outlier: 4.216A pdb=" N SER P 777 " --> pdb=" O GLY P 773 " (cutoff:3.500A) Processing helix chain 'P' and resid 794 through 799 Processing helix chain 'P' and resid 802 through 807 removed outlier: 3.808A pdb=" N GLN P 807 " --> pdb=" O ASN P 803 " (cutoff:3.500A) Processing helix chain 'P' and resid 808 through 817 Processing helix chain 'P' and resid 851 through 853 No H-bonds generated for 'chain 'P' and resid 851 through 853' Processing helix chain 'P' and resid 860 through 864 removed outlier: 3.931A pdb=" N ASN P 863 " --> pdb=" O SER P 860 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG P 864 " --> pdb=" O ASP P 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 860 through 864' Processing helix chain 'P' and resid 872 through 888 removed outlier: 4.261A pdb=" N VAL P 876 " --> pdb=" O SER P 872 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS P 877 " --> pdb=" O GLU P 873 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS P 878 " --> pdb=" O GLU P 874 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET P 879 " --> pdb=" O VAL P 875 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN P 881 " --> pdb=" O LYS P 877 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TYR P 882 " --> pdb=" O LYS P 878 " (cutoff:3.500A) Processing helix chain 'P' and resid 893 through 901 Processing helix chain 'P' and resid 902 through 906 removed outlier: 3.733A pdb=" N ARG P 905 " --> pdb=" O LYS P 902 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY P 906 " --> pdb=" O ALA P 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 902 through 906' Processing helix chain 'P' and resid 909 through 922 Processing helix chain 'P' and resid 925 through 940 removed outlier: 3.686A pdb=" N LYS P 929 " --> pdb=" O ARG P 925 " (cutoff:3.500A) Processing helix chain 'P' and resid 959 through 971 removed outlier: 4.408A pdb=" N VAL P 963 " --> pdb=" O LYS P 959 " (cutoff:3.500A) Processing helix chain 'P' and resid 981 through 1001 removed outlier: 3.594A pdb=" N ALA P 991 " --> pdb=" O ALA P 987 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA P 996 " --> pdb=" O VAL P 992 " (cutoff:3.500A) Processing helix chain 'P' and resid 1004 through 1009 removed outlier: 4.134A pdb=" N PHE P1008 " --> pdb=" O LEU P1004 " (cutoff:3.500A) Processing helix chain 'P' and resid 1025 through 1030 removed outlier: 3.512A pdb=" N ILE P1029 " --> pdb=" O SER P1025 " (cutoff:3.500A) Processing helix chain 'P' and resid 1041 through 1047 removed outlier: 3.739A pdb=" N ASN P1044 " --> pdb=" O ASN P1041 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE P1045 " --> pdb=" O ILE P1042 " (cutoff:3.500A) Processing helix chain 'P' and resid 1076 through 1089 removed outlier: 3.933A pdb=" N PHE P1080 " --> pdb=" O LYS P1076 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA P1081 " --> pdb=" O GLY P1077 " (cutoff:3.500A) Processing helix chain 'P' and resid 1170 through 1177 removed outlier: 3.570A pdb=" N ASN P1177 " --> pdb=" O SER P1173 " (cutoff:3.500A) Processing helix chain 'P' and resid 1177 through 1186 Processing helix chain 'P' and resid 1207 through 1209 No H-bonds generated for 'chain 'P' and resid 1207 through 1209' Processing helix chain 'P' and resid 1229 through 1241 Processing helix chain 'P' and resid 1248 through 1262 removed outlier: 3.902A pdb=" N HIS P1262 " --> pdb=" O PHE P1258 " (cutoff:3.500A) Processing helix chain 'P' and resid 1264 through 1280 Processing helix chain 'P' and resid 1283 through 1297 Processing helix chain 'P' and resid 1301 through 1313 removed outlier: 3.570A pdb=" N GLU P1307 " --> pdb=" O ARG P1303 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN P1308 " --> pdb=" O GLU P1304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 954 through 957 removed outlier: 3.782A pdb=" N ILE P 759 " --> pdb=" O LYS P 954 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 956 " --> pdb=" O ILE P 759 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE P 7 " --> pdb=" O ASN P 758 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE P 11 " --> pdb=" O GLU P 762 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER P 6 " --> pdb=" O ILE P 21 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY P 8 " --> pdb=" O ALA P 19 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA P 19 " --> pdb=" O GLY P 8 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP P 10 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY P 17 " --> pdb=" O ASP P 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 29 through 30 Processing sheet with id=AA3, first strand: chain 'P' and resid 35 through 36 removed outlier: 3.561A pdb=" N LEU P 35 " --> pdb=" O GLU P1357 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR P1358 " --> pdb=" O HIS P1349 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU P1203 " --> pdb=" O ILE P1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 837 through 840 removed outlier: 3.764A pdb=" N ASP P 837 " --> pdb=" O THR P 858 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR P 858 " --> pdb=" O ASP P 837 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP P 839 " --> pdb=" O VAL P 856 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL P 856 " --> pdb=" O ASP P 839 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'P' and resid 1063 through 1065 removed outlier: 6.627A pdb=" N GLU P1064 " --> pdb=" O VAL P1073 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 1157 through 1167 removed outlier: 3.740A pdb=" N VAL P1145 " --> pdb=" O GLU P1162 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU P1164 " --> pdb=" O VAL P1143 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE P1166 " --> pdb=" O TYR P1141 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR P1141 " --> pdb=" O ILE P1166 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU P1144 " --> pdb=" O ILE P1196 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE P1196 " --> pdb=" O LEU P1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 1324 through 1325 removed outlier: 3.738A pdb=" N PHE P1324 " --> pdb=" O ILE P1331 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2961 1.34 - 1.46: 2224 1.46 - 1.58: 5215 1.58 - 1.70: 146 1.70 - 1.82: 31 Bond restraints: 10577 Sorted by residual: bond pdb=" N LYS P 65 " pdb=" CA LYS P 65 " ideal model delta sigma weight residual 1.456 1.527 -0.071 1.40e-02 5.10e+03 2.55e+01 bond pdb=" CA SER P 409 " pdb=" CB SER P 409 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.69e-02 3.50e+03 1.01e+01 bond pdb=" N LEU P 334 " pdb=" CA LEU P 334 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 8.93e+00 bond pdb=" N LEU P 306 " pdb=" CA LEU P 306 " ideal model delta sigma weight residual 1.463 1.500 -0.037 1.27e-02 6.20e+03 8.40e+00 bond pdb=" C LEU P 64 " pdb=" N LYS P 65 " ideal model delta sigma weight residual 1.328 1.370 -0.042 1.51e-02 4.39e+03 7.79e+00 ... (remaining 10572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 14306 2.54 - 5.08: 219 5.08 - 7.61: 39 7.61 - 10.15: 21 10.15 - 12.69: 5 Bond angle restraints: 14590 Sorted by residual: angle pdb=" O3' A B 14 " pdb=" C3' A B 14 " pdb=" C2' A B 14 " ideal model delta sigma weight residual 109.50 98.46 11.04 1.50e+00 4.44e-01 5.42e+01 angle pdb=" C1' U B 9 " pdb=" N1 U B 9 " pdb=" C2 U B 9 " ideal model delta sigma weight residual 117.70 126.38 -8.68 1.20e+00 6.94e-01 5.23e+01 angle pdb=" N1 C B 7 " pdb=" C2 C B 7 " pdb=" O2 C B 7 " ideal model delta sigma weight residual 118.90 122.78 -3.88 6.00e-01 2.78e+00 4.19e+01 angle pdb=" O2 C B 7 " pdb=" C2 C B 7 " pdb=" N3 C B 7 " ideal model delta sigma weight residual 121.90 117.41 4.49 7.00e-01 2.04e+00 4.12e+01 angle pdb=" C1' U B 9 " pdb=" N1 U B 9 " pdb=" C6 U B 9 " ideal model delta sigma weight residual 121.20 112.96 8.24 1.40e+00 5.10e-01 3.46e+01 ... (remaining 14585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 5666 22.19 - 44.38: 655 44.38 - 66.56: 187 66.56 - 88.75: 31 88.75 - 110.94: 6 Dihedral angle restraints: 6545 sinusoidal: 3420 harmonic: 3125 Sorted by residual: dihedral pdb=" O4' A B 14 " pdb=" C1' A B 14 " pdb=" N9 A B 14 " pdb=" C4 A B 14 " ideal model delta sinusoidal sigma weight residual -106.00 -175.61 69.61 1 1.70e+01 3.46e-03 2.16e+01 dihedral pdb=" C ARG P 307 " pdb=" N ARG P 307 " pdb=" CA ARG P 307 " pdb=" CB ARG P 307 " ideal model delta harmonic sigma weight residual -122.60 -112.46 -10.14 0 2.50e+00 1.60e-01 1.64e+01 dihedral pdb=" CA VAL P1280 " pdb=" C VAL P1280 " pdb=" N ILE P1281 " pdb=" CA ILE P1281 " ideal model delta harmonic sigma weight residual 180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 6542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1466 0.065 - 0.131: 199 0.131 - 0.196: 12 0.196 - 0.261: 2 0.261 - 0.327: 3 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CA ARG P 307 " pdb=" N ARG P 307 " pdb=" C ARG P 307 " pdb=" CB ARG P 307 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA GLU P1268 " pdb=" N GLU P1268 " pdb=" C GLU P1268 " pdb=" CB GLU P1268 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB VAL P 339 " pdb=" CA VAL P 339 " pdb=" CG1 VAL P 339 " pdb=" CG2 VAL P 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1679 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG P 63 " 0.065 2.00e-02 2.50e+03 1.30e-01 1.69e+02 pdb=" C ARG P 63 " -0.225 2.00e-02 2.50e+03 pdb=" O ARG P 63 " 0.088 2.00e-02 2.50e+03 pdb=" N LEU P 64 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE P 305 " 0.030 2.00e-02 2.50e+03 5.75e-02 3.31e+01 pdb=" C ILE P 305 " -0.100 2.00e-02 2.50e+03 pdb=" O ILE P 305 " 0.036 2.00e-02 2.50e+03 pdb=" N LEU P 306 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR P 249 " -0.046 5.00e-02 4.00e+02 6.96e-02 7.76e+00 pdb=" N PRO P 250 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO P 250 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO P 250 " -0.038 5.00e-02 4.00e+02 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 362 2.69 - 3.24: 10090 3.24 - 3.79: 16218 3.79 - 4.35: 20344 4.35 - 4.90: 30642 Nonbonded interactions: 77656 Sorted by model distance: nonbonded pdb=" O GLU P1271 " pdb=" OG SER P1274 " model vdw 2.137 3.040 nonbonded pdb=" OH TYR P 5 " pdb=" O HIS P 754 " model vdw 2.228 3.040 nonbonded pdb=" OG SER P 909 " pdb=" OD2 ASP P 912 " model vdw 2.233 3.040 nonbonded pdb=" O GLN P 774 " pdb=" OG SER P 777 " model vdw 2.238 3.040 nonbonded pdb=" OE2 GLU P 762 " pdb=" OG SER P 960 " model vdw 2.273 3.040 ... (remaining 77651 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.660 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4199 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 : 0.004 0.098 10577 Z= 0.226 Angle : 0.872 12.687 14590 Z= 0.545 Chirality : 0.045 0.327 1682 Planarity : 0.006 0.130 1593 Dihedral : 19.384 110.940 4523 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.99 % Rotamer: Outliers : 1.05 % Allowed : 28.11 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.25), residues: 1056 helix: -0.31 (0.22), residues: 508 sheet: -0.83 (0.49), residues: 118 loop : -1.75 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 884 TYR 0.023 0.002 TYR P1237 PHE 0.019 0.002 PHE P 916 TRP 0.009 0.001 TRP P 883 HIS 0.006 0.001 HIS P 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.23 (10577) covalent geometry : angle 0.87172 / 0.54 (14590) hydrogen bonds : bond 0.14699 / 13.83 ( 401) hydrogen bonds : angle 5.92156 / 7.50 ( 1130) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 404 THR cc_start: 0.4229 (p) cc_final: 0.3370 (m) REVERT: P 965 ASP cc_start: 0.7705 (m-30) cc_final: 0.6752 (m-30) outliers start: 10 outliers final: 1 residues processed: 159 average time/residue: 0.0995 time to fit residues: 21.3920 Evaluate side-chains 75 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 306 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 37 ASN ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN P 265 GLN ** P 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 413 GLN ** P 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 721 HIS ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 803 ASN ** P 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 990 ASN P1254 GLN P1262 HIS P1297 HIS ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1350 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.084297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.065701 restraints weight = 71248.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.067348 restraints weight = 42211.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.068335 restraints weight = 30250.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.068964 restraints weight = 24536.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.069321 restraints weight = 21488.784| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 10577 Z= 0.306 Angle : 0.985 15.449 14590 Z= 0.509 Chirality : 0.050 0.275 1682 Planarity : 0.007 0.132 1593 Dihedral : 17.504 115.204 2277 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 7.16 % Allowed : 24.63 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.23), residues: 1056 helix: -0.96 (0.21), residues: 513 sheet: -2.07 (0.52), residues: 91 loop : -1.77 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG P1060 TYR 0.032 0.003 TYR P1141 PHE 0.030 0.003 PHE P1313 TRP 0.019 0.004 TRP P1074 HIS 0.015 0.003 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.31 (10577) covalent geometry : angle 0.98530 / 0.51 (14590) hydrogen bonds : bond 0.07491 / 7.17 ( 401) hydrogen bonds : angle 6.03529 / 7.77 ( 1130) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 74 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 161 MET cc_start: 0.8830 (mmm) cc_final: 0.8563 (mmt) REVERT: P 173 ASP cc_start: 0.8875 (m-30) cc_final: 0.8440 (t70) REVERT: P 822 MET cc_start: 0.8948 (pmm) cc_final: 0.8537 (pmm) REVERT: P 879 MET cc_start: 0.8529 (mpp) cc_final: 0.8212 (mpp) REVERT: P 929 LYS cc_start: 0.7647 (mttt) cc_final: 0.7417 (ptpt) REVERT: P 1043 MET cc_start: 0.7706 (mtm) cc_final: 0.6975 (mmp) REVERT: P 1062 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8069 (tp) outliers start: 68 outliers final: 30 residues processed: 129 average time/residue: 0.0842 time to fit residues: 16.0667 Evaluate side-chains 87 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 72 TYR Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 136 TYR Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 266 LEU Chi-restraints excluded: chain P residue 282 ILE Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 347 TYR Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 803 ASN Chi-restraints excluded: chain P residue 818 ASN Chi-restraints excluded: chain P residue 849 ASP Chi-restraints excluded: chain P residue 992 VAL Chi-restraints excluded: chain P residue 993 VAL Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1094 ILE Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1168 ILE Chi-restraints excluded: chain P residue 1173 SER Chi-restraints excluded: chain P residue 1213 MET Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1348 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 803 ASN P 818 ASN P 844 GLN P 885 GLN P 983 HIS ** P 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1241 HIS ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.082481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.063569 restraints weight = 72371.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.065111 restraints weight = 42061.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.066136 restraints weight = 30003.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.066800 restraints weight = 24192.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.067250 restraints weight = 21190.248| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10577 Z= 0.201 Angle : 0.714 10.601 14590 Z= 0.372 Chirality : 0.042 0.278 1682 Planarity : 0.005 0.060 1593 Dihedral : 17.358 114.088 2275 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 5.37 % Allowed : 24.11 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.24), residues: 1056 helix: -0.59 (0.21), residues: 512 sheet: -1.94 (0.51), residues: 97 loop : -1.55 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 753 TYR 0.018 0.002 TYR P 359 PHE 0.041 0.002 PHE P1313 TRP 0.017 0.003 TRP P1074 HIS 0.013 0.002 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (10577) covalent geometry : angle 0.71378 / 0.37 (14590) hydrogen bonds : bond 0.05745 / 5.62 ( 401) hydrogen bonds : angle 5.49965 / 7.20 ( 1130) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 61 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 140 LYS cc_start: 0.5960 (OUTLIER) cc_final: 0.5572 (mttp) REVERT: P 173 ASP cc_start: 0.8767 (m-30) cc_final: 0.8457 (t70) REVERT: P 762 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.5852 (tp30) REVERT: P 822 MET cc_start: 0.9037 (pmm) cc_final: 0.8827 (pmm) REVERT: P 879 MET cc_start: 0.8601 (mpp) cc_final: 0.8211 (mpp) REVERT: P 1043 MET cc_start: 0.7800 (mtm) cc_final: 0.6942 (mmp) outliers start: 51 outliers final: 36 residues processed: 103 average time/residue: 0.0783 time to fit residues: 11.9940 Evaluate side-chains 90 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 52 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 72 TYR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 136 TYR Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 266 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 388 GLU Chi-restraints excluded: chain P residue 733 ILE Chi-restraints excluded: chain P residue 762 GLU Chi-restraints excluded: chain P residue 818 ASN Chi-restraints excluded: chain P residue 876 VAL Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 928 THR Chi-restraints excluded: chain P residue 977 GLU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1094 ILE Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1168 ILE Chi-restraints excluded: chain P residue 1173 SER Chi-restraints excluded: chain P residue 1187 TYR Chi-restraints excluded: chain P residue 1213 MET Chi-restraints excluded: chain P residue 1238 LEU Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1348 ILE Chi-restraints excluded: chain P residue 1360 ILE Chi-restraints excluded: chain P residue 1361 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 93 optimal weight: 0.2980 chunk 1 optimal weight: 40.0000 chunk 74 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 37 ASN P 281 GLN ** P 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.083769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.064683 restraints weight = 71656.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.066333 restraints weight = 40920.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.067393 restraints weight = 29034.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.068041 restraints weight = 23372.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.068530 restraints weight = 20366.090| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10577 Z= 0.125 Angle : 0.621 10.506 14590 Z= 0.317 Chirality : 0.039 0.230 1682 Planarity : 0.004 0.056 1593 Dihedral : 17.195 112.354 2275 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.32 % Allowed : 25.26 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.25), residues: 1056 helix: -0.14 (0.22), residues: 513 sheet: -1.46 (0.48), residues: 107 loop : -1.44 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P1058 TYR 0.016 0.001 TYR P 359 PHE 0.023 0.001 PHE P1008 TRP 0.007 0.001 TRP P1074 HIS 0.005 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10577) covalent geometry : angle 0.62130 / 0.32 (14590) hydrogen bonds : bond 0.04474 / 4.27 ( 401) hydrogen bonds : angle 5.16088 / 6.75 ( 1130) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 59 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 161 MET cc_start: 0.8858 (mmm) cc_final: 0.8616 (mmt) REVERT: P 173 ASP cc_start: 0.8756 (m-30) cc_final: 0.8478 (t70) REVERT: P 762 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.5746 (tp30) REVERT: P 822 MET cc_start: 0.8991 (pmm) cc_final: 0.8781 (pmm) REVERT: P 879 MET cc_start: 0.8500 (mpp) cc_final: 0.8094 (mpp) REVERT: P 1043 MET cc_start: 0.7722 (mtm) cc_final: 0.6879 (mmp) outliers start: 41 outliers final: 29 residues processed: 92 average time/residue: 0.0703 time to fit residues: 9.8078 Evaluate side-chains 81 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 51 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 136 TYR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 221 ARG Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 266 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 733 ILE Chi-restraints excluded: chain P residue 762 GLU Chi-restraints excluded: chain P residue 876 VAL Chi-restraints excluded: chain P residue 977 GLU Chi-restraints excluded: chain P residue 993 VAL Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1026 GLU Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1173 SER Chi-restraints excluded: chain P residue 1187 TYR Chi-restraints excluded: chain P residue 1213 MET Chi-restraints excluded: chain P residue 1238 LEU Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1348 ILE Chi-restraints excluded: chain P residue 1360 ILE Chi-restraints excluded: chain P residue 1361 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 0.0570 chunk 103 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 109 optimal weight: 0.0870 chunk 105 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.082851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.063696 restraints weight = 71338.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.065312 restraints weight = 41115.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.066341 restraints weight = 29314.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.066971 restraints weight = 23787.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.067430 restraints weight = 20909.482| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10577 Z= 0.132 Angle : 0.591 10.533 14590 Z= 0.305 Chirality : 0.038 0.215 1682 Planarity : 0.004 0.045 1593 Dihedral : 17.123 111.879 2275 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.00 % Allowed : 26.00 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.25), residues: 1056 helix: 0.10 (0.22), residues: 511 sheet: -1.33 (0.48), residues: 107 loop : -1.43 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P1058 TYR 0.018 0.001 TYR P 359 PHE 0.029 0.001 PHE P1008 TRP 0.012 0.002 TRP P1074 HIS 0.007 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10577) covalent geometry : angle 0.59074 / 0.30 (14590) hydrogen bonds : bond 0.04404 / 4.12 ( 401) hydrogen bonds : angle 5.08623 / 6.62 ( 1130) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 54 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 161 MET cc_start: 0.8867 (mmm) cc_final: 0.8642 (mmt) REVERT: P 173 ASP cc_start: 0.8778 (m-30) cc_final: 0.8471 (t70) REVERT: P 762 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.5903 (tp30) REVERT: P 879 MET cc_start: 0.8534 (mpp) cc_final: 0.8137 (mpp) REVERT: P 1043 MET cc_start: 0.7715 (mtm) cc_final: 0.6894 (mmp) REVERT: P 1045 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8300 (p90) outliers start: 38 outliers final: 22 residues processed: 89 average time/residue: 0.0723 time to fit residues: 9.6200 Evaluate side-chains 77 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 266 LEU Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 733 ILE Chi-restraints excluded: chain P residue 762 GLU Chi-restraints excluded: chain P residue 876 VAL Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 998 ILE Chi-restraints excluded: chain P residue 1045 PHE Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1094 ILE Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1173 SER Chi-restraints excluded: chain P residue 1187 TYR Chi-restraints excluded: chain P residue 1213 MET Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1361 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 9.9990 chunk 24 optimal weight: 0.1980 chunk 93 optimal weight: 0.1980 chunk 22 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 228 GLN ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.081627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.063436 restraints weight = 72384.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.065213 restraints weight = 39641.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.065190 restraints weight = 27604.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.065475 restraints weight = 25932.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.065533 restraints weight = 23741.982| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10577 Z= 0.141 Angle : 0.604 10.450 14590 Z= 0.312 Chirality : 0.039 0.227 1682 Planarity : 0.004 0.048 1593 Dihedral : 17.104 111.425 2275 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.32 % Allowed : 26.21 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.25), residues: 1056 helix: 0.13 (0.23), residues: 511 sheet: -1.45 (0.51), residues: 99 loop : -1.39 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P1359 TYR 0.018 0.002 TYR P 359 PHE 0.032 0.002 PHE P 97 TRP 0.011 0.002 TRP P1074 HIS 0.006 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10577) covalent geometry : angle 0.60350 / 0.31 (14590) hydrogen bonds : bond 0.04425 / 4.15 ( 401) hydrogen bonds : angle 5.05589 / 6.52 ( 1130) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 58 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 173 ASP cc_start: 0.8894 (m-30) cc_final: 0.8548 (t70) REVERT: P 380 LEU cc_start: 0.9218 (mm) cc_final: 0.8510 (tt) REVERT: P 762 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6113 (tp30) REVERT: P 879 MET cc_start: 0.8570 (mpp) cc_final: 0.8353 (mpp) REVERT: P 1043 MET cc_start: 0.7641 (mtm) cc_final: 0.6812 (mmp) REVERT: P 1045 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8415 (p90) REVERT: P 1357 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6773 (mm-30) outliers start: 41 outliers final: 28 residues processed: 93 average time/residue: 0.0905 time to fit residues: 12.3535 Evaluate side-chains 85 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 336 LYS Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 404 THR Chi-restraints excluded: chain P residue 762 GLU Chi-restraints excluded: chain P residue 876 VAL Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 992 VAL Chi-restraints excluded: chain P residue 993 VAL Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 998 ILE Chi-restraints excluded: chain P residue 1026 GLU Chi-restraints excluded: chain P residue 1045 PHE Chi-restraints excluded: chain P residue 1094 ILE Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1173 SER Chi-restraints excluded: chain P residue 1187 TYR Chi-restraints excluded: chain P residue 1213 MET Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1361 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 51 optimal weight: 0.0670 chunk 95 optimal weight: 0.0030 chunk 21 optimal weight: 9.9990 overall best weight: 1.7932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1066 ASN ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.081168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.063284 restraints weight = 71872.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.065020 restraints weight = 38767.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.065080 restraints weight = 26915.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.065352 restraints weight = 25388.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.065401 restraints weight = 23408.972| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10577 Z= 0.128 Angle : 0.593 11.010 14590 Z= 0.303 Chirality : 0.039 0.269 1682 Planarity : 0.004 0.048 1593 Dihedral : 17.065 110.520 2275 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.37 % Allowed : 27.26 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.25), residues: 1056 helix: 0.20 (0.23), residues: 511 sheet: -1.26 (0.52), residues: 97 loop : -1.36 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 938 TYR 0.018 0.001 TYR P 359 PHE 0.017 0.001 PHE P1008 TRP 0.013 0.002 TRP P 18 HIS 0.005 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10577) covalent geometry : angle 0.59304 / 0.30 (14590) hydrogen bonds : bond 0.04223 / 3.90 ( 401) hydrogen bonds : angle 5.02875 / 6.56 ( 1130) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 56 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 173 ASP cc_start: 0.8964 (m-30) cc_final: 0.8592 (t70) REVERT: P 200 PRO cc_start: 0.8597 (Cg_exo) cc_final: 0.8336 (Cg_endo) REVERT: P 762 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6147 (tp30) REVERT: P 879 MET cc_start: 0.8507 (mpp) cc_final: 0.8110 (mpp) REVERT: P 1043 MET cc_start: 0.7564 (mtm) cc_final: 0.6714 (mmp) REVERT: P 1045 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8464 (p90) outliers start: 32 outliers final: 23 residues processed: 84 average time/residue: 0.0847 time to fit residues: 10.7487 Evaluate side-chains 77 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 336 LYS Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 762 GLU Chi-restraints excluded: chain P residue 876 VAL Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 992 VAL Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 998 ILE Chi-restraints excluded: chain P residue 1026 GLU Chi-restraints excluded: chain P residue 1045 PHE Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1173 SER Chi-restraints excluded: chain P residue 1187 TYR Chi-restraints excluded: chain P residue 1202 SER Chi-restraints excluded: chain P residue 1213 MET Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1361 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 46 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 95 optimal weight: 0.0570 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 chunk 53 optimal weight: 0.0270 chunk 88 optimal weight: 3.9990 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 199 ASN P 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.082465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.063640 restraints weight = 70673.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.065288 restraints weight = 40521.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.066250 restraints weight = 28802.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.067002 restraints weight = 23319.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.067391 restraints weight = 20309.622| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.6402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10577 Z= 0.108 Angle : 0.590 11.059 14590 Z= 0.296 Chirality : 0.038 0.219 1682 Planarity : 0.004 0.050 1593 Dihedral : 16.965 108.661 2275 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.95 % Allowed : 27.26 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.26), residues: 1056 helix: 0.37 (0.23), residues: 510 sheet: -0.96 (0.53), residues: 97 loop : -1.31 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 938 TYR 0.020 0.001 TYR P 359 PHE 0.024 0.001 PHE P 97 TRP 0.016 0.002 TRP P 18 HIS 0.003 0.001 HIS P 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (10577) covalent geometry : angle 0.58985 / 0.30 (14590) hydrogen bonds : bond 0.03628 / 3.31 ( 401) hydrogen bonds : angle 4.86053 / 6.32 ( 1130) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 173 ASP cc_start: 0.8901 (m-30) cc_final: 0.8611 (t70) REVERT: P 879 MET cc_start: 0.8424 (mpp) cc_final: 0.8222 (mpp) REVERT: P 1043 MET cc_start: 0.7577 (mtm) cc_final: 0.6666 (mmp) outliers start: 28 outliers final: 17 residues processed: 82 average time/residue: 0.0832 time to fit residues: 10.2048 Evaluate side-chains 71 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 404 THR Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 998 ILE Chi-restraints excluded: chain P residue 1026 GLU Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1353 THR Chi-restraints excluded: chain P residue 1361 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 415 HIS ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.079829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.062716 restraints weight = 71530.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.063670 restraints weight = 43014.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.064156 restraints weight = 32197.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.064265 restraints weight = 30482.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.064636 restraints weight = 27402.960| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.6929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10577 Z= 0.155 Angle : 0.607 10.424 14590 Z= 0.315 Chirality : 0.040 0.273 1682 Planarity : 0.004 0.046 1593 Dihedral : 16.967 109.460 2275 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.84 % Allowed : 28.00 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.92 (0.25), residues: 1056 helix: 0.19 (0.23), residues: 510 sheet: -1.34 (0.51), residues: 97 loop : -1.30 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 403 TYR 0.019 0.002 TYR P 988 PHE 0.026 0.002 PHE P 238 TRP 0.016 0.002 TRP P1074 HIS 0.007 0.001 HIS P 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (10577) covalent geometry : angle 0.60734 / 0.32 (14590) hydrogen bonds : bond 0.04768 / 4.45 ( 401) hydrogen bonds : angle 5.08284 / 6.54 ( 1130) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 173 ASP cc_start: 0.9001 (m-30) cc_final: 0.8643 (t70) REVERT: P 321 MET cc_start: 0.6938 (ttm) cc_final: 0.6069 (ttm) REVERT: P 762 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6167 (tp30) REVERT: P 879 MET cc_start: 0.8470 (mpp) cc_final: 0.8082 (mpp) REVERT: P 1043 MET cc_start: 0.7613 (mtm) cc_final: 0.6778 (mmp) outliers start: 27 outliers final: 24 residues processed: 79 average time/residue: 0.0823 time to fit residues: 9.9554 Evaluate side-chains 81 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 404 THR Chi-restraints excluded: chain P residue 762 GLU Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 998 ILE Chi-restraints excluded: chain P residue 1026 GLU Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1173 SER Chi-restraints excluded: chain P residue 1187 TYR Chi-restraints excluded: chain P residue 1202 SER Chi-restraints excluded: chain P residue 1213 MET Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1353 THR Chi-restraints excluded: chain P residue 1361 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 3 optimal weight: 30.0000 chunk 101 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 105 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 415 HIS P 723 HIS P 818 ASN ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.080319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.063346 restraints weight = 71044.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.064277 restraints weight = 39440.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.064893 restraints weight = 31716.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.065085 restraints weight = 27999.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.065209 restraints weight = 25828.313| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10577 Z= 0.117 Angle : 0.596 12.720 14590 Z= 0.302 Chirality : 0.039 0.212 1682 Planarity : 0.004 0.048 1593 Dihedral : 16.956 108.599 2275 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.32 % Allowed : 29.16 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.26), residues: 1056 helix: 0.32 (0.23), residues: 509 sheet: -1.18 (0.53), residues: 97 loop : -1.33 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P1058 TYR 0.016 0.001 TYR P 359 PHE 0.033 0.001 PHE P1008 TRP 0.009 0.002 TRP P 18 HIS 0.004 0.001 HIS P 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (10577) covalent geometry : angle 0.59633 / 0.30 (14590) hydrogen bonds : bond 0.04012 / 3.70 ( 401) hydrogen bonds : angle 4.97680 / 6.46 ( 1130) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 161 MET cc_start: 0.8308 (mmt) cc_final: 0.7963 (mpp) REVERT: P 173 ASP cc_start: 0.9052 (m-30) cc_final: 0.8717 (t70) REVERT: P 762 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6117 (tp30) REVERT: P 879 MET cc_start: 0.8428 (mpp) cc_final: 0.8059 (mpp) REVERT: P 1043 MET cc_start: 0.7552 (mtm) cc_final: 0.6724 (mmp) outliers start: 22 outliers final: 20 residues processed: 76 average time/residue: 0.0795 time to fit residues: 9.2160 Evaluate side-chains 77 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 404 THR Chi-restraints excluded: chain P residue 762 GLU Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 998 ILE Chi-restraints excluded: chain P residue 1026 GLU Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1187 TYR Chi-restraints excluded: chain P residue 1213 MET Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1353 THR Chi-restraints excluded: chain P residue 1361 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 3 optimal weight: 30.0000 chunk 37 optimal weight: 0.0170 chunk 86 optimal weight: 0.0970 chunk 57 optimal weight: 9.9990 overall best weight: 1.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 415 HIS P 723 HIS ** P 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.079588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.062857 restraints weight = 71517.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.063719 restraints weight = 39036.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.063840 restraints weight = 33334.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.064150 restraints weight = 30774.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.064795 restraints weight = 27252.908| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.7520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10577 Z= 0.126 Angle : 0.591 10.535 14590 Z= 0.301 Chirality : 0.039 0.222 1682 Planarity : 0.004 0.046 1593 Dihedral : 16.903 107.206 2275 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.32 % Allowed : 28.84 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.26), residues: 1056 helix: 0.36 (0.23), residues: 510 sheet: -1.21 (0.52), residues: 97 loop : -1.34 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 403 TYR 0.014 0.001 TYR P 988 PHE 0.043 0.002 PHE P1008 TRP 0.008 0.002 TRP P1074 HIS 0.004 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10577) covalent geometry : angle 0.59087 / 0.30 (14590) hydrogen bonds : bond 0.04120 / 3.80 ( 401) hydrogen bonds : angle 4.89605 / 6.36 ( 1130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2473.92 seconds wall clock time: 43 minutes 10.24 seconds (2590.24 seconds total)