Starting phenix.real_space_refine on Fri Feb 14 00:16:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lr0_31583/02_2025/6lr0_31583.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lr0_31583/02_2025/6lr0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6lr0_31583/02_2025/6lr0_31583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lr0_31583/02_2025/6lr0_31583.map" model { file = "/net/cci-nas-00/data/ceres_data/6lr0_31583/02_2025/6lr0_31583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lr0_31583/02_2025/6lr0_31583.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.43, per 1000 atoms: 0.57 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: 2.46 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.00 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: 2.64 Time building geometry restraints manager: 2.84 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: 0.420 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.910 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- 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= 0.698 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.35 (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 TRP 0.027 0.003 TRP U 846 HIS 0.007 0.002 HIS U 717 PHE 0.046 0.004 PHE U 383 TYR 0.027 0.003 TYR U 145 ARG 0.010 0.001 ARG U 317 *********************** 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 : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 76 GLN cc_start: 0.8450 (tp40) cc_final: 0.8100 (tp-100) REVERT: U 97 LEU cc_start: 0.8465 (tp) cc_final: 0.8217 (tt) REVERT: U 228 ILE cc_start: 0.9055 (tp) cc_final: 0.8829 (mt) REVERT: U 922 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6947 (tp) outliers start: 9 outliers final: 2 residues processed: 214 average time/residue: 0.2609 time to fit residues: 75.0598 Evaluate side-chains 125 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 103 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 58 optimal weight: 0.0570 chunk 71 optimal weight: 0.5980 chunk 111 optimal weight: 0.4980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 49 GLN U 207 ASN U 372 ASN U 466 GLN ** U 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 536 ASN U 546 GLN 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 938 GLN ** U1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.214826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.171631 restraints weight = 11285.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.166808 restraints weight = 19501.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163021 restraints weight = 17634.848| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2712 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= 0.174 Angle : 0.712 8.441 13199 Z= 0.368 Chirality : 0.043 0.241 1502 Planarity : 0.005 0.053 1689 Dihedral : 7.210 56.603 1333 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.61 % Allowed : 13.74 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.64 (0.18), residues: 1224 helix: -4.34 (0.11), residues: 654 sheet: -3.11 (0.77), residues: 31 loop : -2.78 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U1071 HIS 0.003 0.001 HIS U 717 PHE 0.023 0.001 PHE U 383 TYR 0.010 0.001 TYR U1208 ARG 0.007 0.001 ARG U1128 *********************** 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 193 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: U 288 MET cc_start: 0.8108 (tpt) cc_final: 0.7768 (tpt) REVERT: U 373 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8926 (tp) REVERT: U 396 THR cc_start: 0.8666 (p) cc_final: 0.7205 (m) REVERT: U 398 ASP cc_start: 0.6926 (t0) cc_final: 0.6719 (t70) REVERT: U 443 MET cc_start: 0.7703 (ppp) cc_final: 0.6600 (ptt) REVERT: U 696 ARG cc_start: 0.7581 (mtp85) cc_final: 0.7306 (mtp85) REVERT: U 743 ARG cc_start: 0.6692 (tpt-90) cc_final: 0.6293 (ttp-170) REVERT: U 834 PHE cc_start: 0.8206 (t80) cc_final: 0.7941 (t80) REVERT: U 891 ILE cc_start: 0.8507 (mm) cc_final: 0.8139 (mt) REVERT: U 900 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8597 (tt) outliers start: 37 outliers final: 13 residues processed: 184 average time/residue: 0.2159 time to fit residues: 57.8033 Evaluate side-chains 130 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 580 LEU Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 643 LEU Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 900 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 49 GLN U 170 GLN U 497 GLN ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 765 ASN U 867 GLN U 938 GLN U1124 GLN U1258 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.212293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.174585 restraints weight = 11340.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165759 restraints weight = 16758.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155265 restraints weight = 16877.492| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9761 Z= 0.222 Angle : 0.691 8.640 13199 Z= 0.349 Chirality : 0.043 0.158 1502 Planarity : 0.004 0.042 1689 Dihedral : 6.538 59.059 1329 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.09 % Allowed : 15.40 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (0.19), residues: 1224 helix: -3.94 (0.14), residues: 659 sheet: -2.72 (0.64), residues: 43 loop : -2.57 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 342 HIS 0.005 0.001 HIS U 717 PHE 0.019 0.002 PHE U1151 TYR 0.012 0.001 TYR U 772 ARG 0.005 0.000 ARG U1128 *********************** 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 167 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 59 ILE cc_start: 0.8800 (tp) cc_final: 0.8516 (tt) REVERT: U 131 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7953 (tt) REVERT: U 183 MET cc_start: 0.7777 (tpp) cc_final: 0.7392 (tpp) REVERT: U 251 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8563 (tt) REVERT: U 288 MET cc_start: 0.8257 (tpt) cc_final: 0.7920 (tpt) REVERT: U 398 ASP cc_start: 0.7162 (t0) cc_final: 0.6861 (t70) REVERT: U 443 MET cc_start: 0.8260 (ppp) cc_final: 0.7697 (ptt) REVERT: U 525 MET cc_start: 0.7515 (tpp) cc_final: 0.7296 (tpp) REVERT: U 696 ARG cc_start: 0.7195 (mtp85) cc_final: 0.6887 (mtp85) REVERT: U 743 ARG cc_start: 0.6700 (tpt-90) cc_final: 0.6212 (ttp-170) REVERT: U 834 PHE cc_start: 0.8401 (t80) cc_final: 0.8128 (t80) REVERT: U 891 ILE cc_start: 0.8196 (mm) cc_final: 0.7865 (mt) REVERT: U 931 GLN cc_start: 0.7285 (mt0) cc_final: 0.7063 (tm-30) REVERT: U 1226 ARG cc_start: 0.7156 (ptm160) cc_final: 0.6824 (ptp-170) REVERT: U 1304 MET cc_start: 0.5789 (mpp) cc_final: 0.5373 (pmm) outliers start: 42 outliers final: 19 residues processed: 158 average time/residue: 0.2058 time to fit residues: 48.0017 Evaluate side-chains 133 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 381 GLU 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 757 VAL Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 777 SER Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 927 SER Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 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 24 optimal weight: 0.0570 chunk 113 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 375 ASN ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 546 GLN ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 576 ASN U 875 GLN U 979 ASN U1258 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.208397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.168733 restraints weight = 11072.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.163181 restraints weight = 20369.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.160963 restraints weight = 17606.038| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9761 Z= 0.333 Angle : 0.718 11.626 13199 Z= 0.360 Chirality : 0.046 0.164 1502 Planarity : 0.004 0.043 1689 Dihedral : 6.551 55.718 1329 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.58 % Allowed : 16.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (0.20), residues: 1224 helix: -3.80 (0.14), residues: 663 sheet: -2.22 (0.71), residues: 43 loop : -2.31 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 846 HIS 0.005 0.001 HIS U 717 PHE 0.017 0.002 PHE U 383 TYR 0.012 0.002 TYR U 178 ARG 0.006 0.001 ARG U1128 *********************** 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 166 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 60 TRP cc_start: 0.7185 (t-100) cc_final: 0.6896 (m100) REVERT: U 153 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7946 (tp) REVERT: U 251 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8419 (tt) REVERT: U 743 ARG cc_start: 0.6730 (tpt-90) cc_final: 0.6258 (ttp-170) REVERT: U 834 PHE cc_start: 0.8438 (t80) cc_final: 0.8216 (t80) REVERT: U 891 ILE cc_start: 0.8492 (mm) cc_final: 0.8064 (mt) outliers start: 47 outliers final: 26 residues processed: 157 average time/residue: 0.2258 time to fit residues: 51.5426 Evaluate side-chains 135 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 153 LEU 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 381 GLU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 479 VAL 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 757 VAL Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 777 SER Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 927 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 22 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 0.2980 chunk 77 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 546 GLN ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 576 ASN U 765 ASN U1258 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.215962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.175948 restraints weight = 11174.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.172454 restraints weight = 21201.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.169556 restraints weight = 16966.471| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9761 Z= 0.154 Angle : 0.642 8.393 13199 Z= 0.321 Chirality : 0.042 0.156 1502 Planarity : 0.004 0.037 1689 Dihedral : 5.915 58.275 1329 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.80 % Allowed : 17.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.21), residues: 1224 helix: -3.53 (0.15), residues: 668 sheet: -2.02 (0.71), residues: 43 loop : -2.15 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP U1071 HIS 0.005 0.001 HIS U 717 PHE 0.017 0.001 PHE U1074 TYR 0.008 0.001 TYR U 274 ARG 0.003 0.000 ARG U 399 *********************** 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 164 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 60 TRP cc_start: 0.7009 (t-100) cc_final: 0.6734 (m100) REVERT: U 67 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8671 (tt) REVERT: U 251 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8364 (tt) REVERT: U 427 PHE cc_start: 0.7902 (t80) cc_final: 0.7697 (t80) REVERT: U 505 PRO cc_start: 0.8397 (Cg_exo) cc_final: 0.8171 (Cg_endo) REVERT: U 743 ARG cc_start: 0.6736 (tpt-90) cc_final: 0.6135 (ttp-170) REVERT: U 891 ILE cc_start: 0.8088 (mm) cc_final: 0.7790 (mt) REVERT: U 955 LYS cc_start: 0.6596 (mmmt) cc_final: 0.6156 (mmmt) REVERT: U 1289 MET cc_start: 0.4461 (mpp) cc_final: 0.4259 (mpp) outliers start: 39 outliers final: 16 residues processed: 154 average time/residue: 0.1938 time to fit residues: 43.2796 Evaluate side-chains 133 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 251 LEU 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 576 ASN 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 777 SER Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 853 SER 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 1160 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 104 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 30.0000 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 466 GLN U 546 GLN ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 576 ASN U 697 GLN U 867 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.213166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.170801 restraints weight = 11032.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.167000 restraints weight = 21256.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.163569 restraints weight = 18726.471| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9761 Z= 0.248 Angle : 0.675 9.385 13199 Z= 0.333 Chirality : 0.044 0.164 1502 Planarity : 0.004 0.043 1689 Dihedral : 5.908 57.630 1329 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.51 % Allowed : 18.52 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.21), residues: 1224 helix: -3.45 (0.15), residues: 678 sheet: -1.56 (0.74), residues: 43 loop : -2.13 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U1071 HIS 0.005 0.001 HIS U 717 PHE 0.018 0.001 PHE U1129 TYR 0.010 0.001 TYR U 178 ARG 0.006 0.000 ARG U 575 *********************** 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 149 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 251 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8360 (tt) REVERT: U 743 ARG cc_start: 0.6729 (tpt-90) cc_final: 0.6145 (ttp-170) REVERT: U 891 ILE cc_start: 0.8319 (mm) cc_final: 0.7948 (mt) REVERT: U 1087 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6813 (t80) outliers start: 36 outliers final: 22 residues processed: 142 average time/residue: 0.1870 time to fit residues: 39.2606 Evaluate side-chains 131 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 100 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 359 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 582 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 777 SER Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 859 THR Chi-restraints excluded: chain U residue 927 SER 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 1159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 0.1980 chunk 118 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 chunk 107 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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** U 576 ASN U1258 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.216945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.175022 restraints weight = 10870.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.170835 restraints weight = 19721.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.167178 restraints weight = 17555.279| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4347 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= 0.168 Angle : 0.648 9.469 13199 Z= 0.320 Chirality : 0.043 0.169 1502 Planarity : 0.003 0.036 1689 Dihedral : 5.628 58.510 1329 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.53 % Allowed : 19.40 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.21), residues: 1224 helix: -3.25 (0.16), residues: 685 sheet: -1.42 (0.76), residues: 43 loop : -2.03 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U 752 HIS 0.004 0.000 HIS U 717 PHE 0.018 0.001 PHE U1074 TYR 0.008 0.001 TYR U 411 ARG 0.007 0.000 ARG U 575 *********************** 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 148 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 251 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8334 (tt) REVERT: U 743 ARG cc_start: 0.6737 (tpt-90) cc_final: 0.6217 (ttp-170) REVERT: U 891 ILE cc_start: 0.7971 (mm) cc_final: 0.7700 (mt) REVERT: U 992 MET cc_start: 0.8115 (tpp) cc_final: 0.7840 (tpp) REVERT: U 1087 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6764 (t80) REVERT: U 1131 ASP cc_start: 0.5665 (t0) cc_final: 0.4899 (t0) REVERT: U 1289 MET cc_start: 0.5059 (OUTLIER) cc_final: 0.3791 (mpp) outliers start: 26 outliers final: 20 residues processed: 141 average time/residue: 0.1989 time to fit residues: 41.1455 Evaluate side-chains 136 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 576 ASN 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 768 VAL Chi-restraints excluded: chain U residue 777 SER Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 927 SER 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 1159 VAL Chi-restraints excluded: chain U residue 1160 SER Chi-restraints excluded: chain U residue 1289 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 77 optimal weight: 0.4980 chunk 61 optimal weight: 7.9990 chunk 99 optimal weight: 0.3980 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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** U 576 ASN U 996 ASN 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 = 0.211712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.169211 restraints weight = 11084.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.164766 restraints weight = 19525.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.160634 restraints weight = 18010.338| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9761 Z= 0.320 Angle : 0.707 11.706 13199 Z= 0.348 Chirality : 0.046 0.177 1502 Planarity : 0.004 0.037 1689 Dihedral : 5.958 57.729 1329 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.80 % Allowed : 18.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.22), residues: 1224 helix: -3.26 (0.16), residues: 685 sheet: -1.36 (0.78), residues: 43 loop : -1.96 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 846 HIS 0.004 0.001 HIS U 717 PHE 0.019 0.002 PHE U1074 TYR 0.015 0.002 TYR U 178 ARG 0.006 0.001 ARG U1128 *********************** 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 148 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 251 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8315 (tt) REVERT: U 743 ARG cc_start: 0.6654 (tpt-90) cc_final: 0.6323 (ttp-170) REVERT: U 891 ILE cc_start: 0.8170 (mm) cc_final: 0.7874 (mt) REVERT: U 992 MET cc_start: 0.8172 (tpp) cc_final: 0.7843 (tpp) REVERT: U 1087 TYR cc_start: 0.7108 (OUTLIER) cc_final: 0.6651 (t80) outliers start: 39 outliers final: 23 residues processed: 141 average time/residue: 0.1876 time to fit residues: 40.0209 Evaluate side-chains 131 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 247 SER 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 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 777 SER Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 859 THR 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 1159 VAL Chi-restraints excluded: chain U residue 1160 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 122 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 60 optimal weight: 30.0000 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 497 GLN ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 576 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.212629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.173932 restraints weight = 10967.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.166508 restraints weight = 17099.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.162197 restraints weight = 16444.121| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9761 Z= 0.259 Angle : 0.690 11.225 13199 Z= 0.338 Chirality : 0.045 0.198 1502 Planarity : 0.004 0.037 1689 Dihedral : 5.865 58.518 1329 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.63 % Allowed : 19.98 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.22), residues: 1224 helix: -3.13 (0.16), residues: 690 sheet: -1.41 (0.77), residues: 43 loop : -1.90 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP U 493 HIS 0.005 0.001 HIS U 717 PHE 0.020 0.002 PHE U1074 TYR 0.012 0.001 TYR U 178 ARG 0.006 0.000 ARG U 920 *********************** 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 138 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: U 251 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8306 (tt) REVERT: U 743 ARG cc_start: 0.6666 (tpt-90) cc_final: 0.6356 (ttp-170) REVERT: U 891 ILE cc_start: 0.8554 (mm) cc_final: 0.8195 (mt) REVERT: U 992 MET cc_start: 0.8151 (tpp) cc_final: 0.7853 (tpp) REVERT: U 1087 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6745 (t80) outliers start: 27 outliers final: 18 residues processed: 133 average time/residue: 0.2034 time to fit residues: 40.6024 Evaluate side-chains 128 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 100 LEU 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 643 LEU Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 777 SER Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 859 THR 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 1159 VAL 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 113 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 172 GLN ** U 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 938 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.208650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169450 restraints weight = 11053.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.161255 restraints weight = 16999.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.156272 restraints weight = 18080.499| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 9761 Z= 0.437 Angle : 0.779 11.144 13199 Z= 0.382 Chirality : 0.048 0.177 1502 Planarity : 0.004 0.039 1689 Dihedral : 6.291 58.189 1329 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.73 % Allowed : 20.37 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.22), residues: 1224 helix: -3.24 (0.16), residues: 695 sheet: -1.38 (0.77), residues: 43 loop : -1.93 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP U 493 HIS 0.005 0.001 HIS U 717 PHE 0.020 0.002 PHE U1074 TYR 0.018 0.002 TYR U 178 ARG 0.008 0.001 ARG U1128 ********************** 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 133 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: U 251 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8269 (tt) REVERT: U 743 ARG cc_start: 0.6728 (tpt-90) cc_final: 0.6173 (ttp-170) REVERT: U 891 ILE cc_start: 0.8100 (mm) cc_final: 0.7778 (mt) REVERT: U 992 MET cc_start: 0.8366 (tpp) cc_final: 0.8099 (tpp) REVERT: U 1087 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6958 (t80) outliers start: 28 outliers final: 22 residues processed: 127 average time/residue: 0.1845 time to fit residues: 35.3797 Evaluate side-chains 130 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 100 LEU 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 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 777 SER Chi-restraints excluded: chain U residue 785 ILE 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 927 SER 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 1159 VAL 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 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 chunk 108 optimal weight: 0.9980 chunk 116 optimal weight: 30.0000 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.214796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.176057 restraints weight = 10902.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.169379 restraints weight = 16548.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.166009 restraints weight = 15724.643| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9761 Z= 0.186 Angle : 0.690 13.258 13199 Z= 0.338 Chirality : 0.043 0.178 1502 Planarity : 0.003 0.038 1689 Dihedral : 5.781 59.162 1329 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.24 % Allowed : 20.86 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.22), residues: 1224 helix: -3.04 (0.17), residues: 690 sheet: -1.37 (0.77), residues: 43 loop : -1.86 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP U 493 HIS 0.004 0.000 HIS U 717 PHE 0.019 0.001 PHE U1074 TYR 0.008 0.001 TYR U 772 ARG 0.006 0.000 ARG U 920 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2882.77 seconds wall clock time: 52 minutes 42.64 seconds (3162.64 seconds total)