Starting phenix.real_space_refine on Thu Feb 13 22:01:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dv5_30870/02_2025/7dv5_30870.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dv5_30870/02_2025/7dv5_30870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dv5_30870/02_2025/7dv5_30870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dv5_30870/02_2025/7dv5_30870.map" model { file = "/net/cci-nas-00/data/ceres_data/7dv5_30870/02_2025/7dv5_30870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dv5_30870/02_2025/7dv5_30870.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 56 5.16 5 C 5977 2.51 5 N 1567 2.21 5 O 1719 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: 9319 Number of models: 1 Model: "" Number of chains: 2 Chain: "U" Number of atoms: 9249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1189, 9249 Classifications: {'peptide': 1189} Link IDs: {'PTRANS': 32, 'TRANS': 1156} Chain breaks: 1 Chain: "U" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'TCH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.65, per 1000 atoms: 0.61 Number of scatterers: 9319 At special positions: 0 Unit cell: (91.91, 157.56, 96.96, 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 56 16.00 O 1719 8.00 N 1567 7.00 C 5977 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.2 seconds 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 44.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'U' and resid 55 through 59 removed outlier: 3.992A pdb=" N ILE U 59 " --> pdb=" O SER U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 87 removed outlier: 4.652A pdb=" N LEU U 80 " --> pdb=" O GLN U 76 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU U 81 " --> pdb=" O PRO U 77 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE U 82 " --> pdb=" O GLY U 78 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR U 87 " --> pdb=" O PHE U 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 92 through 99 removed outlier: 4.158A pdb=" N GLU U 96 " --> pdb=" O ASP U 92 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 149 removed outlier: 3.701A pdb=" N ILE U 139 " --> pdb=" O GLU U 135 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS U 140 " --> pdb=" O SER U 136 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER U 143 " --> pdb=" O ILE U 139 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR U 144 " --> pdb=" O LYS U 140 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA U 146 " --> pdb=" O ALA U 142 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY U 147 " --> pdb=" O SER U 143 " (cutoff:3.500A) Processing helix chain 'U' and resid 149 through 154 Processing helix chain 'U' and resid 157 through 162 Processing helix chain 'U' and resid 164 through 168 removed outlier: 3.656A pdb=" N ALA U 167 " --> pdb=" O VAL U 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 170 through 182 removed outlier: 3.914A pdb=" N LYS U 176 " --> pdb=" O GLN U 172 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE U 179 " --> pdb=" O ARG U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 192 removed outlier: 3.609A pdb=" N ASP U 191 " --> pdb=" O ILE U 187 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS U 192 " --> pdb=" O GLY U 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 187 through 192' Processing helix chain 'U' and resid 214 through 222 removed outlier: 4.600A pdb=" N ALA U 218 " --> pdb=" O ALA U 214 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU U 219 " --> pdb=" O ASP U 215 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE U 220 " --> pdb=" O GLN U 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 236 removed outlier: 3.835A pdb=" N GLY U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 243 removed outlier: 3.716A pdb=" N THR U 242 " --> pdb=" O GLY U 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 244 through 248 Processing helix chain 'U' and resid 250 through 255 removed outlier: 3.777A pdb=" N GLY U 255 " --> pdb=" O LEU U 251 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 275 removed outlier: 3.984A pdb=" N TYR U 269 " --> pdb=" O LYS U 265 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU U 271 " --> pdb=" O THR U 267 " (cutoff:3.500A) Processing helix chain 'U' and resid 287 through 294 removed outlier: 3.902A pdb=" N VAL U 291 " --> pdb=" O SER U 287 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA U 292 " --> pdb=" O MET U 288 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA U 293 " --> pdb=" O ARG U 289 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE U 294 " --> pdb=" O THR U 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 287 through 294' Processing helix chain 'U' and resid 296 through 301 removed outlier: 4.044A pdb=" N VAL U 301 " --> pdb=" O GLU U 297 " (cutoff:3.500A) Processing helix chain 'U' and resid 301 through 306 Processing helix chain 'U' and resid 320 through 335 removed outlier: 3.834A pdb=" N THR U 326 " --> pdb=" O MET U 322 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY U 327 " --> pdb=" O GLY U 323 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU U 332 " --> pdb=" O PHE U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 336 through 341 Processing helix chain 'U' and resid 342 through 350 removed outlier: 3.935A pdb=" N THR U 346 " --> pdb=" O TRP U 342 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU U 347 " --> pdb=" O TYR U 343 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL U 348 " --> pdb=" O GLY U 344 " (cutoff:3.500A) Processing helix chain 'U' and resid 362 through 375 removed outlier: 3.609A pdb=" N VAL U 366 " --> pdb=" O ILE U 362 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN U 372 " --> pdb=" O VAL U 368 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU U 373 " --> pdb=" O GLY U 369 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY U 374 " --> pdb=" O ALA U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 381 through 390 Processing helix chain 'U' and resid 392 through 397 removed outlier: 3.501A pdb=" N THR U 396 " --> pdb=" O SER U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 490 through 497 removed outlier: 3.924A pdb=" N ASP U 496 " --> pdb=" O GLN U 492 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN U 497 " --> pdb=" O TRP U 493 " (cutoff:3.500A) Processing helix chain 'U' and resid 524 through 535 removed outlier: 3.962A pdb=" N VAL U 529 " --> pdb=" O MET U 525 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN U 530 " --> pdb=" O GLU U 526 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA U 531 " --> pdb=" O ASP U 527 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU U 534 " --> pdb=" O GLN U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 537 through 543 removed outlier: 3.862A pdb=" N ASP U 543 " --> pdb=" O ASN U 539 " (cutoff:3.500A) Processing helix chain 'U' and resid 560 through 563 Processing helix chain 'U' and resid 564 through 574 removed outlier: 3.687A pdb=" N ALA U 568 " --> pdb=" O LYS U 564 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE U 569 " --> pdb=" O GLN U 565 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA U 570 " --> pdb=" O ARG U 566 " (cutoff:3.500A) Processing helix chain 'U' and resid 593 through 603 removed outlier: 3.682A pdb=" N VAL U 600 " --> pdb=" O MET U 596 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU U 601 " --> pdb=" O VAL U 597 " (cutoff:3.500A) Processing helix chain 'U' and resid 652 through 656 removed outlier: 3.811A pdb=" N THR U 655 " --> pdb=" O THR U 652 " (cutoff:3.500A) Processing helix chain 'U' and resid 742 through 748 Processing helix chain 'U' and resid 749 through 752 removed outlier: 3.908A pdb=" N TRP U 752 " --> pdb=" O ALA U 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 749 through 752' Processing helix chain 'U' and resid 753 through 761 Processing helix chain 'U' and resid 767 through 780 removed outlier: 3.519A pdb=" N TYR U 772 " --> pdb=" O VAL U 768 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA U 773 " --> pdb=" O THR U 769 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE U 774 " --> pdb=" O PRO U 770 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER U 777 " --> pdb=" O ALA U 773 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN U 778 " --> pdb=" O PHE U 774 " (cutoff:3.500A) Processing helix chain 'U' and resid 789 through 794 removed outlier: 3.741A pdb=" N SER U 793 " --> pdb=" O GLU U 789 " (cutoff:3.500A) Processing helix chain 'U' and resid 802 through 810 removed outlier: 3.884A pdb=" N VAL U 808 " --> pdb=" O ALA U 804 " (cutoff:3.500A) Processing helix chain 'U' and resid 811 through 819 Processing helix chain 'U' and resid 819 through 841 removed outlier: 3.828A pdb=" N GLY U 824 " --> pdb=" O PHE U 820 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU U 825 " --> pdb=" O ALA U 821 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR U 828 " --> pdb=" O GLY U 824 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG U 830 " --> pdb=" O LEU U 826 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG U 832 " --> pdb=" O THR U 828 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS U 833 " --> pdb=" O LYS U 829 " (cutoff:3.500A) Processing helix chain 'U' and resid 868 through 880 removed outlier: 3.920A pdb=" N ALA U 872 " --> pdb=" O VAL U 868 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N SER U 874 " --> pdb=" O GLY U 870 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLN U 875 " --> pdb=" O ALA U 871 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE U 876 " --> pdb=" O ALA U 872 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY U 877 " --> pdb=" O GLY U 873 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET U 878 " --> pdb=" O SER U 874 " (cutoff:3.500A) Processing helix chain 'U' and resid 887 through 897 removed outlier: 3.910A pdb=" N PHE U 896 " --> pdb=" O ILE U 892 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER U 897 " --> pdb=" O ALA U 893 " (cutoff:3.500A) Processing helix chain 'U' and resid 900 through 905 removed outlier: 3.881A pdb=" N ILE U 904 " --> pdb=" O LEU U 900 " (cutoff:3.500A) Processing helix chain 'U' and resid 908 through 917 removed outlier: 3.593A pdb=" N ALA U 912 " --> pdb=" O PHE U 908 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU U 913 " --> pdb=" O PRO U 909 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER U 914 " --> pdb=" O PHE U 910 " (cutoff:3.500A) Processing helix chain 'U' and resid 922 through 926 Processing helix chain 'U' and resid 929 through 933 Processing helix chain 'U' and resid 935 through 940 Processing helix chain 'U' and resid 947 through 952 removed outlier: 3.518A pdb=" N ALA U 951 " --> pdb=" O ILE U 947 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY U 952 " --> pdb=" O ARG U 948 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 947 through 952' Processing helix chain 'U' and resid 965 through 967 No H-bonds generated for 'chain 'U' and resid 965 through 967' Processing helix chain 'U' and resid 968 through 973 removed outlier: 3.682A pdb=" N THR U 973 " --> pdb=" O LYS U 969 " (cutoff:3.500A) Processing helix chain 'U' and resid 991 through 996 Processing helix chain 'U' and resid 996 through 1009 removed outlier: 3.733A pdb=" N ARG U1001 " --> pdb=" O SER U 997 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR U1002 " --> pdb=" O ALA U 998 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU U1006 " --> pdb=" O TYR U1002 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER U1008 " --> pdb=" O GLY U1004 " (cutoff:3.500A) Processing helix chain 'U' and resid 1014 through 1019 removed outlier: 3.921A pdb=" N PHE U1018 " --> pdb=" O PHE U1014 " (cutoff:3.500A) Processing helix chain 'U' and resid 1029 through 1034 removed outlier: 3.612A pdb=" N ALA U1034 " --> pdb=" O ALA U1030 " (cutoff:3.500A) Processing helix chain 'U' and resid 1047 through 1056 removed outlier: 3.771A pdb=" N PHE U1051 " --> pdb=" O SER U1047 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE U1052 " --> pdb=" O ALA U1048 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN U1053 " --> pdb=" O ALA U1049 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP U1056 " --> pdb=" O PHE U1052 " (cutoff:3.500A) Processing helix chain 'U' and resid 1119 through 1125 removed outlier: 3.570A pdb=" N ILE U1123 " --> pdb=" O LYS U1119 " (cutoff:3.500A) Processing helix chain 'U' and resid 1148 through 1154 removed outlier: 3.514A pdb=" N LEU U1152 " --> pdb=" O ASN U1148 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER U1154 " --> pdb=" O GLN U1150 " (cutoff:3.500A) Processing helix chain 'U' and resid 1170 through 1176 Processing helix chain 'U' and resid 1185 through 1191 removed outlier: 4.029A pdb=" N ILE U1189 " --> pdb=" O MET U1185 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA U1190 " --> pdb=" O GLU U1186 " (cutoff:3.500A) Processing helix chain 'U' and resid 1220 through 1223 Processing helix chain 'U' and resid 1224 through 1234 removed outlier: 3.604A pdb=" N ALA U1230 " --> pdb=" O ARG U1226 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA U1232 " --> pdb=" O ALA U1228 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE U1233 " --> pdb=" O ILE U1229 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL U1234 " --> pdb=" O ALA U1230 " (cutoff:3.500A) Processing helix chain 'U' and resid 1250 through 1264 removed outlier: 3.717A pdb=" N THR U1256 " --> pdb=" O GLU U1252 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA U1260 " --> pdb=" O THR U1256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP U1262 " --> pdb=" O GLN U1258 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS U1263 " --> pdb=" O VAL U1259 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA U1264 " --> pdb=" O ALA U1260 " (cutoff:3.500A) Processing helix chain 'U' and resid 1299 through 1303 removed outlier: 3.734A pdb=" N LEU U1303 " --> pdb=" O HIS U1300 " (cutoff:3.500A) Processing helix chain 'U' and resid 1308 through 1315 removed outlier: 3.644A pdb=" N LYS U1312 " --> pdb=" O GLY U1308 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU U1313 " --> pdb=" O ALA U1309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'U' and resid 420 through 426 removed outlier: 3.627A pdb=" N ILE U 420 " --> pdb=" O ILE U 445 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET U 443 " --> pdb=" O PHE U 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN U 424 " --> pdb=" O LEU U 441 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU U 441 " --> pdb=" O ASN U 424 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N THR U 426 " --> pdb=" O ASN U 439 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASN U 439 " --> pdb=" O THR U 426 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 498 through 501 removed outlier: 6.236A pdb=" N LEU U 580 " --> pdb=" O ILE U 611 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 1156 through 1159 removed outlier: 6.775A pdb=" N GLY U1157 " --> pdb=" O LEU U1241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 183 hydrogen bonds defined for protein. 513 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: 2.74 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2531 1.33 - 1.45: 1907 1.45 - 1.57: 4975 1.57 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 9503 Sorted by residual: bond pdb=" CG1 ILE U 171 " pdb=" CD1 ILE U 171 " ideal model delta sigma weight residual 1.513 1.365 0.148 3.90e-02 6.57e+02 1.43e+01 bond pdb=" O3S TCH U1401 " pdb=" S26 TCH U1401 " ideal model delta sigma weight residual 1.475 1.548 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O3S TCH U1402 " pdb=" S26 TCH U1402 " ideal model delta sigma weight residual 1.475 1.547 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" N VAL U 348 " pdb=" CA VAL U 348 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.22e-02 6.72e+03 9.19e+00 bond pdb=" N ILE U1280 " pdb=" CA ILE U1280 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.25e-02 6.40e+03 8.69e+00 ... (remaining 9498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.13: 12820 8.13 - 16.26: 39 16.26 - 24.39: 4 24.39 - 32.52: 1 32.52 - 40.65: 2 Bond angle restraints: 12866 Sorted by residual: angle pdb=" N ARG U 920 " pdb=" CA ARG U 920 " pdb=" C ARG U 920 " ideal model delta sigma weight residual 110.80 151.45 -40.65 2.13e+00 2.20e-01 3.64e+02 angle pdb=" N ILE U 112 " pdb=" CA ILE U 112 " pdb=" C ILE U 112 " ideal model delta sigma weight residual 110.62 132.26 -21.64 1.14e+00 7.69e-01 3.60e+02 angle pdb=" C ARG U 920 " pdb=" CA ARG U 920 " pdb=" CB ARG U 920 " ideal model delta sigma weight residual 110.42 75.84 34.58 1.99e+00 2.53e-01 3.02e+02 angle pdb=" N THR U 111 " pdb=" CA THR U 111 " pdb=" C THR U 111 " ideal model delta sigma weight residual 108.00 82.83 25.17 1.48e+00 4.57e-01 2.89e+02 angle pdb=" C THR U 111 " pdb=" CA THR U 111 " pdb=" CB THR U 111 " ideal model delta sigma weight residual 116.34 137.97 -21.63 1.40e+00 5.10e-01 2.39e+02 ... (remaining 12861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.37: 5479 24.37 - 48.75: 250 48.75 - 73.12: 22 73.12 - 97.49: 8 97.49 - 121.87: 3 Dihedral angle restraints: 5762 sinusoidal: 2351 harmonic: 3411 Sorted by residual: dihedral pdb=" C THR U1279 " pdb=" N THR U1279 " pdb=" CA THR U1279 " pdb=" CB THR U1279 " ideal model delta harmonic sigma weight residual -122.00 -98.92 -23.08 0 2.50e+00 1.60e-01 8.52e+01 dihedral pdb=" C ARG U 920 " pdb=" N ARG U 920 " pdb=" CA ARG U 920 " pdb=" CB ARG U 920 " ideal model delta harmonic sigma weight residual -122.60 -100.02 -22.58 0 2.50e+00 1.60e-01 8.16e+01 dihedral pdb=" N MET U 921 " pdb=" C MET U 921 " pdb=" CA MET U 921 " pdb=" CB MET U 921 " ideal model delta harmonic sigma weight residual 122.80 102.72 20.08 0 2.50e+00 1.60e-01 6.45e+01 ... (remaining 5759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 1441 0.194 - 0.388: 27 0.388 - 0.581: 1 0.581 - 0.775: 3 0.775 - 0.969: 1 Chirality restraints: 1473 Sorted by residual: chirality pdb=" CA ARG U 920 " pdb=" N ARG U 920 " pdb=" C ARG U 920 " pdb=" CB ARG U 920 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CA THR U1279 " pdb=" N THR U1279 " pdb=" C THR U1279 " pdb=" CB THR U1279 " both_signs ideal model delta sigma weight residual False 2.53 3.22 -0.69 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA ILE U 112 " pdb=" N ILE U 112 " pdb=" C ILE U 112 " pdb=" CB ILE U 112 " both_signs ideal model delta sigma weight residual False 2.43 1.76 0.67 2.00e-01 2.50e+01 1.14e+01 ... (remaining 1470 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C23 TCH U1401 " -0.113 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" C24 TCH U1401 " 0.043 2.00e-02 2.50e+03 pdb=" C25 TCH U1401 " -0.153 2.00e-02 2.50e+03 pdb=" N24 TCH U1401 " 0.203 2.00e-02 2.50e+03 pdb=" O24 TCH U1401 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR U 769 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO U 770 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO U 770 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO U 770 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS U 969 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.35e+00 pdb=" N PRO U 970 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO U 970 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO U 970 " -0.041 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 56 2.53 - 3.12: 6619 3.12 - 3.71: 13728 3.71 - 4.31: 18822 4.31 - 4.90: 30814 Nonbonded interactions: 70039 Sorted by model distance: nonbonded pdb=" O ARG U 920 " pdb=" CB ARG U 920 " model vdw 1.936 2.752 nonbonded pdb=" OD1 ASP U 350 " pdb=" N GLU U 351 " model vdw 2.014 3.120 nonbonded pdb=" N THR U 111 " pdb=" O THR U 111 " model vdw 2.079 2.496 nonbonded pdb=" N THR U1279 " pdb=" O THR U1279 " model vdw 2.257 2.496 nonbonded pdb=" C SER U1278 " pdb=" O THR U1279 " model vdw 2.272 3.270 ... (remaining 70034 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: 0.380 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.420 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 0.148 9503 Z= 0.669 Angle : 1.462 40.646 12866 Z= 0.824 Chirality : 0.083 0.969 1473 Planarity : 0.008 0.126 1632 Dihedral : 14.003 121.866 3572 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.73 % Favored : 88.19 % Rotamer: Outliers : 2.23 % Allowed : 8.81 % Favored : 88.97 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.60 (0.15), residues: 1185 helix: -4.90 (0.07), residues: 634 sheet: -4.65 (0.54), residues: 26 loop : -3.52 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP U 163 HIS 0.009 0.002 HIS U 72 PHE 0.026 0.003 PHE U 629 TYR 0.028 0.003 TYR U 981 ARG 0.014 0.001 ARG U1001 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: U 268 ASP cc_start: 0.7978 (m-30) cc_final: 0.7694 (t0) REVERT: U 424 ASN cc_start: 0.5405 (p0) cc_final: 0.4738 (p0) REVERT: U 426 THR cc_start: 0.7168 (t) cc_final: 0.6866 (p) REVERT: U 478 MET cc_start: 0.6556 (ppp) cc_final: 0.5941 (mmt) REVERT: U 516 ILE cc_start: 0.9009 (mt) cc_final: 0.8714 (mm) REVERT: U 533 LYS cc_start: 0.7873 (tttm) cc_final: 0.7367 (pttt) REVERT: U 913 LEU cc_start: 0.8530 (tm) cc_final: 0.8062 (mt) REVERT: U 918 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.5912 (tp-100) REVERT: U 925 PHE cc_start: 0.5698 (OUTLIER) cc_final: 0.3421 (p90) REVERT: U 946 ASN cc_start: 0.8606 (p0) cc_final: 0.8400 (p0) REVERT: U 1033 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7449 (ttp80) REVERT: U 1037 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.6996 (m-10) REVERT: U 1145 LYS cc_start: 0.8217 (mmmm) cc_final: 0.7573 (ptmt) REVERT: U 1161 GLN cc_start: 0.6938 (tt0) cc_final: 0.6568 (tp40) REVERT: U 1221 ARG cc_start: 0.6777 (ttp-170) cc_final: 0.6565 (ttp-170) REVERT: U 1261 LEU cc_start: 0.8459 (mp) cc_final: 0.8224 (mt) outliers start: 22 outliers final: 10 residues processed: 206 average time/residue: 0.2763 time to fit residues: 74.6741 Evaluate side-chains 128 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 343 TYR Chi-restraints excluded: chain U residue 347 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 651 PHE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 921 MET Chi-restraints excluded: chain U residue 925 PHE Chi-restraints excluded: chain U residue 1029 THR Chi-restraints excluded: chain U residue 1033 ARG Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1126 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.0970 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 72 HIS U 110 ASN U 372 ASN ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 867 GLN U1107 GLN U1124 GLN U1258 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.168921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127635 restraints weight = 13535.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126494 restraints weight = 9386.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127640 restraints weight = 9198.172| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9503 Z= 0.169 Angle : 0.678 8.302 12866 Z= 0.349 Chirality : 0.042 0.164 1473 Planarity : 0.004 0.051 1632 Dihedral : 9.928 134.285 1464 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.94 % Allowed : 13.46 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.75 (0.17), residues: 1185 helix: -4.14 (0.12), residues: 638 sheet: -3.74 (0.72), residues: 26 loop : -3.23 (0.23), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 330 HIS 0.004 0.001 HIS U1142 PHE 0.012 0.001 PHE U1085 TYR 0.019 0.002 TYR U 157 ARG 0.004 0.001 ARG U1128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 123 MET cc_start: 0.0344 (mmt) cc_final: 0.0119 (mmt) REVERT: U 144 TYR cc_start: 0.8194 (m-10) cc_final: 0.7921 (m-80) REVERT: U 154 ILE cc_start: 0.8823 (tp) cc_final: 0.8269 (tp) REVERT: U 173 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8341 (mtmm) REVERT: U 424 ASN cc_start: 0.5274 (p0) cc_final: 0.4921 (p0) REVERT: U 472 TYR cc_start: 0.8537 (m-80) cc_final: 0.8331 (m-80) REVERT: U 478 MET cc_start: 0.6436 (ppp) cc_final: 0.5745 (mmt) REVERT: U 533 LYS cc_start: 0.7627 (tttm) cc_final: 0.7309 (pttt) REVERT: U 576 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7343 (t0) REVERT: U 610 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8014 (mp) REVERT: U 913 LEU cc_start: 0.8445 (tm) cc_final: 0.7982 (mt) REVERT: U 918 GLN cc_start: 0.6356 (OUTLIER) cc_final: 0.5483 (tp-100) REVERT: U 920 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.5077 (mtt90) REVERT: U 921 MET cc_start: 0.5582 (tpt) cc_final: 0.4460 (ttp) REVERT: U 928 ARG cc_start: 0.7110 (tpt170) cc_final: 0.6048 (ptp90) REVERT: U 946 ASN cc_start: 0.8369 (p0) cc_final: 0.8117 (p0) REVERT: U 1006 LEU cc_start: 0.9024 (mp) cc_final: 0.8791 (mt) REVERT: U 1037 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7056 (m-10) REVERT: U 1145 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7472 (ptmt) REVERT: U 1161 GLN cc_start: 0.6862 (tt0) cc_final: 0.6491 (tp40) REVERT: U 1171 MET cc_start: 0.8114 (tmm) cc_final: 0.7812 (tmm) REVERT: U 1270 CYS cc_start: 0.7459 (t) cc_final: 0.6820 (m) outliers start: 29 outliers final: 8 residues processed: 162 average time/residue: 0.2466 time to fit residues: 53.4968 Evaluate side-chains 127 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 347 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.168376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127514 restraints weight = 13599.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126390 restraints weight = 11337.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.127446 restraints weight = 11331.421| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9503 Z= 0.219 Angle : 0.638 7.968 12866 Z= 0.328 Chirality : 0.043 0.146 1473 Planarity : 0.004 0.043 1632 Dihedral : 9.110 134.945 1448 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.05 % Allowed : 14.37 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.19), residues: 1185 helix: -3.57 (0.14), residues: 647 sheet: -3.37 (0.73), residues: 26 loop : -3.19 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP U 846 HIS 0.003 0.001 HIS U1142 PHE 0.015 0.001 PHE U1014 TYR 0.015 0.001 TYR U 274 ARG 0.005 0.000 ARG U 792 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 144 TYR cc_start: 0.8152 (m-10) cc_final: 0.7944 (m-80) REVERT: U 154 ILE cc_start: 0.8865 (tp) cc_final: 0.8333 (tp) REVERT: U 173 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8355 (mtmm) REVERT: U 424 ASN cc_start: 0.5237 (p0) cc_final: 0.4899 (p0) REVERT: U 478 MET cc_start: 0.6434 (ppp) cc_final: 0.5793 (mmt) REVERT: U 533 LYS cc_start: 0.7559 (tttm) cc_final: 0.7277 (pttt) REVERT: U 576 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7260 (t0) REVERT: U 578 LYS cc_start: 0.8069 (mppt) cc_final: 0.7562 (mmtt) REVERT: U 878 MET cc_start: 0.8180 (tmm) cc_final: 0.7926 (tmm) REVERT: U 913 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7971 (mt) REVERT: U 918 GLN cc_start: 0.6367 (OUTLIER) cc_final: 0.5478 (tp-100) REVERT: U 920 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.5202 (mtt90) REVERT: U 921 MET cc_start: 0.5952 (tpt) cc_final: 0.4626 (ttp) REVERT: U 928 ARG cc_start: 0.7273 (tpt170) cc_final: 0.6301 (ptp90) REVERT: U 1031 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8484 (tt) REVERT: U 1037 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: U 1145 LYS cc_start: 0.7923 (mmmm) cc_final: 0.7366 (ptmt) REVERT: U 1161 GLN cc_start: 0.6926 (tt0) cc_final: 0.6347 (tp40) REVERT: U 1171 MET cc_start: 0.8118 (tmm) cc_final: 0.7836 (tmm) REVERT: U 1270 CYS cc_start: 0.7389 (t) cc_final: 0.6883 (m) outliers start: 40 outliers final: 17 residues processed: 160 average time/residue: 0.2353 time to fit residues: 51.6351 Evaluate side-chains 136 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 347 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 960 ILE Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1279 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 98 GLN ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.168101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126589 restraints weight = 13329.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125105 restraints weight = 10548.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126127 restraints weight = 10617.708| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9503 Z= 0.245 Angle : 0.639 9.944 12866 Z= 0.325 Chirality : 0.043 0.168 1473 Planarity : 0.004 0.042 1632 Dihedral : 8.986 134.374 1448 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 5.36 % Allowed : 15.79 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.20), residues: 1185 helix: -3.22 (0.16), residues: 653 sheet: -3.05 (0.73), residues: 26 loop : -3.08 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 846 HIS 0.003 0.001 HIS U1142 PHE 0.030 0.001 PHE U 427 TYR 0.023 0.002 TYR U 538 ARG 0.004 0.000 ARG U1128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: U 154 ILE cc_start: 0.8870 (tp) cc_final: 0.8311 (tp) REVERT: U 173 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8331 (mtmm) REVERT: U 183 MET cc_start: 0.8901 (mmm) cc_final: 0.8475 (mmm) REVERT: U 373 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8817 (tp) REVERT: U 424 ASN cc_start: 0.5371 (p0) cc_final: 0.5071 (p0) REVERT: U 478 MET cc_start: 0.6472 (ppp) cc_final: 0.5866 (mmt) REVERT: U 533 LYS cc_start: 0.7541 (tttm) cc_final: 0.7248 (pttt) REVERT: U 576 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7192 (t0) REVERT: U 578 LYS cc_start: 0.8128 (mppt) cc_final: 0.7618 (mmtt) REVERT: U 610 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8104 (mp) REVERT: U 878 MET cc_start: 0.8198 (tmm) cc_final: 0.7873 (tmm) REVERT: U 913 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7972 (mt) REVERT: U 918 GLN cc_start: 0.6476 (OUTLIER) cc_final: 0.5504 (tp-100) REVERT: U 920 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.5034 (mtt90) REVERT: U 921 MET cc_start: 0.5975 (tpt) cc_final: 0.4700 (ttp) REVERT: U 928 ARG cc_start: 0.7250 (tpt170) cc_final: 0.6129 (ptp90) REVERT: U 933 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7936 (tt) REVERT: U 1031 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8490 (tt) REVERT: U 1037 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7222 (m-10) REVERT: U 1145 LYS cc_start: 0.7867 (mmmm) cc_final: 0.7368 (ptmt) REVERT: U 1161 GLN cc_start: 0.7033 (tt0) cc_final: 0.6352 (tp40) REVERT: U 1221 ARG cc_start: 0.6989 (tmm160) cc_final: 0.6705 (ppt170) REVERT: U 1270 CYS cc_start: 0.7455 (t) cc_final: 0.6910 (m) outliers start: 53 outliers final: 22 residues processed: 166 average time/residue: 0.2397 time to fit residues: 54.2129 Evaluate side-chains 146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 426 THR Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 960 ILE Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1025 VAL Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1265 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 41 optimal weight: 0.0020 chunk 83 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 64 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 515 ASN U 631 HIS U 946 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.172529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.130293 restraints weight = 13232.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129598 restraints weight = 9617.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130753 restraints weight = 7928.518| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 9503 Z= 0.160 Angle : 0.599 9.830 12866 Z= 0.299 Chirality : 0.040 0.149 1473 Planarity : 0.003 0.035 1632 Dihedral : 8.562 135.021 1446 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.76 % Allowed : 16.90 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.20), residues: 1185 helix: -2.87 (0.17), residues: 649 sheet: -2.72 (0.76), residues: 26 loop : -2.97 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP U 846 HIS 0.006 0.001 HIS U 631 PHE 0.016 0.001 PHE U 427 TYR 0.012 0.001 TYR U1005 ARG 0.003 0.000 ARG U 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 0.874 Fit side-chains REVERT: U 80 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8395 (mm) REVERT: U 154 ILE cc_start: 0.8835 (tp) cc_final: 0.8299 (tp) REVERT: U 173 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8328 (mtmm) REVERT: U 183 MET cc_start: 0.8932 (mmm) cc_final: 0.8427 (mmm) REVERT: U 373 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8802 (tp) REVERT: U 424 ASN cc_start: 0.5295 (p0) cc_final: 0.4921 (p0) REVERT: U 478 MET cc_start: 0.6461 (ppp) cc_final: 0.5833 (mmt) REVERT: U 533 LYS cc_start: 0.7560 (tttm) cc_final: 0.7205 (pttt) REVERT: U 576 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7210 (t0) REVERT: U 578 LYS cc_start: 0.8068 (mppt) cc_final: 0.7583 (mmtt) REVERT: U 610 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8027 (mp) REVERT: U 878 MET cc_start: 0.8193 (tmm) cc_final: 0.7868 (tmm) REVERT: U 913 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7948 (mt) REVERT: U 918 GLN cc_start: 0.6361 (OUTLIER) cc_final: 0.5466 (tp-100) REVERT: U 920 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.5056 (mtt90) REVERT: U 921 MET cc_start: 0.5711 (tpt) cc_final: 0.4571 (ttp) REVERT: U 933 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7544 (tt) REVERT: U 946 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8274 (p0) REVERT: U 1031 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8457 (tt) REVERT: U 1037 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7184 (m-10) REVERT: U 1145 LYS cc_start: 0.7785 (mmmm) cc_final: 0.7282 (ptmt) REVERT: U 1161 GLN cc_start: 0.7021 (tt0) cc_final: 0.6292 (tp40) REVERT: U 1270 CYS cc_start: 0.7433 (t) cc_final: 0.6881 (m) outliers start: 47 outliers final: 20 residues processed: 158 average time/residue: 0.2295 time to fit residues: 49.9645 Evaluate side-chains 143 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1025 VAL Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1174 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 515 ASN U 640 HIS U 946 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.161579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120529 restraints weight = 13220.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118484 restraints weight = 11111.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119652 restraints weight = 11890.023| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 9503 Z= 0.468 Angle : 0.754 8.490 12866 Z= 0.387 Chirality : 0.050 0.197 1473 Planarity : 0.005 0.051 1632 Dihedral : 9.176 133.892 1446 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 6.07 % Allowed : 17.91 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.20), residues: 1185 helix: -3.00 (0.17), residues: 651 sheet: -3.28 (0.68), residues: 27 loop : -2.99 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP U 493 HIS 0.003 0.001 HIS U 484 PHE 0.019 0.002 PHE U1014 TYR 0.018 0.002 TYR U 144 ARG 0.009 0.001 ARG U 566 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 122 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8568 (mm) REVERT: U 154 ILE cc_start: 0.8883 (tp) cc_final: 0.8413 (tp) REVERT: U 173 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8534 (mtmm) REVERT: U 183 MET cc_start: 0.8942 (mmm) cc_final: 0.8454 (mmm) REVERT: U 224 MET cc_start: 0.8081 (tpt) cc_final: 0.7708 (tpt) REVERT: U 299 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7888 (tmm-80) REVERT: U 373 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8856 (tp) REVERT: U 424 ASN cc_start: 0.5295 (p0) cc_final: 0.4880 (p0) REVERT: U 533 LYS cc_start: 0.7624 (tttm) cc_final: 0.7325 (pttt) REVERT: U 576 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7285 (t0) REVERT: U 610 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8274 (mp) REVERT: U 631 HIS cc_start: 0.5144 (m-70) cc_final: 0.4938 (m170) REVERT: U 839 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7887 (ttp) REVERT: U 913 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.7923 (mp) REVERT: U 918 GLN cc_start: 0.6570 (OUTLIER) cc_final: 0.5459 (tp-100) REVERT: U 920 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.4975 (mtt90) REVERT: U 921 MET cc_start: 0.6400 (tpt) cc_final: 0.4722 (ttp) REVERT: U 928 ARG cc_start: 0.7297 (tpt170) cc_final: 0.6005 (ptp90) REVERT: U 933 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7967 (tt) REVERT: U 946 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8391 (p0) REVERT: U 1031 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8560 (tt) REVERT: U 1145 LYS cc_start: 0.7803 (mmmm) cc_final: 0.7412 (ptmt) REVERT: U 1161 GLN cc_start: 0.7233 (tt0) cc_final: 0.6518 (tp40) REVERT: U 1162 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7206 (tm-30) REVERT: U 1238 LYS cc_start: 0.7572 (mmpt) cc_final: 0.7203 (mttt) REVERT: U 1270 CYS cc_start: 0.7704 (t) cc_final: 0.7042 (m) REVERT: U 1289 MET cc_start: 0.3386 (pmm) cc_final: 0.2486 (mmt) outliers start: 60 outliers final: 33 residues processed: 168 average time/residue: 0.2412 time to fit residues: 55.3998 Evaluate side-chains 159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 407 SER Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 426 THR Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 515 ASN Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 767 THR Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 863 THR Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 903 VAL Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1021 ILE Chi-restraints excluded: chain U residue 1025 VAL Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1174 ILE Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 515 ASN ** U 946 ASN ** 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 = 0.3985 r_free = 0.3985 target = 0.166604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126473 restraints weight = 13225.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124840 restraints weight = 12370.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125986 restraints weight = 11073.379| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9503 Z= 0.154 Angle : 0.602 8.280 12866 Z= 0.304 Chirality : 0.041 0.185 1473 Planarity : 0.003 0.037 1632 Dihedral : 8.551 134.680 1444 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.25 % Allowed : 20.65 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.21), residues: 1185 helix: -2.62 (0.18), residues: 640 sheet: -2.69 (0.78), residues: 26 loop : -2.85 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP U 846 HIS 0.002 0.000 HIS U1142 PHE 0.018 0.001 PHE U1014 TYR 0.033 0.001 TYR U 538 ARG 0.005 0.000 ARG U 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8436 (mm) REVERT: U 154 ILE cc_start: 0.8796 (tp) cc_final: 0.8262 (tp) REVERT: U 173 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8362 (mtmm) REVERT: U 299 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7785 (tmm-80) REVERT: U 373 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8689 (tp) REVERT: U 424 ASN cc_start: 0.5104 (p0) cc_final: 0.4659 (p0) REVERT: U 478 MET cc_start: 0.6580 (ptt) cc_final: 0.5747 (mmt) REVERT: U 533 LYS cc_start: 0.7537 (tttm) cc_final: 0.7280 (pttt) REVERT: U 576 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7347 (t0) REVERT: U 610 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8181 (mp) REVERT: U 878 MET cc_start: 0.8163 (tmm) cc_final: 0.7809 (tmm) REVERT: U 913 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7942 (mt) REVERT: U 918 GLN cc_start: 0.6218 (OUTLIER) cc_final: 0.5347 (tp-100) REVERT: U 920 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.4858 (mtt90) REVERT: U 921 MET cc_start: 0.6031 (tpt) cc_final: 0.4419 (ttp) REVERT: U 933 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7696 (tt) REVERT: U 1031 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8490 (tt) REVERT: U 1145 LYS cc_start: 0.7714 (mmmm) cc_final: 0.7349 (ptmt) REVERT: U 1161 GLN cc_start: 0.7146 (tt0) cc_final: 0.6855 (tp40) REVERT: U 1221 ARG cc_start: 0.6968 (tmm160) cc_final: 0.6557 (ppt170) REVERT: U 1226 ARG cc_start: 0.6714 (mtm180) cc_final: 0.6489 (mmm-85) REVERT: U 1270 CYS cc_start: 0.7642 (t) cc_final: 0.7028 (m) outliers start: 42 outliers final: 21 residues processed: 144 average time/residue: 0.2413 time to fit residues: 47.4090 Evaluate side-chains 138 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 846 TRP Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1021 ILE Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.6316 > 50: distance: 59 - 65: 8.378 distance: 66 - 67: 5.142 distance: 66 - 69: 10.358 distance: 67 - 68: 14.078 distance: 67 - 73: 17.451 distance: 69 - 70: 3.697 distance: 70 - 71: 9.042 distance: 70 - 72: 5.972 distance: 73 - 74: 11.559 distance: 74 - 75: 8.837 distance: 74 - 77: 3.972 distance: 75 - 76: 17.457 distance: 75 - 84: 4.283 distance: 77 - 78: 8.595 distance: 78 - 79: 12.487 distance: 79 - 80: 5.927 distance: 80 - 81: 4.470 distance: 81 - 83: 6.279 distance: 84 - 85: 5.115 distance: 85 - 86: 7.094 distance: 85 - 88: 8.454 distance: 86 - 87: 12.146 distance: 86 - 93: 12.194 distance: 88 - 89: 3.380 distance: 89 - 90: 11.013 distance: 90 - 91: 4.917 distance: 90 - 92: 5.915 distance: 93 - 94: 20.645 distance: 93 - 99: 11.480 distance: 94 - 95: 28.810 distance: 94 - 97: 16.298 distance: 95 - 96: 38.542 distance: 95 - 100: 24.097 distance: 97 - 98: 7.104 distance: 98 - 99: 18.669 distance: 100 - 101: 4.005 distance: 100 - 106: 19.552 distance: 101 - 102: 13.343 distance: 101 - 104: 18.487 distance: 102 - 103: 8.602 distance: 102 - 107: 6.823 distance: 104 - 105: 6.774 distance: 105 - 106: 19.606 distance: 107 - 108: 7.521 distance: 108 - 111: 5.043 distance: 109 - 110: 11.791 distance: 109 - 115: 6.427 distance: 111 - 112: 4.398 distance: 112 - 114: 9.407 distance: 115 - 116: 5.329 distance: 116 - 117: 5.673 distance: 116 - 119: 12.437 distance: 117 - 118: 8.640 distance: 117 - 121: 10.082 distance: 119 - 120: 16.740 distance: 121 - 122: 19.776 distance: 122 - 123: 7.102 distance: 122 - 125: 24.994 distance: 123 - 124: 8.275 distance: 123 - 128: 22.979 distance: 125 - 126: 6.736 distance: 125 - 127: 14.239 distance: 128 - 129: 8.798 distance: 129 - 130: 9.532 distance: 129 - 132: 16.779 distance: 130 - 131: 17.060 distance: 130 - 140: 7.190 distance: 132 - 133: 9.170 distance: 133 - 134: 11.715 distance: 133 - 135: 5.536 distance: 134 - 136: 3.851 distance: 135 - 137: 8.976 distance: 137 - 138: 7.643 distance: 138 - 139: 6.616 distance: 140 - 141: 7.520 distance: 141 - 144: 6.267 distance: 142 - 143: 3.917 distance: 142 - 148: 6.621 distance: 144 - 145: 8.015 distance: 145 - 146: 6.919 distance: 145 - 147: 6.622