Starting phenix.real_space_refine on Thu Sep 18 21:29:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h3j_0134/09_2025/6h3j_0134.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h3j_0134/09_2025/6h3j_0134.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 { model { file = "/net/cci-nas-00/data/ceres_data/6h3j_0134/09_2025/6h3j_0134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h3j_0134/09_2025/6h3j_0134.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6h3j_0134/09_2025/6h3j_0134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h3j_0134/09_2025/6h3j_0134.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 47 5.16 5 C 12715 2.51 5 N 3389 2.21 5 O 3938 1.98 5 H 212 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20301 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 15853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1988, 15853 Classifications: {'peptide': 1988} Link IDs: {'PTRANS': 90, 'TRANS': 1897} Chain breaks: 17 Chain: "B" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1185 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3263 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 12, 'TRANS': 384} Time building chain proxies: 4.46, per 1000 atoms: 0.22 Number of scatterers: 20301 At special positions: 0 Unit cell: (124.64, 132.84, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 O 3938 8.00 N 3389 7.00 C 12715 6.00 H 212 1.00 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: 1.58 Conformation dependent library (CDL) restraints added in 890.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4694 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 47 sheets defined 10.0% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.601A pdb=" N GLN A 202 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 4.105A pdb=" N LYS A 307 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASN A 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 308' Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.055A pdb=" N ASN A 386 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.926A pdb=" N ILE A 393 " --> pdb=" O PRO A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 414 removed outlier: 3.857A pdb=" N ALA A 410 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LYS A 411 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 413 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A 414 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 removed outlier: 4.054A pdb=" N ASN A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 623 through 634 removed outlier: 4.890A pdb=" N ILE A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 630 " --> pdb=" O GLY A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.580A pdb=" N THR A 646 " --> pdb=" O ASP A 643 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 643 through 647' Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.858A pdb=" N MET A 659 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 819 removed outlier: 3.804A pdb=" N THR A 814 " --> pdb=" O VAL A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 944 Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1081 through 1089 removed outlier: 4.414A pdb=" N ASN A1087 " --> pdb=" O ASP A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1103 Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 3.777A pdb=" N TYR A1132 " --> pdb=" O VAL A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1417 Processing helix chain 'A' and resid 1427 through 1438 removed outlier: 3.503A pdb=" N THR A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A1432 " --> pdb=" O ASP A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1613 removed outlier: 3.541A pdb=" N LEU A1611 " --> pdb=" O LYS A1607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1624 removed outlier: 3.884A pdb=" N ASN A1623 " --> pdb=" O ALA A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1861 removed outlier: 3.726A pdb=" N SER A1860 " --> pdb=" O SER A1856 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A1861 " --> pdb=" O THR A1857 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1856 through 1861' Processing helix chain 'A' and resid 1989 through 1995 Processing helix chain 'A' and resid 2072 through 2076 removed outlier: 3.604A pdb=" N ALA A2075 " --> pdb=" O ILE A2072 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE A2076 " --> pdb=" O LYS A2073 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2072 through 2076' Processing helix chain 'A' and resid 2084 through 2104 removed outlier: 3.967A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A2098 " --> pdb=" O ARG A2094 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A2104 " --> pdb=" O ARG A2100 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2135 removed outlier: 3.822A pdb=" N TYR A2133 " --> pdb=" O ASN A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2151 through 2159 Processing helix chain 'A' and resid 2185 through 2189 removed outlier: 4.139A pdb=" N MET A2188 " --> pdb=" O ASN A2185 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A2189 " --> pdb=" O GLY A2186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2185 through 2189' Processing helix chain 'B' and resid 28 through 42 Processing helix chain 'B' and resid 126 through 133 removed outlier: 3.668A pdb=" N LYS B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.715A pdb=" N ILE C 172 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN C 173 " --> pdb=" O SER C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 173' Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.684A pdb=" N LYS C 339 " --> pdb=" O PRO C 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 208 removed outlier: 3.878A pdb=" N ALA A 208 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 144 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET A 180 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 222 removed outlier: 3.764A pdb=" N LYS A 219 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 252 through 253 removed outlier: 3.842A pdb=" N THR A 253 " --> pdb=" O GLU A 763 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 344 removed outlier: 4.898A pdb=" N ARG A 342 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 430 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 471 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 342 through 344 removed outlier: 4.898A pdb=" N ARG A 342 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 430 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA9, first strand: chain 'A' and resid 544 through 545 removed outlier: 3.725A pdb=" N ASN A 544 " --> pdb=" O ARG A 679 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 771 through 772 Processing sheet with id=AB2, first strand: chain 'A' and resid 831 through 832 Processing sheet with id=AB3, first strand: chain 'A' and resid 866 through 869 removed outlier: 3.553A pdb=" N LEU A1259 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A1009 " --> pdb=" O PHE A1216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 990 through 991 removed outlier: 3.706A pdb=" N ILE A 990 " --> pdb=" O MET A1241 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A1034 " --> pdb=" O ARG A1237 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1201 through 1202 removed outlier: 3.758A pdb=" N VAL A1201 " --> pdb=" O THR A1209 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A1209 " --> pdb=" O VAL A1201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1286 through 1290 removed outlier: 3.734A pdb=" N ALA A1288 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A1329 " --> pdb=" O ALA A1288 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1363 through 1364 Processing sheet with id=AB8, first strand: chain 'A' and resid 1383 through 1386 removed outlier: 4.875A pdb=" N GLY A1386 " --> pdb=" O ASN A1485 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A1485 " --> pdb=" O GLY A1386 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1540 through 1541 Processing sheet with id=AC1, first strand: chain 'A' and resid 1559 through 1560 Processing sheet with id=AC2, first strand: chain 'A' and resid 1565 through 1569 removed outlier: 3.872A pdb=" N ASN A1638 " --> pdb=" O ASN A1587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1565 through 1569 Processing sheet with id=AC4, first strand: chain 'A' and resid 1663 through 1664 removed outlier: 3.856A pdb=" N SER A1663 " --> pdb=" O ALA A1687 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A1732 " --> pdb=" O GLN A1767 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1787 through 1789 removed outlier: 6.321A pdb=" N ASN A1787 " --> pdb=" O ASN A1817 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1822 through 1824 Processing sheet with id=AC7, first strand: chain 'A' and resid 1851 through 1852 removed outlier: 4.169A pdb=" N MET A1851 " --> pdb=" O GLN A1877 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1882 through 1883 removed outlier: 3.529A pdb=" N TYR A2037 " --> pdb=" O LYS A2013 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A2066 " --> pdb=" O SER A2036 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A2038 " --> pdb=" O MET A2064 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A2063 " --> pdb=" O PHE A2215 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE A2065 " --> pdb=" O ASN A2213 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASN A2213 " --> pdb=" O PHE A2065 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1948 through 1949 Processing sheet with id=AD1, first strand: chain 'A' and resid 2007 through 2008 removed outlier: 6.789A pdb=" N SER A2042 " --> pdb=" O PRO A2059 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A2044 " --> pdb=" O LEU A2057 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 2199 through 2200 removed outlier: 3.554A pdb=" N ARG A2199 " --> pdb=" O GLU A2258 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 2248 through 2249 Processing sheet with id=AD4, first strand: chain 'A' and resid 2293 through 2297 Processing sheet with id=AD5, first strand: chain 'A' and resid 2300 through 2301 removed outlier: 3.558A pdb=" N ASP A2320 " --> pdb=" O SER A2362 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 2332 through 2333 removed outlier: 3.827A pdb=" N GLN A2350 " --> pdb=" O ASN A2332 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 2353 through 2354 removed outlier: 3.847A pdb=" N TRP A2353 " --> pdb=" O PHE A2377 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 2370 through 2371 removed outlier: 3.636A pdb=" N THR A2396 " --> pdb=" O ILE A2370 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 47 through 48 removed outlier: 3.805A pdb=" N GLN B 47 " --> pdb=" O TYR B 55 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 55 " --> pdb=" O GLN B 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 102 through 104 removed outlier: 6.675A pdb=" N GLY B 103 " --> pdb=" O PHE B 111 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 142 through 146 Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 50 removed outlier: 3.976A pdb=" N ASN C 132 " --> pdb=" O CYS C 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS C 76 " --> pdb=" O ASN C 132 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 59 through 61 Processing sheet with id=AE5, first strand: chain 'C' and resid 159 through 164 Processing sheet with id=AE6, first strand: chain 'C' and resid 159 through 164 Processing sheet with id=AE7, first strand: chain 'C' and resid 198 through 201 removed outlier: 6.427A pdb=" N ILE C 392 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS C 409 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL C 394 " --> pdb=" O ILE C 407 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 198 through 201 Processing sheet with id=AE9, first strand: chain 'C' and resid 240 through 244 removed outlier: 4.266A pdb=" N ASN C 244 " --> pdb=" O GLY C 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 358 " --> pdb=" O ASN C 244 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AF2, first strand: chain 'C' and resid 257 through 258 removed outlier: 3.540A pdb=" N ILE C 355 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 351 " --> pdb=" O PHE C 310 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 789 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: 4.72 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 212 1.03 - 1.23: 36 1.23 - 1.42: 8923 1.42 - 1.61: 11472 1.61 - 1.81: 90 Bond restraints: 20733 Sorted by residual: bond pdb=" CG1 ILE A1876 " pdb=" CD1 ILE A1876 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.72e+00 bond pdb=" CB PHE A1242 " pdb=" CG PHE A1242 " ideal model delta sigma weight residual 1.502 1.458 0.044 2.30e-02 1.89e+03 3.66e+00 bond pdb=" CB TYR A1048 " pdb=" CG TYR A1048 " ideal model delta sigma weight residual 1.512 1.471 0.041 2.20e-02 2.07e+03 3.39e+00 bond pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 1.512 1.474 0.038 2.20e-02 2.07e+03 2.98e+00 bond pdb=" C SER A1097 " pdb=" N SER A1098 " ideal model delta sigma weight residual 1.333 1.309 0.025 1.49e-02 4.50e+03 2.73e+00 ... (remaining 20728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 26612 1.70 - 3.40: 1348 3.40 - 5.10: 207 5.10 - 6.79: 50 6.79 - 8.49: 10 Bond angle restraints: 28227 Sorted by residual: angle pdb=" N ILE C 415 " pdb=" CA ILE C 415 " pdb=" C ILE C 415 " ideal model delta sigma weight residual 112.29 106.80 5.49 9.40e-01 1.13e+00 3.41e+01 angle pdb=" N ILE A 216 " pdb=" CA ILE A 216 " pdb=" C ILE A 216 " ideal model delta sigma weight residual 113.71 108.23 5.48 9.50e-01 1.11e+00 3.32e+01 angle pdb=" N SER A2250 " pdb=" CA SER A2250 " pdb=" C SER A2250 " ideal model delta sigma weight residual 109.41 101.33 8.08 1.53e+00 4.27e-01 2.79e+01 angle pdb=" N ASN A 650 " pdb=" CA ASN A 650 " pdb=" C ASN A 650 " ideal model delta sigma weight residual 112.68 106.77 5.91 1.33e+00 5.65e-01 1.98e+01 angle pdb=" N THR A2160 " pdb=" CA THR A2160 " pdb=" C THR A2160 " ideal model delta sigma weight residual 114.64 107.93 6.71 1.52e+00 4.33e-01 1.95e+01 ... (remaining 28222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 11593 14.94 - 29.88: 615 29.88 - 44.82: 141 44.82 - 59.76: 20 59.76 - 74.70: 9 Dihedral angle restraints: 12378 sinusoidal: 5039 harmonic: 7339 Sorted by residual: dihedral pdb=" CA SER A 563 " pdb=" C SER A 563 " pdb=" N PHE A 564 " pdb=" CA PHE A 564 " ideal model delta harmonic sigma weight residual -180.00 -140.01 -39.99 0 5.00e+00 4.00e-02 6.40e+01 dihedral pdb=" CA GLY A 394 " pdb=" C GLY A 394 " pdb=" N GLN A 395 " pdb=" CA GLN A 395 " ideal model delta harmonic sigma weight residual -180.00 -143.28 -36.72 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA SER A2250 " pdb=" C SER A2250 " pdb=" N PRO A2251 " pdb=" CA PRO A2251 " ideal model delta harmonic sigma weight residual -180.00 -144.64 -35.36 0 5.00e+00 4.00e-02 5.00e+01 ... (remaining 12375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2048 0.044 - 0.088: 681 0.088 - 0.133: 258 0.133 - 0.177: 34 0.177 - 0.221: 5 Chirality restraints: 3026 Sorted by residual: chirality pdb=" CA PHE C 119 " pdb=" N PHE C 119 " pdb=" C PHE C 119 " pdb=" CB PHE C 119 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ASN A 998 " pdb=" N ASN A 998 " pdb=" C ASN A 998 " pdb=" CB ASN A 998 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO A2178 " pdb=" N PRO A2178 " pdb=" C PRO A2178 " pdb=" CB PRO A2178 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 3023 not shown) Planarity restraints: 3795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 564 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO A 565 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2250 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO A2251 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A2251 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A2251 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1996 " 0.020 2.00e-02 2.50e+03 1.69e-02 7.12e+00 pdb=" CG TRP A1996 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A1996 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A1996 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1996 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1996 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1996 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1996 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1996 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1996 " 0.002 2.00e-02 2.50e+03 ... (remaining 3792 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 103 2.30 - 2.87: 8671 2.87 - 3.45: 24767 3.45 - 4.02: 37434 4.02 - 4.60: 56237 Nonbonded interactions: 127212 Sorted by model distance: nonbonded pdb=" O THR B 98 " pdb=" H VAL B 173 " model vdw 1.719 2.450 nonbonded pdb=" O TYR B 54 " pdb=" H PHE B 145 " model vdw 1.733 2.450 nonbonded pdb=" O LEU B 93 " pdb="HH11 ARG B 123 " model vdw 1.791 2.450 nonbonded pdb=" O TYR B 27 " pdb="HD21 ASN B 31 " model vdw 1.796 2.450 nonbonded pdb=" HG SER B 51 " pdb=" OE1 GLU B 131 " model vdw 1.842 2.450 ... (remaining 127207 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.770 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: 0.200 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.780 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.007 0.075 20521 Z= 0.320 Angle : 0.874 8.492 27849 Z= 0.495 Chirality : 0.051 0.221 3026 Planarity : 0.005 0.078 3678 Dihedral : 10.174 74.698 7511 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 43.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 23.77 % Favored : 76.18 % Rotamer: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.63 (0.13), residues: 2469 helix: -3.98 (0.22), residues: 205 sheet: -4.89 (0.12), residues: 830 loop : -4.29 (0.13), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 402 TYR 0.030 0.002 TYR A 528 PHE 0.039 0.003 PHE C 119 TRP 0.046 0.003 TRP A1996 HIS 0.005 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00696 (20521) covalent geometry : angle 0.87363 (27849) hydrogen bonds : bond 0.28205 ( 304) hydrogen bonds : angle 12.13866 ( 789) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ASN cc_start: 0.8618 (p0) cc_final: 0.8405 (m-40) REVERT: C 158 THR cc_start: 0.8846 (m) cc_final: 0.8504 (p) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.1807 time to fit residues: 69.0783 Evaluate side-chains 112 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.0470 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 203 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 GLN A1018 ASN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 ASN A1087 ASN A1136 ASN ** A1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1210 ASN ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1562 GLN ** A1587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1604 GLN ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1623 ASN A1667 ASN A1668 GLN A1740 ASN A1767 GLN A1787 ASN A1805 ASN A1819 HIS A1821 GLN A1826 ASN A1874 ASN ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1889 ASN ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2052 ASN ** A2083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2213 ASN A2214 GLN ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2375 HIS A2400 ASN B 31 ASN C 41 ASN C 44 ASN C 104 ASN C 110 GLN C 126 GLN C 232 GLN C 261 ASN C 271 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.057055 restraints weight = 64582.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.058640 restraints weight = 35009.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.059721 restraints weight = 23130.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060461 restraints weight = 17227.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.060811 restraints weight = 13968.404| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20521 Z= 0.188 Angle : 0.605 6.144 27849 Z= 0.328 Chirality : 0.044 0.164 3026 Planarity : 0.004 0.072 3678 Dihedral : 6.104 37.502 2753 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 52.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.47 % Favored : 78.53 % Rotamer: Outliers : 1.40 % Allowed : 8.33 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.21 (0.14), residues: 2469 helix: -3.15 (0.27), residues: 230 sheet: -4.62 (0.13), residues: 828 loop : -4.07 (0.14), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2392 TYR 0.014 0.001 TYR A1120 PHE 0.021 0.001 PHE A 564 TRP 0.018 0.002 TRP A1996 HIS 0.004 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00401 (20521) covalent geometry : angle 0.60463 (27849) hydrogen bonds : bond 0.03525 ( 304) hydrogen bonds : angle 7.68459 ( 789) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 471 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8712 (mtpp) REVERT: A 762 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9017 (pt) REVERT: A 1508 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8772 (tt) REVERT: C 158 THR cc_start: 0.9098 (m) cc_final: 0.8770 (p) outliers start: 31 outliers final: 15 residues processed: 149 average time/residue: 0.1496 time to fit residues: 36.0397 Evaluate side-chains 132 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 471 LYS Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1394 TYR Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2334 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 354 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 87 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 236 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN A 584 ASN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1443 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 GLN A1672 HIS A1740 ASN ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2332 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.063122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.053072 restraints weight = 66458.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.054601 restraints weight = 36354.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.055656 restraints weight = 24150.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.056372 restraints weight = 18155.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.056851 restraints weight = 14858.445| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 20521 Z= 0.397 Angle : 0.791 8.064 27849 Z= 0.421 Chirality : 0.048 0.241 3026 Planarity : 0.005 0.073 3678 Dihedral : 6.620 37.221 2753 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 55.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.10 % Favored : 72.90 % Rotamer: Outliers : 2.34 % Allowed : 9.95 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.20 (0.14), residues: 2469 helix: -3.01 (0.29), residues: 223 sheet: -4.65 (0.13), residues: 852 loop : -4.03 (0.14), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1234 TYR 0.025 0.002 TYR C 390 PHE 0.031 0.002 PHE A 564 TRP 0.026 0.002 TRP A1996 HIS 0.005 0.002 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00875 (20521) covalent geometry : angle 0.79118 (27849) hydrogen bonds : bond 0.03800 ( 304) hydrogen bonds : angle 7.33280 ( 789) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 106 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9239 (pp) REVERT: A 350 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8692 (tm) REVERT: A 762 ILE cc_start: 0.9544 (OUTLIER) cc_final: 0.9120 (pt) REVERT: A 1394 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8333 (m-10) REVERT: A 1508 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8779 (tt) REVERT: A 2187 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8202 (tt) REVERT: C 158 THR cc_start: 0.9115 (m) cc_final: 0.8759 (p) outliers start: 52 outliers final: 29 residues processed: 149 average time/residue: 0.1411 time to fit residues: 34.8468 Evaluate side-chains 132 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1394 TYR Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2253 ILE Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 108 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 chunk 230 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN ** A1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2282 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.066917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.056895 restraints weight = 64338.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058531 restraints weight = 34585.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.059654 restraints weight = 22688.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.060401 restraints weight = 16810.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.060897 restraints weight = 13624.731| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20521 Z= 0.117 Angle : 0.531 5.521 27849 Z= 0.287 Chirality : 0.043 0.152 3026 Planarity : 0.003 0.058 3678 Dihedral : 5.611 31.636 2753 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 51.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.23 % Favored : 81.77 % Rotamer: Outliers : 1.71 % Allowed : 11.26 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.62 (0.15), residues: 2469 helix: -2.56 (0.31), residues: 216 sheet: -4.23 (0.15), residues: 801 loop : -3.73 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2091 TYR 0.011 0.001 TYR A2373 PHE 0.020 0.001 PHE C 119 TRP 0.013 0.001 TRP A1264 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00248 (20521) covalent geometry : angle 0.53119 (27849) hydrogen bonds : bond 0.02491 ( 304) hydrogen bonds : angle 6.59634 ( 789) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 341 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9212 (pp) REVERT: A 900 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7317 (pp20) REVERT: A 1394 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7947 (m-10) REVERT: A 1508 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8698 (tt) REVERT: C 158 THR cc_start: 0.9091 (m) cc_final: 0.8713 (p) outliers start: 38 outliers final: 17 residues processed: 147 average time/residue: 0.1410 time to fit residues: 34.2312 Evaluate side-chains 127 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1394 TYR Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 252 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 132 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 229 optimal weight: 0.0020 chunk 181 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 chunk 67 optimal weight: 0.2980 chunk 238 optimal weight: 3.9990 overall best weight: 1.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2332 ASN C 299 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.067237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.057177 restraints weight = 64314.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.058824 restraints weight = 34520.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.059954 restraints weight = 22604.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.060687 restraints weight = 16787.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.061206 restraints weight = 13635.314| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20521 Z= 0.118 Angle : 0.510 7.611 27849 Z= 0.273 Chirality : 0.042 0.151 3026 Planarity : 0.003 0.050 3678 Dihedral : 5.181 30.471 2753 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 49.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.60 % Favored : 80.40 % Rotamer: Outliers : 1.80 % Allowed : 11.80 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.35 (0.15), residues: 2469 helix: -2.35 (0.32), residues: 217 sheet: -4.07 (0.15), residues: 822 loop : -3.49 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2100 TYR 0.013 0.001 TYR A 447 PHE 0.017 0.001 PHE A 564 TRP 0.009 0.001 TRP A1264 HIS 0.003 0.000 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00254 (20521) covalent geometry : angle 0.50982 (27849) hydrogen bonds : bond 0.02302 ( 304) hydrogen bonds : angle 6.20052 ( 789) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8588 (tm) REVERT: A 762 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9046 (pt) REVERT: A 1394 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: B 27 TYR cc_start: 0.8190 (m-10) cc_final: 0.7960 (m-10) REVERT: B 131 GLU cc_start: 0.8172 (tp30) cc_final: 0.7966 (tp30) REVERT: C 158 THR cc_start: 0.9089 (m) cc_final: 0.8662 (p) outliers start: 40 outliers final: 27 residues processed: 147 average time/residue: 0.1397 time to fit residues: 33.8861 Evaluate side-chains 133 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1394 TYR Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 227 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 chunk 220 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 240 optimal weight: 0.2980 chunk 89 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.054999 restraints weight = 64953.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.056568 restraints weight = 35373.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.057668 restraints weight = 23402.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.058403 restraints weight = 17457.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058894 restraints weight = 14212.333| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 20521 Z= 0.227 Angle : 0.594 6.158 27849 Z= 0.316 Chirality : 0.044 0.169 3026 Planarity : 0.004 0.057 3678 Dihedral : 5.495 31.426 2753 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 51.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.41 % Favored : 76.59 % Rotamer: Outliers : 2.48 % Allowed : 12.43 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.35 (0.15), residues: 2469 helix: -2.22 (0.33), residues: 211 sheet: -4.07 (0.15), residues: 830 loop : -3.52 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2100 TYR 0.013 0.001 TYR C 390 PHE 0.022 0.002 PHE A 564 TRP 0.013 0.001 TRP A1996 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00498 (20521) covalent geometry : angle 0.59365 (27849) hydrogen bonds : bond 0.02576 ( 304) hydrogen bonds : angle 6.25382 ( 789) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 104 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7960 (ptt180) REVERT: A 350 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8606 (tm) REVERT: A 762 ILE cc_start: 0.9508 (OUTLIER) cc_final: 0.9068 (pt) REVERT: A 1394 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8368 (m-10) REVERT: A 1508 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8720 (tt) REVERT: B 131 GLU cc_start: 0.8218 (tp30) cc_final: 0.8005 (tp30) REVERT: C 158 THR cc_start: 0.9096 (m) cc_final: 0.8703 (p) outliers start: 55 outliers final: 40 residues processed: 148 average time/residue: 0.1439 time to fit residues: 35.1150 Evaluate side-chains 146 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 101 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 892 PHE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1366 GLU Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1394 TYR Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1496 HIS Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain A residue 2223 SER Chi-restraints excluded: chain A residue 2253 ILE Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 246 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN A1767 GLN ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.054586 restraints weight = 65237.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.056154 restraints weight = 35625.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.057243 restraints weight = 23608.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.057919 restraints weight = 17703.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.058452 restraints weight = 14571.589| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 20521 Z= 0.240 Angle : 0.600 6.235 27849 Z= 0.321 Chirality : 0.044 0.178 3026 Planarity : 0.004 0.053 3678 Dihedral : 5.586 31.466 2753 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 51.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.57 % Favored : 76.43 % Rotamer: Outliers : 3.47 % Allowed : 12.52 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.33 (0.15), residues: 2469 helix: -2.26 (0.32), residues: 217 sheet: -4.02 (0.15), residues: 840 loop : -3.50 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2100 TYR 0.013 0.001 TYR C 390 PHE 0.022 0.002 PHE A 564 TRP 0.012 0.001 TRP A1996 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00527 (20521) covalent geometry : angle 0.60016 (27849) hydrogen bonds : bond 0.02562 ( 304) hydrogen bonds : angle 6.26591 ( 789) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 101 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7908 (ptt180) REVERT: A 350 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8598 (tm) REVERT: A 523 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7884 (tpt) REVERT: A 762 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9091 (pt) REVERT: A 1394 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.8333 (m-10) REVERT: A 1508 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8704 (tt) REVERT: B 131 GLU cc_start: 0.8297 (tp30) cc_final: 0.8092 (tp30) REVERT: C 158 THR cc_start: 0.9103 (m) cc_final: 0.8708 (p) outliers start: 77 outliers final: 50 residues processed: 161 average time/residue: 0.1450 time to fit residues: 38.0150 Evaluate side-chains 155 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 99 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 892 PHE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1266 ARG Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1366 GLU Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1394 TYR Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1483 VAL Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain A residue 2223 SER Chi-restraints excluded: chain A residue 2253 ILE Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 168 optimal weight: 0.0050 chunk 105 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2375 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.064765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.054705 restraints weight = 65433.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.056278 restraints weight = 35389.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.057371 restraints weight = 23399.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058090 restraints weight = 17497.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.058590 restraints weight = 14283.880| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 20521 Z= 0.222 Angle : 0.587 6.151 27849 Z= 0.313 Chirality : 0.044 0.170 3026 Planarity : 0.004 0.061 3678 Dihedral : 5.549 31.311 2753 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 51.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.73 % Favored : 76.27 % Rotamer: Outliers : 3.33 % Allowed : 12.70 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.28 (0.15), residues: 2469 helix: -2.15 (0.32), residues: 217 sheet: -3.99 (0.15), residues: 833 loop : -3.49 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2100 TYR 0.012 0.001 TYR C 390 PHE 0.021 0.001 PHE A 564 TRP 0.010 0.001 TRP A1996 HIS 0.002 0.001 HIS A2375 Details of bonding type rmsd covalent geometry : bond 0.00487 (20521) covalent geometry : angle 0.58695 (27849) hydrogen bonds : bond 0.02481 ( 304) hydrogen bonds : angle 6.22136 ( 789) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 104 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7891 (ptt180) REVERT: A 350 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8638 (tm) REVERT: A 523 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.7887 (tpt) REVERT: A 762 ILE cc_start: 0.9527 (OUTLIER) cc_final: 0.9115 (pt) REVERT: A 1035 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: A 1171 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8077 (mp) REVERT: A 1394 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8350 (m-10) REVERT: A 1508 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8831 (tt) REVERT: C 158 THR cc_start: 0.9094 (m) cc_final: 0.8700 (p) REVERT: C 227 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.7474 (p90) outliers start: 74 outliers final: 54 residues processed: 163 average time/residue: 0.1482 time to fit residues: 39.1456 Evaluate side-chains 165 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 102 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1035 GLU Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1175 TYR Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1266 ARG Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1366 GLU Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1394 TYR Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1483 VAL Chi-restraints excluded: chain A residue 1496 HIS Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain A residue 2375 HIS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 48 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 174 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 230 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 0.2980 chunk 83 optimal weight: 7.9990 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2375 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.066434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.056309 restraints weight = 63937.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.057945 restraints weight = 34431.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.059055 restraints weight = 22629.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.059782 restraints weight = 16896.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.060192 restraints weight = 13754.311| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20521 Z= 0.125 Angle : 0.518 5.670 27849 Z= 0.277 Chirality : 0.042 0.146 3026 Planarity : 0.003 0.054 3678 Dihedral : 5.184 29.398 2753 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 50.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.56 % Favored : 80.44 % Rotamer: Outliers : 2.43 % Allowed : 13.87 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.05 (0.16), residues: 2469 helix: -1.91 (0.34), residues: 217 sheet: -3.84 (0.16), residues: 818 loop : -3.37 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2100 TYR 0.018 0.001 TYR A2373 PHE 0.016 0.001 PHE C 119 TRP 0.010 0.001 TRP A1264 HIS 0.004 0.001 HIS A2375 Details of bonding type rmsd covalent geometry : bond 0.00271 (20521) covalent geometry : angle 0.51780 (27849) hydrogen bonds : bond 0.02216 ( 304) hydrogen bonds : angle 5.94769 ( 789) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 112 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7779 (ptt180) REVERT: A 523 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.7909 (tpt) REVERT: A 762 ILE cc_start: 0.9518 (OUTLIER) cc_final: 0.9091 (pt) REVERT: A 1171 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8025 (mp) REVERT: A 1394 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.8241 (m-10) REVERT: A 1508 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8633 (tt) REVERT: B 27 TYR cc_start: 0.8236 (m-10) cc_final: 0.7911 (m-10) REVERT: C 158 THR cc_start: 0.9075 (m) cc_final: 0.8622 (p) outliers start: 54 outliers final: 41 residues processed: 154 average time/residue: 0.1463 time to fit residues: 36.7053 Evaluate side-chains 151 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1266 ARG Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1366 GLU Chi-restraints excluded: chain A residue 1394 TYR Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain A residue 2253 ILE Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain A residue 2375 HIS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 242 optimal weight: 0.0670 chunk 96 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 chunk 193 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 132 optimal weight: 0.0060 overall best weight: 3.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2375 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.065151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.055084 restraints weight = 65220.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.056661 restraints weight = 35359.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.057748 restraints weight = 23366.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058467 restraints weight = 17447.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.058941 restraints weight = 14256.851| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20521 Z= 0.202 Angle : 0.567 5.806 27849 Z= 0.302 Chirality : 0.043 0.156 3026 Planarity : 0.004 0.059 3678 Dihedral : 5.296 30.158 2753 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 50.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.80 % Favored : 77.20 % Rotamer: Outliers : 2.48 % Allowed : 14.05 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.07 (0.16), residues: 2469 helix: -1.82 (0.34), residues: 211 sheet: -3.86 (0.16), residues: 832 loop : -3.37 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2100 TYR 0.013 0.001 TYR A2210 PHE 0.020 0.001 PHE A 564 TRP 0.009 0.001 TRP A1996 HIS 0.002 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00445 (20521) covalent geometry : angle 0.56657 (27849) hydrogen bonds : bond 0.02367 ( 304) hydrogen bonds : angle 5.99132 ( 789) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 106 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7897 (ptt180) REVERT: A 523 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.7872 (tpt) REVERT: A 762 ILE cc_start: 0.9528 (OUTLIER) cc_final: 0.9121 (pt) REVERT: A 1035 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: A 1171 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8104 (mp) REVERT: A 1394 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8291 (m-10) REVERT: A 1508 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8668 (tt) REVERT: B 27 TYR cc_start: 0.8229 (m-10) cc_final: 0.7900 (m-10) REVERT: C 158 THR cc_start: 0.9091 (m) cc_final: 0.8690 (p) outliers start: 55 outliers final: 43 residues processed: 151 average time/residue: 0.1468 time to fit residues: 36.0223 Evaluate side-chains 155 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 105 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1035 GLU Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1266 ARG Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1366 GLU Chi-restraints excluded: chain A residue 1394 TYR Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1772 PHE Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain A residue 2375 HIS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 77 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 229 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2375 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.065671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.055657 restraints weight = 64776.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.057217 restraints weight = 35643.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.058280 restraints weight = 23773.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.058993 restraints weight = 17919.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.059412 restraints weight = 14643.629| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20521 Z= 0.168 Angle : 0.541 5.555 27849 Z= 0.289 Chirality : 0.043 0.148 3026 Planarity : 0.003 0.057 3678 Dihedral : 5.233 29.431 2753 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 50.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.14 % Favored : 78.86 % Rotamer: Outliers : 2.48 % Allowed : 14.14 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.00 (0.16), residues: 2469 helix: -1.77 (0.35), residues: 211 sheet: -3.79 (0.16), residues: 829 loop : -3.33 (0.15), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2264 TYR 0.011 0.001 TYR A2373 PHE 0.018 0.001 PHE A 564 TRP 0.009 0.001 TRP A1264 HIS 0.008 0.001 HIS A2375 Details of bonding type rmsd covalent geometry : bond 0.00368 (20521) covalent geometry : angle 0.54137 (27849) hydrogen bonds : bond 0.02295 ( 304) hydrogen bonds : angle 5.92517 ( 789) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3002.29 seconds wall clock time: 53 minutes 40.22 seconds (3220.22 seconds total)