Starting phenix.real_space_refine on Sun May 3 14:13:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wd7_65885/05_2026/9wd7_65885_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wd7_65885/05_2026/9wd7_65885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wd7_65885/05_2026/9wd7_65885_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wd7_65885/05_2026/9wd7_65885_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wd7_65885/05_2026/9wd7_65885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wd7_65885/05_2026/9wd7_65885.map" } resolution = 2.34 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= 0.001 sd= 0.039 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 4270 2.51 5 N 1158 2.21 5 O 1311 1.98 5 H 6514 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13309 Number of models: 1 Model: "" Number of chains: 4 Chain: "a" Number of atoms: 6651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 6651 Classifications: {'peptide': 431} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain breaks: 1 Chain: "b" Number of atoms: 6592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6592 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "a" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.77, per 1000 atoms: 0.21 Number of scatterers: 13309 At special positions: 0 Unit cell: (74.5446, 74.5446, 113.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 48 16.00 P 6 15.00 Mg 2 11.99 O 1311 8.00 N 1158 7.00 C 4270 6.00 H 6514 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: 1.15 Conformation dependent library (CDL) restraints added in 466.7 milliseconds 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 53.6% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'a' and resid 10 through 28 removed outlier: 3.687A pdb=" N ALA a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) Processing helix chain 'a' and resid 71 through 81 removed outlier: 4.697A pdb=" N ILE a 75 " --> pdb=" O GLU a 71 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU a 77 " --> pdb=" O THR a 73 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL a 78 " --> pdb=" O VAL a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 90 No H-bonds generated for 'chain 'a' and resid 88 through 90' Processing helix chain 'a' and resid 102 through 108 Processing helix chain 'a' and resid 110 through 113 Processing helix chain 'a' and resid 114 through 127 Processing helix chain 'a' and resid 147 through 161 removed outlier: 3.852A pdb=" N VAL a 159 " --> pdb=" O GLU a 155 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP a 160 " --> pdb=" O ARG a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 182 through 190 Processing helix chain 'a' and resid 190 through 197 removed outlier: 3.500A pdb=" N THR a 194 " --> pdb=" O THR a 190 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 216 Processing helix chain 'a' and resid 223 through 239 removed outlier: 3.611A pdb=" N LEU a 230 " --> pdb=" O ASN a 226 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR a 239 " --> pdb=" O VAL a 235 " (cutoff:3.500A) Processing helix chain 'a' and resid 239 through 244 removed outlier: 3.765A pdb=" N ARG a 243 " --> pdb=" O THR a 239 " (cutoff:3.500A) Processing helix chain 'a' and resid 251 through 258 removed outlier: 3.722A pdb=" N ASN a 258 " --> pdb=" O GLU a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 279 through 284 removed outlier: 3.922A pdb=" N TYR a 282 " --> pdb=" O GLU a 279 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU a 284 " --> pdb=" O ALA a 281 " (cutoff:3.500A) Processing helix chain 'a' and resid 287 through 295 removed outlier: 3.582A pdb=" N CYS a 295 " --> pdb=" O ILE a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 296 through 301 removed outlier: 6.110A pdb=" N ALA a 299 " --> pdb=" O PHE a 296 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN a 301 " --> pdb=" O PRO a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 306 through 310 Processing helix chain 'a' and resid 324 through 336 Processing helix chain 'a' and resid 384 through 401 removed outlier: 3.686A pdb=" N TRP a 388 " --> pdb=" O ILE a 384 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS a 401 " --> pdb=" O LEU a 397 " (cutoff:3.500A) Processing helix chain 'a' and resid 404 through 410 removed outlier: 4.107A pdb=" N TYR a 408 " --> pdb=" O PHE a 404 " (cutoff:3.500A) Processing helix chain 'a' and resid 415 through 435 removed outlier: 4.210A pdb=" N SER a 419 " --> pdb=" O GLU a 415 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 29 removed outlier: 3.524A pdb=" N ASP b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS b 28 " --> pdb=" O ILE b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 41 through 46 removed outlier: 3.749A pdb=" N GLU b 45 " --> pdb=" O ASP b 41 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG b 46 " --> pdb=" O LEU b 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 41 through 46' Processing helix chain 'b' and resid 47 through 49 No H-bonds generated for 'chain 'b' and resid 47 through 49' Processing helix chain 'b' and resid 70 through 78 removed outlier: 3.535A pdb=" N SER b 75 " --> pdb=" O GLY b 71 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER b 78 " --> pdb=" O ASP b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 85 removed outlier: 3.700A pdb=" N LEU b 84 " --> pdb=" O PHE b 81 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE b 85 " --> pdb=" O GLY b 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 81 through 85' Processing helix chain 'b' and resid 86 through 88 No H-bonds generated for 'chain 'b' and resid 86 through 88' Processing helix chain 'b' and resid 100 through 106 Processing helix chain 'b' and resid 107 through 126 removed outlier: 3.891A pdb=" N GLU b 111 " --> pdb=" O THR b 107 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU b 112 " --> pdb=" O GLU b 108 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP b 114 " --> pdb=" O ALA b 110 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER b 115 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL b 116 " --> pdb=" O LEU b 112 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN b 126 " --> pdb=" O LYS b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 159 removed outlier: 3.531A pdb=" N LEU b 150 " --> pdb=" O GLY b 146 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 196 removed outlier: 3.528A pdb=" N ILE b 189 " --> pdb=" O ALA b 185 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS b 190 " --> pdb=" O THR b 186 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLN b 191 " --> pdb=" O LEU b 187 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR b 196 " --> pdb=" O LEU b 192 " (cutoff:3.500A) Processing helix chain 'b' and resid 204 through 214 Processing helix chain 'b' and resid 221 through 237 removed outlier: 3.825A pdb=" N THR b 237 " --> pdb=" O MET b 233 " (cutoff:3.500A) Processing helix chain 'b' and resid 238 through 241 Processing helix chain 'b' and resid 249 through 258 Processing helix chain 'b' and resid 276 through 282 removed outlier: 3.644A pdb=" N GLN b 279 " --> pdb=" O ARG b 276 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN b 280 " --> pdb=" O GLY b 277 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG b 282 " --> pdb=" O GLN b 279 " (cutoff:3.500A) Processing helix chain 'b' and resid 285 through 294 Processing helix chain 'b' and resid 295 through 299 removed outlier: 3.785A pdb=" N MET b 299 " --> pdb=" O ALA b 296 " (cutoff:3.500A) Processing helix chain 'b' and resid 304 through 308 Processing helix chain 'b' and resid 322 through 337 removed outlier: 3.890A pdb=" N GLN b 334 " --> pdb=" O MET b 330 " (cutoff:3.500A) Processing helix chain 'b' and resid 338 through 341 removed outlier: 3.586A pdb=" N PHE b 341 " --> pdb=" O SER b 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 338 through 341' Processing helix chain 'b' and resid 374 through 392 removed outlier: 3.868A pdb=" N PHE b 378 " --> pdb=" O ILE b 374 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG b 391 " --> pdb=" O ALA b 387 " (cutoff:3.500A) Processing helix chain 'b' and resid 394 through 400 removed outlier: 4.255A pdb=" N TYR b 398 " --> pdb=" O PHE b 394 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 425 removed outlier: 3.882A pdb=" N THR b 409 " --> pdb=" O GLU b 405 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR b 425 " --> pdb=" O GLU b 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 92 through 94 removed outlier: 8.256A pdb=" N ILE a 93 " --> pdb=" O ALA a 65 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE a 67 " --> pdb=" O ILE a 93 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N VAL a 66 " --> pdb=" O CYS a 4 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER a 6 " --> pdb=" O VAL a 66 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL a 68 " --> pdb=" O SER a 6 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS a 8 " --> pdb=" O VAL a 68 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU a 3 " --> pdb=" O LEU a 132 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY a 134 " --> pdb=" O GLU a 3 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N SER a 140 " --> pdb=" O VAL a 9 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLN a 133 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU a 167 " --> pdb=" O GLN a 133 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE a 135 " --> pdb=" O LEU a 167 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE a 169 " --> pdb=" O PHE a 135 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL a 137 " --> pdb=" O PHE a 169 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE a 171 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N HIS a 139 " --> pdb=" O ILE a 171 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS a 166 " --> pdb=" O CYS a 200 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE a 202 " --> pdb=" O LYS a 166 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU a 168 " --> pdb=" O PHE a 202 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL a 204 " --> pdb=" O GLU a 168 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER a 170 " --> pdb=" O VAL a 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'a' and resid 269 through 273 removed outlier: 3.769A pdb=" N ALA a 314 " --> pdb=" O ASN a 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 90 through 92 removed outlier: 8.284A pdb=" N ILE b 91 " --> pdb=" O ALA b 63 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU b 65 " --> pdb=" O ILE b 91 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ILE b 64 " --> pdb=" O ILE b 4 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N HIS b 6 " --> pdb=" O ILE b 64 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL b 66 " --> pdb=" O HIS b 6 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN b 8 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLU b 3 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE b 133 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL b 5 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU b 135 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE b 7 " --> pdb=" O LEU b 135 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N HIS b 137 " --> pdb=" O ILE b 7 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ALA b 9 " --> pdb=" O HIS b 137 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN b 131 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ASN b 165 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE b 133 " --> pdb=" O ASN b 165 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N PHE b 167 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU b 135 " --> pdb=" O PHE b 167 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL b 169 " --> pdb=" O LEU b 135 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS b 137 " --> pdb=" O VAL b 169 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET b 164 " --> pdb=" O GLU b 198 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N TYR b 200 " --> pdb=" O MET b 164 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR b 166 " --> pdb=" O TYR b 200 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE b 202 " --> pdb=" O THR b 166 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER b 168 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR b 199 " --> pdb=" O PHE b 266 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N CYS b 201 " --> pdb=" O PRO b 268 " (cutoff:3.500A) removed outlier: 10.810A pdb=" N PHE b 270 " --> pdb=" O CYS b 201 " (cutoff:3.500A) removed outlier: 14.080A pdb=" N ASP b 203 " --> pdb=" O PHE b 270 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE b 265 " --> pdb=" O SER b 371 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER b 371 " --> pdb=" O PHE b 265 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER b 364 " --> pdb=" O PHE b 317 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE b 317 " --> pdb=" O SER b 364 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR b 366 " --> pdb=" O THR b 315 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR b 315 " --> pdb=" O THR b 366 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE b 368 " --> pdb=" O VAL b 313 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL b 313 " --> pdb=" O ILE b 368 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN b 370 " --> pdb=" O LEU b 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 51 through 53 283 hydrogen bonds defined for protein. 813 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: 3.36 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 6494 1.06 - 1.29: 1166 1.29 - 1.51: 3403 1.51 - 1.74: 2321 1.74 - 1.96: 79 Bond restraints: 13463 Sorted by residual: bond pdb=" O5' G2P b 501 " pdb=" PA G2P b 501 " ideal model delta sigma weight residual 1.656 1.861 -0.205 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C3A G2P b 501 " pdb=" PA G2P b 501 " ideal model delta sigma weight residual 1.818 1.686 0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" C3A G2P b 501 " pdb=" PB G2P b 501 " ideal model delta sigma weight residual 1.850 1.963 -0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" O3B G2P b 501 " pdb=" PG G2P b 501 " ideal model delta sigma weight residual 1.716 1.822 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C5' G2P b 501 " pdb=" O5' G2P b 501 " ideal model delta sigma weight residual 1.399 1.316 0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 13458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.38: 24194 5.38 - 10.75: 21 10.75 - 16.13: 4 16.13 - 21.50: 3 21.50 - 26.88: 3 Bond angle restraints: 24225 Sorted by residual: angle pdb=" CG2 THR b 178 " pdb=" CB THR b 178 " pdb=" HB THR b 178 " ideal model delta sigma weight residual 108.00 81.12 26.88 3.00e+00 1.11e-01 8.03e+01 angle pdb=" OG1 THR b 178 " pdb=" CB THR b 178 " pdb=" HB THR b 178 " ideal model delta sigma weight residual 109.00 82.98 26.02 3.00e+00 1.11e-01 7.52e+01 angle pdb=" CA THR b 178 " pdb=" CB THR b 178 " pdb=" HB THR b 178 " ideal model delta sigma weight residual 109.00 83.50 25.50 3.00e+00 1.11e-01 7.22e+01 angle pdb=" O1A G2P b 501 " pdb=" PA G2P b 501 " pdb=" O5' G2P b 501 " ideal model delta sigma weight residual 109.23 88.95 20.28 3.00e+00 1.11e-01 4.57e+01 angle pdb=" C3A G2P b 501 " pdb=" PB G2P b 501 " pdb=" O3B G2P b 501 " ideal model delta sigma weight residual 99.71 116.75 -17.04 3.00e+00 1.11e-01 3.23e+01 ... (remaining 24220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.22: 6106 32.22 - 64.45: 279 64.45 - 96.67: 23 96.67 - 128.89: 1 128.89 - 161.11: 3 Dihedral angle restraints: 6412 sinusoidal: 3469 harmonic: 2943 Sorted by residual: dihedral pdb=" C8 GTP a 501 " pdb=" C1' GTP a 501 " pdb=" N9 GTP a 501 " pdb=" O4' GTP a 501 " ideal model delta sinusoidal sigma weight residual 104.59 -56.52 161.11 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O3B GTP a 501 " pdb=" O3A GTP a 501 " pdb=" PB GTP a 501 " pdb=" PA GTP a 501 " ideal model delta sinusoidal sigma weight residual -68.92 75.19 -144.11 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O3A GTP a 501 " pdb=" O3B GTP a 501 " pdb=" PB GTP a 501 " pdb=" PG GTP a 501 " ideal model delta sinusoidal sigma weight residual 303.79 166.85 136.94 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 6409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.282: 1030 0.282 - 0.564: 0 0.564 - 0.846: 0 0.846 - 1.128: 0 1.128 - 1.410: 1 Chirality restraints: 1031 Sorted by residual: chirality pdb=" CB THR b 178 " pdb=" CA THR b 178 " pdb=" OG1 THR b 178 " pdb=" CG2 THR b 178 " both_signs ideal model delta sigma weight residual False 2.55 1.14 1.41 2.00e-01 2.50e+01 4.97e+01 chirality pdb=" C2' G2P b 501 " pdb=" C1' G2P b 501 " pdb=" C3' G2P b 501 " pdb=" O2' G2P b 501 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C3' GTP a 501 " pdb=" C2' GTP a 501 " pdb=" C4' GTP a 501 " pdb=" O3' GTP a 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1028 not shown) Planarity restraints: 2039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE a 267 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO a 268 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO a 268 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO a 268 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL a 324 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO a 325 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO a 325 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO a 325 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR a 172 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO a 173 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO a 173 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO a 173 " 0.018 5.00e-02 4.00e+02 ... (remaining 2036 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 3266 2.32 - 2.89: 28907 2.89 - 3.46: 32993 3.46 - 4.03: 47806 4.03 - 4.60: 71394 Nonbonded interactions: 184366 Sorted by model distance: nonbonded pdb=" HA THR b 178 " pdb=" HB THR b 178 " model vdw 1.747 1.952 nonbonded pdb=" HB THR b 178 " pdb="HG23 THR b 178 " model vdw 1.750 1.952 nonbonded pdb="HE22 GLN b 334 " pdb=" H ASN b 348 " model vdw 1.787 2.100 nonbonded pdb="HD22 ASN a 101 " pdb="HD21 ASN b 256 " model vdw 1.854 2.100 nonbonded pdb=" HH TYR b 50 " pdb=" HG1 THR b 237 " model vdw 1.856 2.100 ... (remaining 184361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 12.700 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: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 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 : 0.006 0.205 6949 Z= 0.278 Angle : 0.790 20.276 9438 Z= 0.341 Chirality : 0.063 1.410 1031 Planarity : 0.004 0.048 1226 Dihedral : 17.552 161.115 2562 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.82 % Allowed : 17.92 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.27), residues: 851 helix: -0.56 (0.26), residues: 363 sheet: 0.26 (0.43), residues: 143 loop : -1.05 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 213 TYR 0.010 0.001 TYR b 59 PHE 0.010 0.001 PHE b 385 TRP 0.010 0.002 TRP a 21 HIS 0.004 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 6949) covalent geometry : angle 0.78988 ( 9438) hydrogen bonds : bond 0.28765 ( 283) hydrogen bonds : angle 7.03018 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.430 Fit side-chains REVERT: a 55 GLU cc_start: 0.7653 (tt0) cc_final: 0.7331 (tm-30) REVERT: a 123 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7777 (ttm110) REVERT: a 176 GLN cc_start: 0.8834 (mt0) cc_final: 0.8579 (mm110) REVERT: a 221 ARG cc_start: 0.7512 (mtm-85) cc_final: 0.7191 (mtt-85) REVERT: a 255 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7661 (t80) REVERT: a 279 GLU cc_start: 0.7879 (mp0) cc_final: 0.7672 (pt0) REVERT: a 285 GLN cc_start: 0.8282 (mt0) cc_final: 0.7919 (mm-40) REVERT: a 322 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7665 (t0) REVERT: a 370 LYS cc_start: 0.8574 (tttm) cc_final: 0.7416 (tptp) REVERT: a 372 GLN cc_start: 0.8664 (mt0) cc_final: 0.7984 (mm110) REVERT: a 414 GLU cc_start: 0.8454 (mp0) cc_final: 0.8114 (tm-30) REVERT: b 320 ARG cc_start: 0.7557 (tpp-160) cc_final: 0.7238 (tpt170) REVERT: b 377 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8368 (mp) REVERT: b 406 MET cc_start: 0.8813 (tpp) cc_final: 0.8415 (tpp) outliers start: 6 outliers final: 3 residues processed: 98 average time/residue: 1.7424 time to fit residues: 177.2863 Evaluate side-chains 100 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 322 ASP Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain b residue 383 GLU Chi-restraints excluded: chain b residue 424 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 99 ASN ** b 334 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 = 0.3498 r_free = 0.3498 target = 0.107655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.087288 restraints weight = 21811.400| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.12 r_work: 0.3068 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6949 Z= 0.132 Angle : 0.560 10.974 9438 Z= 0.296 Chirality : 0.060 1.377 1031 Planarity : 0.004 0.044 1226 Dihedral : 10.747 145.799 990 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.82 % Allowed : 17.51 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.28), residues: 851 helix: 0.82 (0.27), residues: 372 sheet: 0.42 (0.42), residues: 145 loop : -0.78 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 213 TYR 0.009 0.001 TYR a 103 PHE 0.014 0.001 PHE b 317 TRP 0.014 0.001 TRP a 21 HIS 0.003 0.001 HIS b 396 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6949) covalent geometry : angle 0.56001 ( 9438) hydrogen bonds : bond 0.07830 ( 283) hydrogen bonds : angle 4.61401 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.330 Fit side-chains REVERT: a 55 GLU cc_start: 0.7666 (tt0) cc_final: 0.7150 (tm-30) REVERT: a 123 ARG cc_start: 0.7261 (ttm-80) cc_final: 0.6886 (ttm110) REVERT: a 176 GLN cc_start: 0.8609 (mt0) cc_final: 0.8307 (mm110) REVERT: a 221 ARG cc_start: 0.7056 (mtm-85) cc_final: 0.6710 (mtt-85) REVERT: a 255 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7359 (t80) REVERT: a 279 GLU cc_start: 0.7749 (mp0) cc_final: 0.7411 (pt0) REVERT: a 285 GLN cc_start: 0.8072 (mt0) cc_final: 0.7686 (mm-40) REVERT: a 370 LYS cc_start: 0.8355 (tttm) cc_final: 0.7126 (tptp) REVERT: a 372 GLN cc_start: 0.8427 (mt0) cc_final: 0.7590 (mm110) REVERT: a 414 GLU cc_start: 0.8182 (mp0) cc_final: 0.7686 (tm-30) REVERT: b 320 ARG cc_start: 0.7411 (tpp-160) cc_final: 0.7088 (tpt170) REVERT: b 330 MET cc_start: 0.8600 (mmp) cc_final: 0.8207 (mmp) outliers start: 6 outliers final: 1 residues processed: 105 average time/residue: 1.5040 time to fit residues: 164.4739 Evaluate side-chains 96 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 340 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 107 HIS ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.106557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.086073 restraints weight = 22115.635| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.12 r_work: 0.3047 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6949 Z= 0.168 Angle : 0.566 10.770 9438 Z= 0.297 Chirality : 0.061 1.397 1031 Planarity : 0.004 0.048 1226 Dihedral : 10.322 152.799 979 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.37 % Allowed : 17.24 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.28), residues: 851 helix: 1.15 (0.28), residues: 373 sheet: 0.55 (0.42), residues: 145 loop : -0.82 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 213 TYR 0.010 0.001 TYR b 59 PHE 0.013 0.001 PHE b 317 TRP 0.013 0.002 TRP a 21 HIS 0.004 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6949) covalent geometry : angle 0.56559 ( 9438) hydrogen bonds : bond 0.07494 ( 283) hydrogen bonds : angle 4.34479 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.333 Fit side-chains REVERT: a 55 GLU cc_start: 0.7716 (tt0) cc_final: 0.7149 (tm-30) REVERT: a 123 ARG cc_start: 0.7358 (ttm-80) cc_final: 0.6959 (ttm110) REVERT: a 176 GLN cc_start: 0.8608 (mt0) cc_final: 0.8301 (mm110) REVERT: a 221 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6761 (mtt-85) REVERT: a 255 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7294 (t80) REVERT: a 279 GLU cc_start: 0.7740 (mp0) cc_final: 0.7387 (pt0) REVERT: a 285 GLN cc_start: 0.8092 (mt0) cc_final: 0.7705 (mm-40) REVERT: a 370 LYS cc_start: 0.8371 (tttm) cc_final: 0.7128 (tptp) REVERT: a 372 GLN cc_start: 0.8413 (mt0) cc_final: 0.7555 (mm110) REVERT: a 414 GLU cc_start: 0.8214 (mp0) cc_final: 0.7708 (tm-30) REVERT: b 147 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8780 (ttp) REVERT: b 320 ARG cc_start: 0.7356 (tpp-160) cc_final: 0.6866 (mpt180) REVERT: b 330 MET cc_start: 0.8505 (mmp) cc_final: 0.8112 (mmp) outliers start: 10 outliers final: 6 residues processed: 99 average time/residue: 1.5287 time to fit residues: 157.6531 Evaluate side-chains 100 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 340 THR Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 383 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.106636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086228 restraints weight = 21915.475| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.11 r_work: 0.3047 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6949 Z= 0.167 Angle : 0.562 10.758 9438 Z= 0.294 Chirality : 0.061 1.391 1031 Planarity : 0.004 0.048 1226 Dihedral : 10.052 153.089 979 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.64 % Allowed : 17.65 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.28), residues: 851 helix: 1.28 (0.28), residues: 373 sheet: 0.63 (0.41), residues: 145 loop : -0.82 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 213 TYR 0.010 0.001 TYR b 59 PHE 0.013 0.001 PHE b 317 TRP 0.013 0.002 TRP a 21 HIS 0.004 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 6949) covalent geometry : angle 0.56152 ( 9438) hydrogen bonds : bond 0.06884 ( 283) hydrogen bonds : angle 4.21344 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.416 Fit side-chains REVERT: a 123 ARG cc_start: 0.7309 (ttm-80) cc_final: 0.6914 (ttm110) REVERT: a 221 ARG cc_start: 0.7054 (mtm-85) cc_final: 0.6740 (mtt-85) REVERT: a 255 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7439 (t80) REVERT: a 279 GLU cc_start: 0.7712 (mp0) cc_final: 0.7355 (pt0) REVERT: a 285 GLN cc_start: 0.8085 (mt0) cc_final: 0.7689 (mm-40) REVERT: a 370 LYS cc_start: 0.8373 (tttm) cc_final: 0.7127 (tptp) REVERT: a 372 GLN cc_start: 0.8467 (mt0) cc_final: 0.7651 (mm110) REVERT: a 414 GLU cc_start: 0.8229 (mp0) cc_final: 0.7652 (tm-30) REVERT: b 320 ARG cc_start: 0.7297 (tpp-160) cc_final: 0.6877 (mpt180) REVERT: b 330 MET cc_start: 0.8458 (mmp) cc_final: 0.8072 (mmp) outliers start: 12 outliers final: 6 residues processed: 101 average time/residue: 1.4456 time to fit residues: 152.4612 Evaluate side-chains 97 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 340 THR Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain b residue 383 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 347 ASN b 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.108237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.087579 restraints weight = 21841.333| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.13 r_work: 0.3115 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6949 Z= 0.157 Angle : 0.553 10.719 9438 Z= 0.289 Chirality : 0.061 1.393 1031 Planarity : 0.004 0.048 1226 Dihedral : 9.876 154.059 979 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.05 % Allowed : 17.51 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.28), residues: 851 helix: 1.34 (0.28), residues: 373 sheet: 0.67 (0.41), residues: 145 loop : -0.80 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 213 TYR 0.010 0.001 TYR b 59 PHE 0.013 0.001 PHE b 317 TRP 0.013 0.002 TRP a 21 HIS 0.004 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6949) covalent geometry : angle 0.55254 ( 9438) hydrogen bonds : bond 0.06578 ( 283) hydrogen bonds : angle 4.13776 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.375 Fit side-chains REVERT: a 123 ARG cc_start: 0.7520 (ttm-80) cc_final: 0.7134 (ttm110) REVERT: a 221 ARG cc_start: 0.7246 (mtm-85) cc_final: 0.6928 (mtt-85) REVERT: a 255 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7732 (t80) REVERT: a 279 GLU cc_start: 0.7797 (mp0) cc_final: 0.7491 (pt0) REVERT: a 285 GLN cc_start: 0.8205 (mt0) cc_final: 0.7829 (mm-40) REVERT: a 322 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7160 (t0) REVERT: a 372 GLN cc_start: 0.8561 (mt0) cc_final: 0.7813 (mm110) REVERT: a 414 GLU cc_start: 0.8333 (mp0) cc_final: 0.7797 (tm-30) REVERT: b 147 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8393 (ttp) REVERT: b 320 ARG cc_start: 0.7430 (tpp-160) cc_final: 0.7104 (mpt180) REVERT: b 330 MET cc_start: 0.8655 (mmp) cc_final: 0.8263 (mmp) outliers start: 15 outliers final: 9 residues processed: 102 average time/residue: 1.5158 time to fit residues: 161.2730 Evaluate side-chains 105 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 322 ASP Chi-restraints excluded: chain a residue 340 THR Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain b residue 288 GLU Chi-restraints excluded: chain b residue 335 SER Chi-restraints excluded: chain b residue 383 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 347 ASN b 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.087604 restraints weight = 21956.957| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.15 r_work: 0.3131 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6949 Z= 0.128 Angle : 0.527 10.786 9438 Z= 0.275 Chirality : 0.060 1.388 1031 Planarity : 0.004 0.047 1226 Dihedral : 9.577 153.293 979 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.92 % Allowed : 17.37 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.29), residues: 851 helix: 1.49 (0.28), residues: 375 sheet: 0.67 (0.41), residues: 145 loop : -0.72 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 213 TYR 0.008 0.001 TYR b 59 PHE 0.013 0.001 PHE b 317 TRP 0.013 0.001 TRP a 21 HIS 0.003 0.001 HIS b 396 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6949) covalent geometry : angle 0.52733 ( 9438) hydrogen bonds : bond 0.05846 ( 283) hydrogen bonds : angle 4.00696 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.442 Fit side-chains REVERT: a 6 SER cc_start: 0.9046 (OUTLIER) cc_final: 0.8834 (t) REVERT: a 123 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.7107 (ttm110) REVERT: a 221 ARG cc_start: 0.7199 (mtm-85) cc_final: 0.6875 (mtt-85) REVERT: a 255 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7792 (t80) REVERT: a 279 GLU cc_start: 0.7807 (mp0) cc_final: 0.7492 (pt0) REVERT: a 285 GLN cc_start: 0.8186 (mt0) cc_final: 0.7803 (mm-40) REVERT: a 372 GLN cc_start: 0.8555 (mt0) cc_final: 0.7793 (mm110) REVERT: a 414 GLU cc_start: 0.8302 (mp0) cc_final: 0.7769 (tm-30) REVERT: b 147 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8385 (ttp) REVERT: b 320 ARG cc_start: 0.7401 (tpp-160) cc_final: 0.7114 (mpt180) REVERT: b 330 MET cc_start: 0.8609 (mmp) cc_final: 0.8247 (mmp) outliers start: 14 outliers final: 8 residues processed: 103 average time/residue: 1.3841 time to fit residues: 149.2494 Evaluate side-chains 105 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 340 THR Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain b residue 288 GLU Chi-restraints excluded: chain b residue 335 SER Chi-restraints excluded: chain b residue 383 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 347 ASN b 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.108627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087950 restraints weight = 21867.025| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.13 r_work: 0.3120 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6949 Z= 0.155 Angle : 0.549 10.719 9438 Z= 0.286 Chirality : 0.061 1.395 1031 Planarity : 0.004 0.048 1226 Dihedral : 9.772 154.675 979 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.92 % Allowed : 17.51 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.29), residues: 851 helix: 1.44 (0.28), residues: 375 sheet: 0.69 (0.41), residues: 145 loop : -0.73 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 213 TYR 0.010 0.001 TYR b 59 PHE 0.010 0.001 PHE b 317 TRP 0.012 0.002 TRP a 21 HIS 0.004 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6949) covalent geometry : angle 0.54926 ( 9438) hydrogen bonds : bond 0.06325 ( 283) hydrogen bonds : angle 4.05900 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: a 123 ARG cc_start: 0.7523 (ttm-80) cc_final: 0.7141 (ttm110) REVERT: a 176 GLN cc_start: 0.8726 (mt0) cc_final: 0.8438 (mm-40) REVERT: a 221 ARG cc_start: 0.7209 (mtm-85) cc_final: 0.6965 (mtt-85) REVERT: a 255 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7775 (t80) REVERT: a 279 GLU cc_start: 0.7810 (mp0) cc_final: 0.7503 (pt0) REVERT: a 285 GLN cc_start: 0.8196 (mt0) cc_final: 0.7810 (mm-40) REVERT: a 372 GLN cc_start: 0.8557 (mt0) cc_final: 0.7807 (mm110) REVERT: a 414 GLU cc_start: 0.8375 (mp0) cc_final: 0.7772 (tm-30) REVERT: b 147 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8425 (ttp) REVERT: b 320 ARG cc_start: 0.7391 (tpp-160) cc_final: 0.7154 (mpt180) outliers start: 14 outliers final: 10 residues processed: 103 average time/residue: 1.4684 time to fit residues: 157.6739 Evaluate side-chains 105 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 340 THR Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 88 ASP Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain b residue 288 GLU Chi-restraints excluded: chain b residue 335 SER Chi-restraints excluded: chain b residue 383 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 67 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 35 optimal weight: 0.0970 chunk 65 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 347 ASN b 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.111537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.090909 restraints weight = 21795.604| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.14 r_work: 0.3185 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6949 Z= 0.092 Angle : 0.495 10.951 9438 Z= 0.256 Chirality : 0.060 1.390 1031 Planarity : 0.004 0.044 1226 Dihedral : 8.854 147.811 979 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.82 % Allowed : 18.47 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.29), residues: 851 helix: 1.84 (0.28), residues: 374 sheet: 0.66 (0.43), residues: 139 loop : -0.58 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 213 TYR 0.006 0.001 TYR a 210 PHE 0.015 0.001 PHE b 317 TRP 0.014 0.001 TRP a 21 HIS 0.002 0.000 HIS a 28 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 6949) covalent geometry : angle 0.49494 ( 9438) hydrogen bonds : bond 0.04600 ( 283) hydrogen bonds : angle 3.79692 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: a 123 ARG cc_start: 0.7475 (ttm-80) cc_final: 0.7112 (ttm110) REVERT: a 176 GLN cc_start: 0.8722 (mt0) cc_final: 0.8422 (mm110) REVERT: a 221 ARG cc_start: 0.7142 (mtm-85) cc_final: 0.6894 (mtt-85) REVERT: a 255 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7892 (t80) REVERT: a 279 GLU cc_start: 0.7799 (mp0) cc_final: 0.7487 (pt0) REVERT: a 285 GLN cc_start: 0.8185 (mt0) cc_final: 0.7800 (mm-40) REVERT: a 372 GLN cc_start: 0.8510 (mt0) cc_final: 0.7742 (mm110) REVERT: a 414 GLU cc_start: 0.8260 (mp0) cc_final: 0.7720 (tm-30) REVERT: b 86 ARG cc_start: 0.8336 (ttm-80) cc_final: 0.7068 (tpm170) REVERT: b 147 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8337 (ttp) REVERT: b 320 ARG cc_start: 0.7456 (tpp-160) cc_final: 0.7223 (mpt180) REVERT: b 330 MET cc_start: 0.8537 (mmp) cc_final: 0.8158 (mmp) REVERT: b 347 ASN cc_start: 0.7864 (t0) cc_final: 0.7007 (p0) outliers start: 6 outliers final: 1 residues processed: 100 average time/residue: 1.5724 time to fit residues: 163.9805 Evaluate side-chains 94 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 340 THR Chi-restraints excluded: chain b residue 147 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.108036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.087173 restraints weight = 22020.060| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.14 r_work: 0.3125 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6949 Z= 0.158 Angle : 0.551 10.727 9438 Z= 0.286 Chirality : 0.061 1.395 1031 Planarity : 0.004 0.047 1226 Dihedral : 9.640 155.880 979 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.82 % Allowed : 18.47 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.29), residues: 851 helix: 1.61 (0.28), residues: 375 sheet: 0.67 (0.41), residues: 145 loop : -0.60 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 213 TYR 0.010 0.001 TYR b 59 PHE 0.012 0.001 PHE b 317 TRP 0.011 0.002 TRP a 21 HIS 0.005 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6949) covalent geometry : angle 0.55057 ( 9438) hydrogen bonds : bond 0.06111 ( 283) hydrogen bonds : angle 3.96288 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.384 Fit side-chains REVERT: a 123 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.7161 (ttm110) REVERT: a 176 GLN cc_start: 0.8723 (mt0) cc_final: 0.8434 (mm-40) REVERT: a 221 ARG cc_start: 0.7154 (mtm-85) cc_final: 0.6906 (mtt-85) REVERT: a 255 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7943 (t80) REVERT: a 279 GLU cc_start: 0.7813 (mp0) cc_final: 0.7500 (pt0) REVERT: a 285 GLN cc_start: 0.8204 (mt0) cc_final: 0.7818 (mm-40) REVERT: a 372 GLN cc_start: 0.8495 (mt0) cc_final: 0.7735 (mm110) REVERT: a 414 GLU cc_start: 0.8349 (mp0) cc_final: 0.7737 (tm-30) REVERT: b 147 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8462 (ttp) REVERT: b 320 ARG cc_start: 0.7486 (tpp-160) cc_final: 0.7234 (mpt180) outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 1.5346 time to fit residues: 148.5860 Evaluate side-chains 94 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 383 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.109216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.088399 restraints weight = 22024.714| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.14 r_work: 0.3146 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6949 Z= 0.119 Angle : 0.523 10.865 9438 Z= 0.272 Chirality : 0.060 1.395 1031 Planarity : 0.004 0.045 1226 Dihedral : 9.403 153.763 979 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.68 % Allowed : 18.74 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.29), residues: 851 helix: 1.72 (0.28), residues: 374 sheet: 0.62 (0.41), residues: 145 loop : -0.57 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 213 TYR 0.007 0.001 TYR b 59 PHE 0.010 0.001 PHE b 317 TRP 0.013 0.001 TRP a 21 HIS 0.003 0.001 HIS b 396 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6949) covalent geometry : angle 0.52271 ( 9438) hydrogen bonds : bond 0.05481 ( 283) hydrogen bonds : angle 3.90460 ( 813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.381 Fit side-chains REVERT: a 123 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7147 (ttm110) REVERT: a 221 ARG cc_start: 0.7136 (mtm-85) cc_final: 0.6894 (mtt-85) REVERT: a 255 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7889 (t80) REVERT: a 279 GLU cc_start: 0.7799 (mp0) cc_final: 0.7485 (pt0) REVERT: a 285 GLN cc_start: 0.8205 (mt0) cc_final: 0.7816 (mm-40) REVERT: a 372 GLN cc_start: 0.8510 (mt0) cc_final: 0.7744 (mm110) REVERT: a 414 GLU cc_start: 0.8328 (mp0) cc_final: 0.7734 (tm-30) REVERT: b 86 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.7090 (tpm170) REVERT: b 147 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8415 (ttp) outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 1.6511 time to fit residues: 158.2946 Evaluate side-chains 92 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 321 MET Chi-restraints excluded: chain b residue 383 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 4 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 16 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.091006 restraints weight = 21788.765| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.14 r_work: 0.3187 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 6949 Z= 0.105 Angle : 0.560 21.290 9438 Z= 0.279 Chirality : 0.060 1.386 1031 Planarity : 0.004 0.044 1226 Dihedral : 8.961 150.033 979 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.68 % Allowed : 19.15 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.29), residues: 851 helix: 1.90 (0.28), residues: 374 sheet: 0.60 (0.43), residues: 139 loop : -0.51 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 320 TYR 0.006 0.001 TYR a 210 PHE 0.038 0.001 PHE b 317 TRP 0.014 0.001 TRP a 21 HIS 0.002 0.000 HIS a 28 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 6949) covalent geometry : angle 0.56031 ( 9438) hydrogen bonds : bond 0.04779 ( 283) hydrogen bonds : angle 3.79116 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5802.91 seconds wall clock time: 98 minutes 51.61 seconds (5931.61 seconds total)