Starting phenix.real_space_refine on Wed Mar 4 00:29:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lr0_31583/03_2026/6lr0_31583.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lr0_31583/03_2026/6lr0_31583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lr0_31583/03_2026/6lr0_31583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lr0_31583/03_2026/6lr0_31583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lr0_31583/03_2026/6lr0_31583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lr0_31583/03_2026/6lr0_31583.map" } resolution = 3.5 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= 0.007 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 6129 2.51 5 N 1627 2.21 5 O 1766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9576 Number of models: 1 Model: "" Number of chains: 1 Chain: "U" Number of atoms: 9576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9576 Classifications: {'peptide': 1230} Link IDs: {'PTRANS': 36, 'TRANS': 1193} Chain breaks: 2 Time building chain proxies: 2.56, per 1000 atoms: 0.27 Number of scatterers: 9576 At special positions: 0 Unit cell: (90.1, 160.06, 112.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1766 8.00 N 1627 7.00 C 6129 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: 0.76 Conformation dependent library (CDL) restraints added in 413.9 milliseconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 4 sheets defined 36.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'U' and resid 46 through 50 Processing helix chain 'U' and resid 79 through 84 Processing helix chain 'U' and resid 88 through 100 removed outlier: 3.716A pdb=" N GLU U 96 " --> pdb=" O ASP U 92 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU U 99 " --> pdb=" O VAL U 95 " (cutoff:3.500A) Processing helix chain 'U' and resid 147 through 155 removed outlier: 4.004A pdb=" N LEU U 153 " --> pdb=" O ALA U 149 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 183 removed outlier: 3.655A pdb=" N PHE U 179 " --> pdb=" O ARG U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 192 removed outlier: 3.734A pdb=" N PHE U 190 " --> pdb=" O ILE U 187 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS U 192 " --> pdb=" O TRP U 189 " (cutoff:3.500A) Processing helix chain 'U' and resid 230 through 238 removed outlier: 3.769A pdb=" N PHE U 236 " --> pdb=" O LEU U 232 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG U 237 " --> pdb=" O LEU U 233 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY U 238 " --> pdb=" O GLY U 234 " (cutoff:3.500A) Processing helix chain 'U' and resid 240 through 245 removed outlier: 3.740A pdb=" N VAL U 244 " --> pdb=" O LYS U 240 " (cutoff:3.500A) Processing helix chain 'U' and resid 248 through 257 removed outlier: 4.183A pdb=" N ILE U 254 " --> pdb=" O PRO U 250 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY U 255 " --> pdb=" O LEU U 251 " (cutoff:3.500A) Processing helix chain 'U' and resid 258 through 263 Processing helix chain 'U' and resid 266 through 275 removed outlier: 3.567A pdb=" N LEU U 271 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS U 272 " --> pdb=" O ASP U 268 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA U 275 " --> pdb=" O LEU U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 277 through 282 removed outlier: 3.706A pdb=" N ASP U 282 " --> pdb=" O GLY U 278 " (cutoff:3.500A) Processing helix chain 'U' and resid 287 through 294 removed outlier: 3.678A pdb=" N VAL U 291 " --> pdb=" O SER U 287 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA U 293 " --> pdb=" O ARG U 289 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE U 294 " --> pdb=" O THR U 290 " (cutoff:3.500A) Processing helix chain 'U' and resid 308 through 312 removed outlier: 3.684A pdb=" N ALA U 311 " --> pdb=" O LEU U 308 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 325 Processing helix chain 'U' and resid 329 through 334 removed outlier: 3.919A pdb=" N PHE U 334 " --> pdb=" O TRP U 330 " (cutoff:3.500A) Processing helix chain 'U' and resid 335 through 344 removed outlier: 3.978A pdb=" N LEU U 339 " --> pdb=" O LEU U 335 " (cutoff:3.500A) Processing helix chain 'U' and resid 363 through 376 removed outlier: 3.621A pdb=" N ILE U 367 " --> pdb=" O PHE U 363 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY U 369 " --> pdb=" O SER U 365 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU U 373 " --> pdb=" O GLY U 369 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY U 374 " --> pdb=" O ALA U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 377 through 386 removed outlier: 4.929A pdb=" N PHE U 383 " --> pdb=" O CYS U 379 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA U 384 " --> pdb=" O LEU U 380 " (cutoff:3.500A) Processing helix chain 'U' and resid 392 through 397 removed outlier: 3.716A pdb=" N THR U 396 " --> pdb=" O SER U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 462 through 467 Processing helix chain 'U' and resid 490 through 495 Processing helix chain 'U' and resid 525 through 535 removed outlier: 3.749A pdb=" N GLN U 530 " --> pdb=" O GLU U 526 " (cutoff:3.500A) Processing helix chain 'U' and resid 540 through 544 removed outlier: 3.508A pdb=" N LEU U 544 " --> pdb=" O ILE U 541 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 575 removed outlier: 3.615A pdb=" N ALA U 570 " --> pdb=" O ARG U 566 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG U 575 " --> pdb=" O ARG U 571 " (cutoff:3.500A) Processing helix chain 'U' and resid 593 through 603 removed outlier: 3.766A pdb=" N VAL U 597 " --> pdb=" O SER U 593 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL U 600 " --> pdb=" O MET U 596 " (cutoff:3.500A) Processing helix chain 'U' and resid 652 through 656 Processing helix chain 'U' and resid 700 through 704 removed outlier: 3.660A pdb=" N SER U 704 " --> pdb=" O SER U 701 " (cutoff:3.500A) Processing helix chain 'U' and resid 742 through 747 Processing helix chain 'U' and resid 748 through 752 Processing helix chain 'U' and resid 775 through 780 removed outlier: 3.556A pdb=" N LEU U 780 " --> pdb=" O PHE U 776 " (cutoff:3.500A) Processing helix chain 'U' and resid 789 through 802 removed outlier: 3.621A pdb=" N ILE U 795 " --> pdb=" O GLN U 791 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN U 796 " --> pdb=" O ARG U 792 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS U 799 " --> pdb=" O ILE U 795 " (cutoff:3.500A) Processing helix chain 'U' and resid 803 through 806 Processing helix chain 'U' and resid 828 through 833 removed outlier: 3.685A pdb=" N LYS U 833 " --> pdb=" O LYS U 829 " (cutoff:3.500A) Processing helix chain 'U' and resid 834 through 836 No H-bonds generated for 'chain 'U' and resid 834 through 836' Processing helix chain 'U' and resid 838 through 842 removed outlier: 3.983A pdb=" N GLN U 842 " --> pdb=" O MET U 839 " (cutoff:3.500A) Processing helix chain 'U' and resid 843 through 847 removed outlier: 4.072A pdb=" N TRP U 846 " --> pdb=" O ASP U 843 " (cutoff:3.500A) Processing helix chain 'U' and resid 875 through 881 Processing helix chain 'U' and resid 885 through 897 removed outlier: 3.825A pdb=" N ALA U 889 " --> pdb=" O ASN U 885 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE U 891 " --> pdb=" O THR U 887 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE U 894 " --> pdb=" O MET U 890 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE U 896 " --> pdb=" O ILE U 892 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER U 897 " --> pdb=" O ALA U 893 " (cutoff:3.500A) Processing helix chain 'U' and resid 904 through 907 Processing helix chain 'U' and resid 908 through 913 Processing helix chain 'U' and resid 925 through 930 removed outlier: 3.774A pdb=" N LYS U 930 " --> pdb=" O ALA U 926 " (cutoff:3.500A) Processing helix chain 'U' and resid 935 through 940 Processing helix chain 'U' and resid 940 through 945 removed outlier: 3.555A pdb=" N SER U 945 " --> pdb=" O ASN U 941 " (cutoff:3.500A) Processing helix chain 'U' and resid 946 through 951 Processing helix chain 'U' and resid 956 through 962 Processing helix chain 'U' and resid 994 through 1007 removed outlier: 3.639A pdb=" N SER U 999 " --> pdb=" O ALA U 995 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR U1000 " --> pdb=" O ASN U 996 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG U1001 " --> pdb=" O SER U 997 " (cutoff:3.500A) Processing helix chain 'U' and resid 1013 through 1015 No H-bonds generated for 'chain 'U' and resid 1013 through 1015' Processing helix chain 'U' and resid 1016 through 1021 removed outlier: 3.614A pdb=" N ILE U1021 " --> pdb=" O VAL U1017 " (cutoff:3.500A) Processing helix chain 'U' and resid 1031 through 1035 removed outlier: 3.917A pdb=" N PHE U1035 " --> pdb=" O GLY U1032 " (cutoff:3.500A) Processing helix chain 'U' and resid 1037 through 1043 removed outlier: 3.558A pdb=" N TYR U1041 " --> pdb=" O TYR U1037 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA U1042 " --> pdb=" O THR U1038 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS U1043 " --> pdb=" O PRO U1039 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 1037 through 1043' Processing helix chain 'U' and resid 1048 through 1053 removed outlier: 3.843A pdb=" N PHE U1052 " --> pdb=" O ALA U1048 " (cutoff:3.500A) Processing helix chain 'U' and resid 1120 through 1125 removed outlier: 3.553A pdb=" N GLN U1124 " --> pdb=" O SER U1120 " (cutoff:3.500A) Processing helix chain 'U' and resid 1148 through 1153 removed outlier: 3.509A pdb=" N LEU U1152 " --> pdb=" O ASN U1148 " (cutoff:3.500A) Processing helix chain 'U' and resid 1171 through 1176 removed outlier: 3.714A pdb=" N LYS U1175 " --> pdb=" O MET U1171 " (cutoff:3.500A) Processing helix chain 'U' and resid 1185 through 1191 removed outlier: 4.306A pdb=" N ILE U1189 " --> pdb=" O MET U1185 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA U1190 " --> pdb=" O GLU U1186 " (cutoff:3.500A) Processing helix chain 'U' and resid 1200 through 1204 removed outlier: 3.822A pdb=" N LEU U1204 " --> pdb=" O VAL U1201 " (cutoff:3.500A) Processing helix chain 'U' and resid 1220 through 1223 Processing helix chain 'U' and resid 1224 through 1233 removed outlier: 3.830A pdb=" N ALA U1228 " --> pdb=" O LYS U1224 " (cutoff:3.500A) Processing helix chain 'U' and resid 1250 through 1264 removed outlier: 3.537A pdb=" N VAL U1257 " --> pdb=" O SER U1253 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL U1259 " --> pdb=" O LYS U1255 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA U1260 " --> pdb=" O THR U1256 " (cutoff:3.500A) Processing helix chain 'U' and resid 1308 through 1314 removed outlier: 3.519A pdb=" N LYS U1312 " --> pdb=" O GLY U1308 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU U1313 " --> pdb=" O ALA U1309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'U' and resid 438 through 445 removed outlier: 6.806A pdb=" N ASN U 439 " --> pdb=" O THR U 426 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR U 426 " --> pdb=" O ASN U 439 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU U 441 " --> pdb=" O ASN U 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN U 424 " --> pdb=" O LEU U 441 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE U 420 " --> pdb=" O ILE U 445 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 450 through 451 removed outlier: 6.175A pdb=" N THR U 451 " --> pdb=" O SER U 612 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU U 580 " --> pdb=" O ILE U 611 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL U 613 " --> pdb=" O LEU U 580 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU U 582 " --> pdb=" O VAL U 613 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 1079 through 1080 Processing sheet with id=AA4, first strand: chain 'U' and resid 1156 through 1159 removed outlier: 6.714A pdb=" N GLY U1157 " --> pdb=" O LEU U1241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 158 hydrogen bonds defined for protein. 420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2048 1.33 - 1.45: 2223 1.45 - 1.57: 5402 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 9761 Sorted by residual: bond pdb=" C GLN U 76 " pdb=" N PRO U 77 " ideal model delta sigma weight residual 1.333 1.378 -0.045 7.80e-03 1.64e+04 3.37e+01 bond pdb=" CG1 ILE U 171 " pdb=" CD1 ILE U 171 " ideal model delta sigma weight residual 1.513 1.363 0.150 3.90e-02 6.57e+02 1.49e+01 bond pdb=" CB VAL U1024 " pdb=" CG2 VAL U1024 " ideal model delta sigma weight residual 1.521 1.421 0.100 3.30e-02 9.18e+02 9.18e+00 bond pdb=" CG ARG U 175 " pdb=" CD ARG U 175 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.22e+00 bond pdb=" CB ILE U 160 " pdb=" CG2 ILE U 160 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.66e+00 ... (remaining 9756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 12553 2.82 - 5.63: 541 5.63 - 8.45: 68 8.45 - 11.27: 29 11.27 - 14.08: 8 Bond angle restraints: 13199 Sorted by residual: angle pdb=" N ILE U1170 " pdb=" CA ILE U1170 " pdb=" C ILE U1170 " ideal model delta sigma weight residual 112.83 104.69 8.14 9.90e-01 1.02e+00 6.75e+01 angle pdb=" N ILE U 213 " pdb=" CA ILE U 213 " pdb=" C ILE U 213 " ideal model delta sigma weight residual 113.71 107.32 6.39 9.50e-01 1.11e+00 4.53e+01 angle pdb=" N LEU U 67 " pdb=" CA LEU U 67 " pdb=" C LEU U 67 " ideal model delta sigma weight residual 113.38 105.94 7.44 1.23e+00 6.61e-01 3.66e+01 angle pdb=" C ASN U 946 " pdb=" N ILE U 947 " pdb=" CA ILE U 947 " ideal model delta sigma weight residual 120.53 127.26 -6.73 1.41e+00 5.03e-01 2.28e+01 angle pdb=" N GLY U 924 " pdb=" CA GLY U 924 " pdb=" C GLY U 924 " ideal model delta sigma weight residual 115.46 107.75 7.71 1.63e+00 3.76e-01 2.24e+01 ... (remaining 13194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 5279 16.28 - 32.56: 428 32.56 - 48.84: 99 48.84 - 65.12: 10 65.12 - 81.40: 7 Dihedral angle restraints: 5823 sinusoidal: 2288 harmonic: 3535 Sorted by residual: dihedral pdb=" CA LEU U 712 " pdb=" C LEU U 712 " pdb=" N ALA U 713 " pdb=" CA ALA U 713 " ideal model delta harmonic sigma weight residual 180.00 135.33 44.67 0 5.00e+00 4.00e-02 7.98e+01 dihedral pdb=" CA TYR U1037 " pdb=" C TYR U1037 " pdb=" N THR U1038 " pdb=" CA THR U1038 " ideal model delta harmonic sigma weight residual -180.00 -142.24 -37.76 0 5.00e+00 4.00e-02 5.70e+01 dihedral pdb=" CA ILE U1271 " pdb=" C ILE U1271 " pdb=" N VAL U1272 " pdb=" CA VAL U1272 " ideal model delta harmonic sigma weight residual -180.00 -146.00 -34.00 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 5820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1305 0.093 - 0.187: 177 0.187 - 0.280: 16 0.280 - 0.374: 3 0.374 - 0.467: 1 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CB ILE U 785 " pdb=" CA ILE U 785 " pdb=" CG1 ILE U 785 " pdb=" CG2 ILE U 785 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CB VAL U 808 " pdb=" CA VAL U 808 " pdb=" CG1 VAL U 808 " pdb=" CG2 VAL U 808 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB VAL U 360 " pdb=" CA VAL U 360 " pdb=" CG1 VAL U 360 " pdb=" CG2 VAL U 360 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1499 not shown) Planarity restraints: 1689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS U 969 " 0.060 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO U 970 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO U 970 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO U 970 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE U 383 " -0.023 2.00e-02 2.50e+03 2.06e-02 7.44e+00 pdb=" CG PHE U 383 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE U 383 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE U 383 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE U 383 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE U 383 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE U 383 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER U 249 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO U 250 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO U 250 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO U 250 " -0.037 5.00e-02 4.00e+02 ... (remaining 1686 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2970 2.81 - 3.33: 8225 3.33 - 3.86: 14900 3.86 - 4.38: 17263 4.38 - 4.90: 29290 Nonbonded interactions: 72648 Sorted by model distance: nonbonded pdb=" O GLN U 546 " pdb=" OG1 THR U 550 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR U 227 " pdb=" O GLY U 369 " model vdw 2.295 3.040 nonbonded pdb=" O SER U1027 " pdb=" OG SER U1027 " model vdw 2.308 3.040 nonbonded pdb=" O GLN U1196 " pdb=" NH2 ARG U1226 " model vdw 2.316 3.120 nonbonded pdb=" O THR U 155 " pdb=" OG1 THR U 155 " model vdw 2.330 3.040 ... (remaining 72643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.900 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.560 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.011 0.150 9761 Z= 0.459 Angle : 1.380 14.085 13199 Z= 0.753 Chirality : 0.066 0.467 1502 Planarity : 0.007 0.090 1689 Dihedral : 13.072 81.405 3551 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.03 % Favored : 88.89 % Rotamer: Outliers : 0.88 % Allowed : 9.26 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.35 (0.16), residues: 1224 helix: -4.96 (0.08), residues: 637 sheet: -3.98 (0.66), residues: 36 loop : -3.12 (0.23), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 317 TYR 0.027 0.003 TYR U 145 PHE 0.046 0.004 PHE U 383 TRP 0.027 0.003 TRP U 846 HIS 0.007 0.002 HIS U 717 Details of bonding type rmsd covalent geometry : bond 0.01076 ( 9761) covalent geometry : angle 1.37967 (13199) hydrogen bonds : bond 0.31650 ( 158) hydrogen bonds : angle 10.56888 ( 420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 76 GLN cc_start: 0.8450 (tp40) cc_final: 0.8102 (tp-100) REVERT: U 97 LEU cc_start: 0.8465 (tp) cc_final: 0.8218 (tt) REVERT: U 228 ILE cc_start: 0.9055 (tp) cc_final: 0.8828 (mt) REVERT: U 922 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6946 (tp) outliers start: 9 outliers final: 2 residues processed: 214 average time/residue: 0.1111 time to fit residues: 32.0040 Evaluate side-chains 126 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1026 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.0670 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.3980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 overall best weight: 1.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 207 ASN U 466 GLN U 492 GLN U 497 GLN ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 536 ASN U 546 GLN ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 576 ASN U 605 GLN U 640 HIS U 697 GLN U 708 HIS U 778 GLN U 791 GLN U 813 GLN U 842 GLN U 875 GLN U 938 GLN ** U1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.209671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.168516 restraints weight = 11334.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.164704 restraints weight = 22524.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.160954 restraints weight = 19542.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159877 restraints weight = 18807.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.157966 restraints weight = 16837.952| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9761 Z= 0.181 Angle : 0.762 9.583 13199 Z= 0.391 Chirality : 0.045 0.238 1502 Planarity : 0.005 0.056 1689 Dihedral : 7.632 59.711 1333 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.74 % Favored : 91.18 % Rotamer: Outliers : 4.00 % Allowed : 13.65 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.58 (0.19), residues: 1224 helix: -4.37 (0.12), residues: 640 sheet: -3.39 (0.61), residues: 41 loop : -2.67 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U1128 TYR 0.012 0.002 TYR U 145 PHE 0.026 0.002 PHE U 383 TRP 0.011 0.001 TRP U1071 HIS 0.004 0.001 HIS U 717 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9761) covalent geometry : angle 0.76198 (13199) hydrogen bonds : bond 0.04137 ( 158) hydrogen bonds : angle 6.20883 ( 420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 59 ILE cc_start: 0.8868 (tp) cc_final: 0.8593 (tt) REVERT: U 288 MET cc_start: 0.8091 (tpt) cc_final: 0.7747 (tpt) REVERT: U 373 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8978 (tp) REVERT: U 443 MET cc_start: 0.7842 (ppp) cc_final: 0.6782 (ptt) REVERT: U 696 ARG cc_start: 0.7602 (mtp85) cc_final: 0.7340 (mtp85) REVERT: U 743 ARG cc_start: 0.6674 (tpt-90) cc_final: 0.6277 (ttp-170) REVERT: U 792 ARG cc_start: 0.7186 (mmm160) cc_final: 0.6710 (tpp80) REVERT: U 922 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7101 (tp) outliers start: 41 outliers final: 16 residues processed: 169 average time/residue: 0.0841 time to fit residues: 20.9267 Evaluate side-chains 138 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 643 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 956 GLU Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1159 VAL Chi-restraints excluded: chain U residue 1160 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 111 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 30.0000 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 chunk 45 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.211100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.167517 restraints weight = 11254.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163837 restraints weight = 20655.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.159811 restraints weight = 18796.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.156186 restraints weight = 19229.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155267 restraints weight = 15447.765| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9761 Z= 0.149 Angle : 0.700 9.938 13199 Z= 0.353 Chirality : 0.043 0.155 1502 Planarity : 0.004 0.046 1689 Dihedral : 6.753 58.454 1331 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.39 % Allowed : 14.91 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.12 (0.20), residues: 1224 helix: -3.96 (0.14), residues: 651 sheet: -2.94 (0.62), residues: 43 loop : -2.47 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U1128 TYR 0.013 0.001 TYR U 772 PHE 0.020 0.001 PHE U1151 TRP 0.007 0.001 TRP U 846 HIS 0.003 0.001 HIS U1275 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9761) covalent geometry : angle 0.69975 (13199) hydrogen bonds : bond 0.03408 ( 158) hydrogen bonds : angle 5.74441 ( 420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 59 ILE cc_start: 0.8819 (tp) cc_final: 0.8522 (tt) REVERT: U 251 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8499 (tt) REVERT: U 398 ASP cc_start: 0.7378 (t0) cc_final: 0.7100 (t70) REVERT: U 696 ARG cc_start: 0.7434 (mtp85) cc_final: 0.7100 (mtp85) REVERT: U 743 ARG cc_start: 0.6652 (tpt-90) cc_final: 0.6073 (ttp-170) REVERT: U 834 PHE cc_start: 0.8429 (t80) cc_final: 0.8129 (t80) REVERT: U 891 ILE cc_start: 0.8430 (mm) cc_final: 0.8043 (mt) outliers start: 45 outliers final: 23 residues processed: 164 average time/residue: 0.0826 time to fit residues: 20.0117 Evaluate side-chains 137 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 153 LEU Chi-restraints excluded: chain U residue 174 MET Chi-restraints excluded: chain U residue 187 ILE Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 643 LEU Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 956 GLU Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 30.0000 chunk 49 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 0.0570 chunk 5 optimal weight: 0.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 375 ASN U 546 GLN ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 576 ASN ** U1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1258 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.209578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.167008 restraints weight = 11164.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.162538 restraints weight = 21063.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.159929 restraints weight = 19944.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157320 restraints weight = 19677.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.155844 restraints weight = 16848.398| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9761 Z= 0.177 Angle : 0.701 10.616 13199 Z= 0.351 Chirality : 0.045 0.151 1502 Planarity : 0.004 0.042 1689 Dihedral : 6.490 57.406 1329 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.68 % Allowed : 16.76 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.90 (0.20), residues: 1224 helix: -3.77 (0.14), residues: 664 sheet: -2.43 (0.67), residues: 43 loop : -2.36 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 957 TYR 0.012 0.001 TYR U 772 PHE 0.016 0.002 PHE U 383 TRP 0.007 0.001 TRP U1071 HIS 0.002 0.001 HIS U 717 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 9761) covalent geometry : angle 0.70142 (13199) hydrogen bonds : bond 0.03216 ( 158) hydrogen bonds : angle 5.43906 ( 420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 121 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 59 ILE cc_start: 0.8915 (tp) cc_final: 0.8567 (tt) REVERT: U 60 TRP cc_start: 0.7220 (t-100) cc_final: 0.6947 (m100) REVERT: U 153 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7809 (tp) REVERT: U 251 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8387 (tt) REVERT: U 427 PHE cc_start: 0.8159 (t80) cc_final: 0.7911 (t80) REVERT: U 610 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7974 (mp) REVERT: U 743 ARG cc_start: 0.6659 (tpt-90) cc_final: 0.6258 (ttp-170) REVERT: U 792 ARG cc_start: 0.7366 (tpp80) cc_final: 0.6898 (tpp80) REVERT: U 891 ILE cc_start: 0.8523 (mm) cc_final: 0.8116 (mt) REVERT: U 1304 MET cc_start: 0.4067 (pmm) cc_final: 0.3258 (pmm) outliers start: 48 outliers final: 30 residues processed: 157 average time/residue: 0.0865 time to fit residues: 19.7162 Evaluate side-chains 147 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 153 LEU Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 174 MET Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 355 THR Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 643 LEU Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 956 GLU Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1159 VAL Chi-restraints excluded: chain U residue 1160 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 20.0000 chunk 22 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 938 GLN ** U1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1258 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.211790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.171960 restraints weight = 11173.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.164323 restraints weight = 17455.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.159255 restraints weight = 16892.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.157971 restraints weight = 18200.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.156393 restraints weight = 15016.377| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9761 Z= 0.137 Angle : 0.662 9.005 13199 Z= 0.331 Chirality : 0.043 0.160 1502 Planarity : 0.004 0.038 1689 Dihedral : 6.141 56.988 1329 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.61 % Allowed : 17.93 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.69 (0.21), residues: 1224 helix: -3.60 (0.15), residues: 669 sheet: -2.23 (0.67), residues: 43 loop : -2.24 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 957 TYR 0.010 0.001 TYR U 772 PHE 0.016 0.001 PHE U1074 TRP 0.006 0.001 TRP U1071 HIS 0.002 0.001 HIS U 717 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9761) covalent geometry : angle 0.66216 (13199) hydrogen bonds : bond 0.02832 ( 158) hydrogen bonds : angle 5.22293 ( 420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 60 TRP cc_start: 0.7132 (t-100) cc_final: 0.6839 (m100) REVERT: U 153 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7815 (tp) REVERT: U 251 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8333 (tt) REVERT: U 395 GLU cc_start: 0.6863 (tp30) cc_final: 0.6590 (tp30) REVERT: U 743 ARG cc_start: 0.6752 (tpt-90) cc_final: 0.6047 (ttp-170) REVERT: U 792 ARG cc_start: 0.7560 (tpp80) cc_final: 0.7189 (tpp80) REVERT: U 891 ILE cc_start: 0.8518 (mm) cc_final: 0.8095 (mt) REVERT: U 1087 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6814 (t80) outliers start: 37 outliers final: 25 residues processed: 151 average time/residue: 0.0846 time to fit residues: 18.4704 Evaluate side-chains 142 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 131 LEU Chi-restraints excluded: chain U residue 153 LEU Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 187 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 355 THR Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 643 LEU Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 956 GLU Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1159 VAL Chi-restraints excluded: chain U residue 1160 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.0170 chunk 114 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 466 GLN ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1124 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 = 0.4390 r_free = 0.4390 target = 0.214745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.172018 restraints weight = 11002.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.167881 restraints weight = 20376.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164174 restraints weight = 16628.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160583 restraints weight = 18462.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.158712 restraints weight = 17903.291| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9761 Z= 0.111 Angle : 0.631 8.993 13199 Z= 0.314 Chirality : 0.042 0.167 1502 Planarity : 0.004 0.037 1689 Dihedral : 5.778 58.717 1329 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.51 % Allowed : 18.32 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.48 (0.21), residues: 1224 helix: -3.40 (0.16), residues: 683 sheet: -1.89 (0.71), residues: 43 loop : -2.17 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 566 TYR 0.008 0.001 TYR U 178 PHE 0.014 0.001 PHE U1074 TRP 0.005 0.001 TRP U1071 HIS 0.001 0.000 HIS U1275 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9761) covalent geometry : angle 0.63130 (13199) hydrogen bonds : bond 0.02558 ( 158) hydrogen bonds : angle 4.94699 ( 420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 67 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8594 (tt) REVERT: U 251 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8298 (tt) REVERT: U 395 GLU cc_start: 0.6798 (tp30) cc_final: 0.6528 (tp30) REVERT: U 743 ARG cc_start: 0.6731 (tpt-90) cc_final: 0.6212 (ttp-170) REVERT: U 751 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7538 (mm-30) REVERT: U 792 ARG cc_start: 0.7601 (tpp80) cc_final: 0.7225 (tpp80) REVERT: U 891 ILE cc_start: 0.8434 (mm) cc_final: 0.8075 (mt) REVERT: U 1087 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6756 (t80) REVERT: U 1289 MET cc_start: 0.5183 (mpp) cc_final: 0.4114 (mpp) REVERT: U 1304 MET cc_start: 0.4399 (pmm) cc_final: 0.3522 (pmm) outliers start: 36 outliers final: 20 residues processed: 152 average time/residue: 0.0919 time to fit residues: 20.3156 Evaluate side-chains 134 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 187 ILE Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 355 THR Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 643 LEU Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 900 LEU Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 956 GLU Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 38 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 442 ASN ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1124 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 = 0.4412 r_free = 0.4412 target = 0.216990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172112 restraints weight = 10950.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.168530 restraints weight = 19565.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164240 restraints weight = 18780.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.162877 restraints weight = 19303.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162299 restraints weight = 15363.059| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9761 Z= 0.110 Angle : 0.633 8.568 13199 Z= 0.315 Chirality : 0.043 0.184 1502 Planarity : 0.003 0.036 1689 Dihedral : 5.613 58.879 1329 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.51 % Allowed : 18.81 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.21), residues: 1224 helix: -3.23 (0.16), residues: 685 sheet: -1.51 (0.77), residues: 43 loop : -2.11 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 957 TYR 0.009 0.001 TYR U 178 PHE 0.031 0.001 PHE U1151 TRP 0.005 0.001 TRP U 342 HIS 0.004 0.000 HIS U1300 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9761) covalent geometry : angle 0.63261 (13199) hydrogen bonds : bond 0.02476 ( 158) hydrogen bonds : angle 4.84390 ( 420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 67 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8632 (tt) REVERT: U 251 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8244 (tt) REVERT: U 743 ARG cc_start: 0.6715 (tpt-90) cc_final: 0.6367 (ttp-170) REVERT: U 792 ARG cc_start: 0.7451 (tpp80) cc_final: 0.7165 (mmm160) REVERT: U 891 ILE cc_start: 0.8420 (mm) cc_final: 0.8073 (mt) REVERT: U 960 ILE cc_start: 0.8701 (tp) cc_final: 0.8229 (mt) REVERT: U 1087 TYR cc_start: 0.7136 (OUTLIER) cc_final: 0.6675 (t80) REVERT: U 1289 MET cc_start: 0.4838 (mpp) cc_final: 0.3986 (mpp) REVERT: U 1304 MET cc_start: 0.4262 (pmm) cc_final: 0.3337 (pmm) outliers start: 36 outliers final: 20 residues processed: 146 average time/residue: 0.0901 time to fit residues: 19.2224 Evaluate side-chains 138 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 187 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 573 LEU Chi-restraints excluded: chain U residue 611 ILE Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 900 LEU Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 956 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 65 optimal weight: 0.0060 chunk 0 optimal weight: 2.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 697 GLN U 867 GLN U1124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.216490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.170158 restraints weight = 10921.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.164850 restraints weight = 19355.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.160195 restraints weight = 15072.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.159624 restraints weight = 16173.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.160762 restraints weight = 12033.492| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9761 Z= 0.127 Angle : 0.650 11.842 13199 Z= 0.319 Chirality : 0.043 0.198 1502 Planarity : 0.003 0.036 1689 Dihedral : 5.564 58.852 1329 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.00 % Allowed : 18.32 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.13 (0.22), residues: 1224 helix: -3.13 (0.16), residues: 688 sheet: -1.25 (0.80), residues: 43 loop : -2.02 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U1128 TYR 0.010 0.001 TYR U 178 PHE 0.034 0.001 PHE U1151 TRP 0.005 0.001 TRP U1071 HIS 0.002 0.000 HIS U1275 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9761) covalent geometry : angle 0.65007 (13199) hydrogen bonds : bond 0.02510 ( 158) hydrogen bonds : angle 4.79956 ( 420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 67 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8610 (tt) REVERT: U 217 MET cc_start: 0.8391 (tpp) cc_final: 0.7875 (tpt) REVERT: U 251 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8243 (tt) REVERT: U 493 TRP cc_start: 0.8151 (t-100) cc_final: 0.7939 (t-100) REVERT: U 743 ARG cc_start: 0.6695 (tpt-90) cc_final: 0.6391 (ttp-170) REVERT: U 792 ARG cc_start: 0.7450 (tpp80) cc_final: 0.7192 (mmm160) REVERT: U 891 ILE cc_start: 0.8344 (mm) cc_final: 0.8011 (mt) REVERT: U 1087 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6688 (t80) REVERT: U 1304 MET cc_start: 0.4326 (pmm) cc_final: 0.3420 (pmm) outliers start: 41 outliers final: 26 residues processed: 151 average time/residue: 0.0842 time to fit residues: 18.9237 Evaluate side-chains 139 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 187 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 573 LEU Chi-restraints excluded: chain U residue 611 ILE Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 859 THR Chi-restraints excluded: chain U residue 900 LEU Chi-restraints excluded: chain U residue 936 VAL Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 956 GLU Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1124 GLN Chi-restraints excluded: chain U residue 1156 ILE Chi-restraints excluded: chain U residue 1159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 109 optimal weight: 7.9990 chunk 77 optimal weight: 0.0970 chunk 121 optimal weight: 0.4980 chunk 98 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 110 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.218378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.172680 restraints weight = 10872.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 89)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.162768 restraints weight = 17290.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154781 restraints weight = 15370.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.156666 restraints weight = 14813.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.156569 restraints weight = 11184.955| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9761 Z= 0.109 Angle : 0.652 11.183 13199 Z= 0.320 Chirality : 0.043 0.174 1502 Planarity : 0.003 0.039 1689 Dihedral : 5.396 59.034 1329 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.02 % Allowed : 19.88 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.22), residues: 1224 helix: -2.96 (0.17), residues: 685 sheet: -1.14 (0.81), residues: 43 loop : -1.97 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 957 TYR 0.011 0.001 TYR U1208 PHE 0.020 0.001 PHE U1074 TRP 0.004 0.001 TRP U1071 HIS 0.002 0.000 HIS U 484 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9761) covalent geometry : angle 0.65205 (13199) hydrogen bonds : bond 0.02448 ( 158) hydrogen bonds : angle 4.69336 ( 420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 67 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8648 (tt) REVERT: U 217 MET cc_start: 0.8263 (tpp) cc_final: 0.7799 (tpt) REVERT: U 251 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8218 (tt) REVERT: U 493 TRP cc_start: 0.8169 (t-100) cc_final: 0.7913 (t-100) REVERT: U 743 ARG cc_start: 0.6707 (tpt-90) cc_final: 0.6439 (ttp-170) REVERT: U 891 ILE cc_start: 0.8420 (mm) cc_final: 0.8103 (mt) REVERT: U 1087 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.6605 (t80) outliers start: 31 outliers final: 21 residues processed: 143 average time/residue: 0.0827 time to fit residues: 17.6973 Evaluate side-chains 139 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 187 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 611 ILE Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 859 THR Chi-restraints excluded: chain U residue 900 LEU Chi-restraints excluded: chain U residue 936 VAL Chi-restraints excluded: chain U residue 956 GLU Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1156 ILE Chi-restraints excluded: chain U residue 1160 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 0.1980 chunk 7 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.217523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.179434 restraints weight = 10865.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.172467 restraints weight = 15981.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.168181 restraints weight = 16163.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.165813 restraints weight = 16960.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164800 restraints weight = 12501.295| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9761 Z= 0.122 Angle : 0.658 12.161 13199 Z= 0.322 Chirality : 0.043 0.181 1502 Planarity : 0.003 0.041 1689 Dihedral : 5.372 57.747 1329 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.73 % Allowed : 20.27 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.22), residues: 1224 helix: -2.84 (0.17), residues: 687 sheet: -1.14 (0.80), residues: 43 loop : -1.93 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 792 TYR 0.009 0.001 TYR U 178 PHE 0.020 0.001 PHE U1074 TRP 0.006 0.001 TRP U1071 HIS 0.001 0.000 HIS U1275 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9761) covalent geometry : angle 0.65811 (13199) hydrogen bonds : bond 0.02445 ( 158) hydrogen bonds : angle 4.67096 ( 420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 67 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8584 (tt) REVERT: U 217 MET cc_start: 0.8418 (tpp) cc_final: 0.7945 (tpt) REVERT: U 251 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8291 (tt) REVERT: U 743 ARG cc_start: 0.6693 (tpt-90) cc_final: 0.6383 (ttp-170) REVERT: U 891 ILE cc_start: 0.8380 (mm) cc_final: 0.8032 (mt) REVERT: U 1087 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.6547 (t80) REVERT: U 1304 MET cc_start: 0.3796 (pmm) cc_final: 0.2801 (pmm) outliers start: 28 outliers final: 21 residues processed: 135 average time/residue: 0.0778 time to fit residues: 15.6778 Evaluate side-chains 129 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 131 LEU Chi-restraints excluded: chain U residue 187 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 611 ILE Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 859 THR Chi-restraints excluded: chain U residue 900 LEU Chi-restraints excluded: chain U residue 956 GLU Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1124 GLN Chi-restraints excluded: chain U residue 1156 ILE Chi-restraints excluded: chain U residue 1160 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 61 optimal weight: 0.0670 chunk 113 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1258 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 = 0.4405 r_free = 0.4405 target = 0.217348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.177942 restraints weight = 10812.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.171262 restraints weight = 16945.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.167321 restraints weight = 17827.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.164865 restraints weight = 17827.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162743 restraints weight = 14743.097| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.332 9761 Z= 0.272 Angle : 0.949 65.877 13199 Z= 0.539 Chirality : 0.047 0.684 1502 Planarity : 0.007 0.239 1689 Dihedral : 5.379 57.795 1329 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.53 % Allowed : 20.66 % Favored : 76.80 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.22), residues: 1224 helix: -2.84 (0.17), residues: 687 sheet: -1.14 (0.80), residues: 43 loop : -1.93 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U1128 TYR 0.009 0.001 TYR U 178 PHE 0.029 0.001 PHE U 179 TRP 0.043 0.003 TRP U 493 HIS 0.001 0.000 HIS U1275 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 9761) covalent geometry : angle 0.94921 (13199) hydrogen bonds : bond 0.02460 ( 158) hydrogen bonds : angle 4.68080 ( 420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1692.14 seconds wall clock time: 29 minutes 54.51 seconds (1794.51 seconds total)