Starting phenix.real_space_refine on Wed Aug 5 23:05:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rxk_19577/08_2026/8rxk_19577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rxk_19577/08_2026/8rxk_19577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rxk_19577/08_2026/8rxk_19577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rxk_19577/08_2026/8rxk_19577.map" model { file = "/net/cci-nas-00/data/ceres_data/8rxk_19577/08_2026/8rxk_19577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rxk_19577/08_2026/8rxk_19577.cif" } resolution = 3.23 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 57 5.49 5 S 63 5.16 5 C 7497 2.51 5 N 2171 2.21 5 O 2374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12162 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3727 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 29, 'TRANS': 456} Chain breaks: 1 Chain: "D" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3679 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 29, 'TRANS': 450} Chain breaks: 2 Chain: "E" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3679 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 29, 'TRANS': 450} Chain breaks: 2 Chain: "Y" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 480 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "Z" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 504 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ANP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.35, per 1000 atoms: 0.19 Number of scatterers: 12162 At special positions: 0 Unit cell: (90.3, 127.065, 114.165, 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 63 16.00 P 57 15.00 O 2374 8.00 N 2171 7.00 C 7497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 519.7 milliseconds 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 15 sheets defined 46.7% alpha, 12.0% beta 15 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 44 through 55 removed outlier: 4.116A pdb=" N ARG C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 97 through 102 removed outlier: 3.511A pdb=" N LEU C 101 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 102 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 159 through 170 Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.791A pdb=" N ASP C 193 " --> pdb=" O ASP C 190 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 194 " --> pdb=" O TRP C 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 190 through 194' Processing helix chain 'C' and resid 197 through 205 removed outlier: 3.519A pdb=" N ALA C 203 " --> pdb=" O HIS C 199 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 235 removed outlier: 4.137A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 234 " --> pdb=" O ARG C 230 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 235 " --> pdb=" O PHE C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 254 removed outlier: 3.785A pdb=" N GLU C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 249 " --> pdb=" O GLU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 308 through 315 removed outlier: 3.613A pdb=" N LEU C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR C 314 " --> pdb=" O GLN C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 321 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.873A pdb=" N TYR C 370 " --> pdb=" O ARG C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 382 Processing helix chain 'C' and resid 392 through 398 Processing helix chain 'C' and resid 406 through 422 Processing helix chain 'C' and resid 444 through 458 Processing helix chain 'C' and resid 461 through 466 removed outlier: 3.522A pdb=" N HIS C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 Processing helix chain 'C' and resid 487 through 494 removed outlier: 3.808A pdb=" N SER C 494 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 56 removed outlier: 4.518A pdb=" N ASP D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.520A pdb=" N ASN D 100 " --> pdb=" O PRO D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 142 through 148 removed outlier: 3.850A pdb=" N LEU D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 169 removed outlier: 3.674A pdb=" N VAL D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 194 removed outlier: 3.639A pdb=" N ASP D 193 " --> pdb=" O ASP D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 211 Processing helix chain 'D' and resid 223 through 232 removed outlier: 4.146A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 252 Processing helix chain 'D' and resid 275 through 280 Processing helix chain 'D' and resid 289 through 294 removed outlier: 3.746A pdb=" N ALA D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.838A pdb=" N THR D 314 " --> pdb=" O GLN D 310 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 315 " --> pdb=" O VAL D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 322 removed outlier: 3.516A pdb=" N GLU D 320 " --> pdb=" O ARG D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 374 removed outlier: 3.744A pdb=" N LEU D 374 " --> pdb=" O TYR D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 380 Processing helix chain 'D' and resid 392 through 398 Processing helix chain 'D' and resid 406 through 425 Processing helix chain 'D' and resid 428 through 432 removed outlier: 3.768A pdb=" N LEU D 432 " --> pdb=" O ASN D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 441 Processing helix chain 'D' and resid 444 through 458 removed outlier: 3.897A pdb=" N PHE D 450 " --> pdb=" O GLU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 479 removed outlier: 3.659A pdb=" N HIS D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 495 removed outlier: 3.794A pdb=" N SER D 494 " --> pdb=" O GLN D 490 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR D 495 " --> pdb=" O GLN D 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 44 through 56 removed outlier: 4.250A pdb=" N ARG E 48 " --> pdb=" O GLU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 159 through 170 Processing helix chain 'E' and resid 190 through 194 Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 224 through 232 removed outlier: 3.695A pdb=" N ARG E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 254 Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 310 through 315 Processing helix chain 'E' and resid 315 through 322 removed outlier: 3.752A pdb=" N GLU E 320 " --> pdb=" O ARG E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 373 removed outlier: 4.616A pdb=" N TYR E 370 " --> pdb=" O ARG E 366 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU E 371 " --> pdb=" O ILE E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 380 Processing helix chain 'E' and resid 393 through 397 removed outlier: 3.907A pdb=" N ILE E 397 " --> pdb=" O GLU E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 425 Processing helix chain 'E' and resid 428 through 432 removed outlier: 3.522A pdb=" N LEU E 432 " --> pdb=" O ASN E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 440 Processing helix chain 'E' and resid 445 through 458 removed outlier: 3.803A pdb=" N LEU E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG E 452 " --> pdb=" O GLN E 448 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU E 453 " --> pdb=" O LEU E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 479 Processing helix chain 'E' and resid 485 through 493 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 12 removed outlier: 3.730A pdb=" N VAL C 15 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU C 22 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR C 33 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 104 through 106 removed outlier: 6.328A pdb=" N LEU C 136 " --> pdb=" O PHE C 155 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ALA C 157 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE C 138 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 110 removed outlier: 3.647A pdb=" N GLU C 109 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 267 through 268 removed outlier: 6.601A pdb=" N ARG C 268 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP C 302 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 218 " --> pdb=" O MET C 345 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU C 215 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE C 388 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER C 217 " --> pdb=" O ILE C 388 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 326 through 327 removed outlier: 3.543A pdb=" N ILE C 326 " --> pdb=" O ILE C 333 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 12 removed outlier: 5.473A pdb=" N SER D 31 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL D 67 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR D 33 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU D 69 " --> pdb=" O THR D 33 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 104 through 106 removed outlier: 6.043A pdb=" N LEU D 136 " --> pdb=" O PHE D 155 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA D 157 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE D 138 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 109 through 110 removed outlier: 4.018A pdb=" N GLU D 109 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 267 through 268 removed outlier: 6.529A pdb=" N ARG D 268 " --> pdb=" O PHE D 300 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU D 215 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE D 388 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER D 217 " --> pdb=" O ILE D 388 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 326 through 327 removed outlier: 3.740A pdb=" N ILE D 326 " --> pdb=" O ILE D 333 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 333 " --> pdb=" O ILE D 326 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 12 removed outlier: 5.901A pdb=" N SER E 31 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL E 67 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR E 33 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU E 69 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL E 35 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 105 through 106 removed outlier: 6.542A pdb=" N GLU E 105 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ALA E 139 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU E 136 " --> pdb=" O PHE E 155 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA E 157 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE E 138 " --> pdb=" O ALA E 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 109 through 110 removed outlier: 3.615A pdb=" N GLU E 109 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 267 through 268 removed outlier: 6.503A pdb=" N ARG E 268 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA E 344 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU E 301 " --> pdb=" O ALA E 344 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE E 214 " --> pdb=" O ALA E 343 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N MET E 345 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU E 216 " --> pdb=" O MET E 345 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU E 215 " --> pdb=" O VAL E 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 323 through 327 433 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3760 1.34 - 1.46: 1799 1.46 - 1.58: 6721 1.58 - 1.70: 112 1.70 - 1.82: 99 Bond restraints: 12491 Sorted by residual: bond pdb=" O3A ANP D 601 " pdb=" PB ANP D 601 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" O3A ANP C 601 " pdb=" PB ANP C 601 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" O3A ANP C 602 " pdb=" PB ANP C 602 " ideal model delta sigma weight residual 1.700 1.560 0.140 2.00e-02 2.50e+03 4.88e+01 bond pdb=" N3B ANP C 601 " pdb=" PG ANP C 601 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" N3B ANP D 601 " pdb=" PG ANP D 601 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 12486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 16999 3.56 - 7.13: 116 7.13 - 10.69: 9 10.69 - 14.25: 4 14.25 - 17.81: 3 Bond angle restraints: 17131 Sorted by residual: angle pdb=" PB ANP C 601 " pdb=" N3B ANP C 601 " pdb=" PG ANP C 601 " ideal model delta sigma weight residual 126.95 109.14 17.81 3.00e+00 1.11e-01 3.53e+01 angle pdb=" PB ANP C 602 " pdb=" N3B ANP C 602 " pdb=" PG ANP C 602 " ideal model delta sigma weight residual 126.95 109.34 17.61 3.00e+00 1.11e-01 3.45e+01 angle pdb=" PB ANP D 601 " pdb=" N3B ANP D 601 " pdb=" PG ANP D 601 " ideal model delta sigma weight residual 126.95 109.68 17.27 3.00e+00 1.11e-01 3.32e+01 angle pdb=" O4' DA Z 29 " pdb=" C1' DA Z 29 " pdb=" N9 DA Z 29 " ideal model delta sigma weight residual 108.00 111.61 -3.61 7.00e-01 2.04e+00 2.66e+01 angle pdb=" N3 DT Y 11 " pdb=" C4 DT Y 11 " pdb=" O4 DT Y 11 " ideal model delta sigma weight residual 119.90 122.80 -2.90 6.00e-01 2.78e+00 2.34e+01 ... (remaining 17126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 6607 21.18 - 42.35: 786 42.35 - 63.53: 231 63.53 - 84.70: 33 84.70 - 105.88: 6 Dihedral angle restraints: 7663 sinusoidal: 3480 harmonic: 4183 Sorted by residual: dihedral pdb=" CA GLY C 70 " pdb=" C GLY C 70 " pdb=" N PRO C 71 " pdb=" CA PRO C 71 " ideal model delta harmonic sigma weight residual 180.00 122.92 57.08 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA LEU E 189 " pdb=" C LEU E 189 " pdb=" N ASP E 190 " pdb=" CA ASP E 190 " ideal model delta harmonic sigma weight residual 180.00 154.77 25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ARG C 467 " pdb=" C ARG C 467 " pdb=" N LEU C 468 " pdb=" CA LEU C 468 " ideal model delta harmonic sigma weight residual 180.00 154.91 25.09 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 7660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 1973 0.185 - 0.369: 3 0.369 - 0.553: 0 0.553 - 0.738: 0 0.738 - 0.922: 1 Chirality restraints: 1977 Sorted by residual: chirality pdb=" C1' ANP C 601 " pdb=" C2' ANP C 601 " pdb=" N9 ANP C 601 " pdb=" O4' ANP C 601 " both_signs ideal model delta sigma weight residual False 2.42 1.50 0.92 2.00e-01 2.50e+01 2.13e+01 chirality pdb=" C3' ANP C 601 " pdb=" C2' ANP C 601 " pdb=" C4' ANP C 601 " pdb=" O3' ANP C 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C3' ANP D 601 " pdb=" C2' ANP D 601 " pdb=" C4' ANP D 601 " pdb=" O3' ANP D 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1974 not shown) Planarity restraints: 2035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 285 " 0.058 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO E 286 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO E 286 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 286 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 452 " -0.210 9.50e-02 1.11e+02 9.42e-02 5.83e+00 pdb=" NE ARG E 452 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG E 452 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 452 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG E 452 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT Y 25 " 0.024 2.00e-02 2.50e+03 1.17e-02 3.42e+00 pdb=" N1 DT Y 25 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DT Y 25 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT Y 25 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT Y 25 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT Y 25 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT Y 25 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT Y 25 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT Y 25 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT Y 25 " -0.005 2.00e-02 2.50e+03 ... (remaining 2032 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 268 2.65 - 3.22: 12044 3.22 - 3.78: 18683 3.78 - 4.34: 25817 4.34 - 4.90: 41934 Nonbonded interactions: 98746 Sorted by model distance: nonbonded pdb=" O ARG E 253 " pdb=" NH1 ARG E 253 " model vdw 2.093 3.120 nonbonded pdb=" O ASN C 346 " pdb=" OH TYR C 370 " model vdw 2.113 3.040 nonbonded pdb=" OE1 GLU D 22 " pdb=" ND2 ASN D 68 " model vdw 2.125 3.120 nonbonded pdb=" ND1 HIS C 212 " pdb=" OD2 ASP C 383 " model vdw 2.132 3.120 nonbonded pdb=" O GLU D 412 " pdb=" OG1 THR D 415 " model vdw 2.178 3.040 ... (remaining 98741 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 180 or resid 187 through 500)) selection = (chain 'D' and resid 1 through 500) selection = chain 'E' } 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: 8.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.840 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.005 0.145 12491 Z= 0.303 Angle : 0.803 17.814 17131 Z= 0.463 Chirality : 0.049 0.922 1977 Planarity : 0.005 0.094 2035 Dihedral : 19.419 105.879 4933 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.13 % Favored : 92.17 % Rotamer: Outliers : 0.25 % Allowed : 18.97 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.95 (0.24), residues: 1430 helix: 0.15 (0.22), residues: 606 sheet: -1.36 (0.34), residues: 235 loop : -1.00 (0.28), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 452 TYR 0.009 0.001 TYR C 187 PHE 0.017 0.001 PHE D 259 TRP 0.007 0.001 TRP E 262 HIS 0.006 0.001 HIS C 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.30 (12491) covalent geometry : angle 0.80330 / 0.46 (17131) hydrogen bonds : bond 0.16511 / 10.82 ( 463) hydrogen bonds : angle 7.04753 / 4.93 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 0.0959 time to fit residues: 16.1372 Evaluate side-chains 96 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.1980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 ASN C 296 HIS C 448 GLN D 135 HIS D 400 ASN D 406 GLN D 421 GLN D 500 HIS E 135 HIS E 271 HIS E 284 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.091246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.062245 restraints weight = 35743.849| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.07 r_work: 0.2826 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12491 Z= 0.181 Angle : 0.758 10.853 17131 Z= 0.389 Chirality : 0.044 0.269 1977 Planarity : 0.005 0.060 2035 Dihedral : 19.059 129.954 2190 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.85 % Favored : 92.45 % Rotamer: Outliers : 2.46 % Allowed : 18.39 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.84 (0.23), residues: 1430 helix: 0.19 (0.22), residues: 637 sheet: -1.02 (0.34), residues: 234 loop : -1.07 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 366 TYR 0.015 0.002 TYR E 370 PHE 0.024 0.001 PHE D 259 TRP 0.011 0.002 TRP D 191 HIS 0.006 0.001 HIS C 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (12491) covalent geometry : angle 0.75829 / 0.39 (17131) hydrogen bonds : bond 0.05382 / 3.28 ( 463) hydrogen bonds : angle 5.67793 / 4.04 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8863 (mm-40) REVERT: C 112 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8846 (mt) REVERT: C 255 LYS cc_start: 0.8173 (ptmm) cc_final: 0.7796 (ptmm) REVERT: C 256 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8238 (mm) REVERT: C 310 GLN cc_start: 0.9353 (mm-40) cc_final: 0.9095 (mm-40) REVERT: C 370 TYR cc_start: 0.8310 (t80) cc_final: 0.7901 (t80) REVERT: C 397 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9271 (mp) REVERT: D 380 ASP cc_start: 0.9393 (OUTLIER) cc_final: 0.9046 (m-30) REVERT: D 417 MET cc_start: 0.9335 (mmm) cc_final: 0.8712 (mmt) REVERT: D 455 MET cc_start: 0.9422 (mmm) cc_final: 0.9093 (tpt) REVERT: E 39 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8950 (mt-10) REVERT: E 227 MET cc_start: 0.9430 (mtp) cc_final: 0.9177 (mpp) REVERT: E 417 MET cc_start: 0.9408 (mmm) cc_final: 0.9035 (mmt) outliers start: 30 outliers final: 13 residues processed: 130 average time/residue: 0.0787 time to fit residues: 15.5937 Evaluate side-chains 114 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 500 HIS Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 468 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 0 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN E 95 GLN E 135 HIS E 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.087789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.059013 restraints weight = 36913.297| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 4.05 r_work: 0.2752 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 12491 Z= 0.344 Angle : 0.815 10.558 17131 Z= 0.414 Chirality : 0.045 0.199 1977 Planarity : 0.005 0.061 2035 Dihedral : 19.085 131.847 2190 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.11 % Favored : 91.19 % Rotamer: Outliers : 3.37 % Allowed : 19.70 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.86 (0.23), residues: 1430 helix: 0.18 (0.21), residues: 637 sheet: -1.14 (0.35), residues: 223 loop : -1.05 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 260 TYR 0.024 0.002 TYR C 187 PHE 0.030 0.002 PHE D 259 TRP 0.015 0.002 TRP D 191 HIS 0.005 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.34 (12491) covalent geometry : angle 0.81493 / 0.41 (17131) hydrogen bonds : bond 0.05783 / 3.50 ( 463) hydrogen bonds : angle 5.54140 / 3.92 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8921 (mm-40) REVERT: C 255 LYS cc_start: 0.8289 (ptmm) cc_final: 0.7926 (ptmm) REVERT: C 256 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8390 (mm) REVERT: C 310 GLN cc_start: 0.9406 (mm-40) cc_final: 0.9111 (mm-40) REVERT: C 370 TYR cc_start: 0.8471 (t80) cc_final: 0.8074 (t80) REVERT: C 397 ILE cc_start: 0.9502 (OUTLIER) cc_final: 0.9298 (mp) REVERT: C 496 LYS cc_start: 0.9075 (tppp) cc_final: 0.8740 (tppp) REVERT: D 112 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8805 (mp) REVERT: D 380 ASP cc_start: 0.9440 (OUTLIER) cc_final: 0.9111 (m-30) REVERT: D 417 MET cc_start: 0.9479 (mmm) cc_final: 0.8937 (mmt) REVERT: E 151 HIS cc_start: 0.7977 (t70) cc_final: 0.7621 (t70) REVERT: E 227 MET cc_start: 0.9452 (mtp) cc_final: 0.9192 (mpp) outliers start: 41 outliers final: 17 residues processed: 127 average time/residue: 0.0801 time to fit residues: 15.8940 Evaluate side-chains 113 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 474 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 130 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 421 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 HIS E 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.090441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.061387 restraints weight = 36213.621| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.11 r_work: 0.2822 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12491 Z= 0.136 Angle : 0.680 9.600 17131 Z= 0.348 Chirality : 0.042 0.193 1977 Planarity : 0.004 0.066 2035 Dihedral : 18.954 132.277 2190 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.64 % Favored : 92.80 % Rotamer: Outliers : 3.45 % Allowed : 18.97 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.64 (0.23), residues: 1430 helix: 0.40 (0.22), residues: 634 sheet: -0.99 (0.36), residues: 209 loop : -1.00 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 253 TYR 0.017 0.002 TYR C 187 PHE 0.022 0.001 PHE D 259 TRP 0.010 0.002 TRP E 191 HIS 0.006 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (12491) covalent geometry : angle 0.67957 / 0.35 (17131) hydrogen bonds : bond 0.04081 / 2.47 ( 463) hydrogen bonds : angle 4.93318 / 3.51 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8884 (mm-40) REVERT: C 44 GLU cc_start: 0.8767 (pm20) cc_final: 0.8439 (pm20) REVERT: C 145 GLU cc_start: 0.8540 (mp0) cc_final: 0.8250 (mp0) REVERT: C 171 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9113 (p) REVERT: C 255 LYS cc_start: 0.8230 (ptmm) cc_final: 0.7868 (ptmm) REVERT: C 256 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8507 (mm) REVERT: C 271 HIS cc_start: 0.8173 (t-90) cc_final: 0.7912 (t70) REVERT: C 310 GLN cc_start: 0.9441 (mm-40) cc_final: 0.9159 (mm-40) REVERT: C 370 TYR cc_start: 0.8432 (t80) cc_final: 0.8154 (t80) REVERT: C 397 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9316 (mp) REVERT: C 496 LYS cc_start: 0.8889 (tppp) cc_final: 0.8568 (tppt) REVERT: D 213 SER cc_start: 0.9112 (m) cc_final: 0.8412 (p) REVERT: D 313 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9166 (mm-30) REVERT: D 380 ASP cc_start: 0.9433 (OUTLIER) cc_final: 0.9089 (m-30) REVERT: D 417 MET cc_start: 0.9458 (mmm) cc_final: 0.8797 (mmt) REVERT: D 455 MET cc_start: 0.9359 (mmm) cc_final: 0.9039 (tpt) REVERT: D 478 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8795 (ttm) REVERT: E 39 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9024 (mt-10) REVERT: E 151 HIS cc_start: 0.7921 (t70) cc_final: 0.7522 (t70) REVERT: E 227 MET cc_start: 0.9387 (mtp) cc_final: 0.9173 (mpp) REVERT: E 417 MET cc_start: 0.9344 (mmm) cc_final: 0.8882 (mmt) outliers start: 42 outliers final: 17 residues processed: 140 average time/residue: 0.0763 time to fit residues: 16.6873 Evaluate side-chains 119 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 468 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.090642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.061561 restraints weight = 36442.804| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.15 r_work: 0.2827 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12491 Z= 0.128 Angle : 0.657 9.098 17131 Z= 0.334 Chirality : 0.041 0.179 1977 Planarity : 0.004 0.063 2035 Dihedral : 18.808 136.598 2188 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.06 % Favored : 92.38 % Rotamer: Outliers : 3.20 % Allowed : 19.21 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.56 (0.23), residues: 1430 helix: 0.44 (0.21), residues: 647 sheet: -0.71 (0.37), residues: 204 loop : -1.06 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 467 TYR 0.023 0.002 TYR E 370 PHE 0.014 0.001 PHE C 307 TRP 0.009 0.001 TRP D 191 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (12491) covalent geometry : angle 0.65650 / 0.33 (17131) hydrogen bonds : bond 0.03857 / 2.35 ( 463) hydrogen bonds : angle 4.73561 / 3.39 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8870 (mm-40) REVERT: C 44 GLU cc_start: 0.8760 (pm20) cc_final: 0.8450 (pm20) REVERT: C 145 GLU cc_start: 0.8521 (mp0) cc_final: 0.8208 (mp0) REVERT: C 171 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.9157 (p) REVERT: C 271 HIS cc_start: 0.8220 (t-90) cc_final: 0.7838 (t70) REVERT: C 310 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9116 (mm-40) REVERT: C 370 TYR cc_start: 0.8408 (t80) cc_final: 0.7993 (t80) REVERT: C 391 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7431 (tt) REVERT: C 397 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9300 (mp) REVERT: C 417 MET cc_start: 0.9182 (mmm) cc_final: 0.8972 (mmm) REVERT: C 449 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9263 (pp) REVERT: C 496 LYS cc_start: 0.8941 (tppp) cc_final: 0.8693 (tppp) REVERT: D 213 SER cc_start: 0.9085 (m) cc_final: 0.8385 (p) REVERT: D 259 PHE cc_start: 0.7864 (t80) cc_final: 0.7559 (t80) REVERT: D 345 MET cc_start: 0.8402 (ptm) cc_final: 0.8119 (tmm) REVERT: D 380 ASP cc_start: 0.9415 (OUTLIER) cc_final: 0.9084 (m-30) REVERT: D 417 MET cc_start: 0.9442 (mmm) cc_final: 0.8683 (mmt) REVERT: D 455 MET cc_start: 0.9368 (mmm) cc_final: 0.9049 (tpt) REVERT: E 39 GLU cc_start: 0.9372 (mt-10) cc_final: 0.9028 (mt-10) REVERT: E 151 HIS cc_start: 0.7956 (t70) cc_final: 0.7531 (t70) REVERT: E 227 MET cc_start: 0.9400 (mtp) cc_final: 0.9190 (mpp) REVERT: E 417 MET cc_start: 0.9354 (mmm) cc_final: 0.8680 (mmt) outliers start: 39 outliers final: 20 residues processed: 133 average time/residue: 0.0833 time to fit residues: 17.3125 Evaluate side-chains 125 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 474 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 144 optimal weight: 20.0000 chunk 127 optimal weight: 0.0470 chunk 45 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 0.0470 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.089202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.060483 restraints weight = 36487.684| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.10 r_work: 0.2799 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12491 Z= 0.186 Angle : 0.662 9.230 17131 Z= 0.338 Chirality : 0.041 0.180 1977 Planarity : 0.004 0.059 2035 Dihedral : 18.850 137.050 2188 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.13 % Favored : 92.31 % Rotamer: Outliers : 3.61 % Allowed : 19.05 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.47 (0.23), residues: 1430 helix: 0.53 (0.22), residues: 648 sheet: -0.71 (0.37), residues: 199 loop : -1.02 (0.28), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 467 TYR 0.017 0.002 TYR E 370 PHE 0.011 0.001 PHE C 307 TRP 0.011 0.001 TRP D 191 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (12491) covalent geometry : angle 0.66249 / 0.34 (17131) hydrogen bonds : bond 0.04102 / 2.50 ( 463) hydrogen bonds : angle 4.74179 / 3.38 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8908 (mm-40) REVERT: C 44 GLU cc_start: 0.8761 (pm20) cc_final: 0.8486 (pm20) REVERT: C 145 GLU cc_start: 0.8488 (mp0) cc_final: 0.8170 (mp0) REVERT: C 171 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.9159 (p) REVERT: C 271 HIS cc_start: 0.8279 (t-90) cc_final: 0.7848 (t70) REVERT: C 310 GLN cc_start: 0.9446 (mm-40) cc_final: 0.9189 (mm-40) REVERT: C 370 TYR cc_start: 0.8448 (t80) cc_final: 0.8150 (t80) REVERT: C 391 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7352 (tt) REVERT: C 397 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9297 (mp) REVERT: C 449 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9274 (pp) REVERT: C 455 MET cc_start: 0.8724 (tpt) cc_final: 0.8440 (ttt) REVERT: D 213 SER cc_start: 0.9125 (m) cc_final: 0.8444 (p) REVERT: D 259 PHE cc_start: 0.7837 (t80) cc_final: 0.7546 (t80) REVERT: D 313 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9063 (mm-30) REVERT: D 345 MET cc_start: 0.8503 (ptm) cc_final: 0.8289 (tmm) REVERT: D 380 ASP cc_start: 0.9416 (OUTLIER) cc_final: 0.9098 (m-30) REVERT: D 417 MET cc_start: 0.9463 (mmm) cc_final: 0.8957 (mmt) REVERT: D 455 MET cc_start: 0.9352 (mmm) cc_final: 0.9024 (tpt) REVERT: E 39 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9040 (mt-10) REVERT: E 227 MET cc_start: 0.9397 (mtp) cc_final: 0.9195 (mpp) outliers start: 44 outliers final: 27 residues processed: 134 average time/residue: 0.0785 time to fit residues: 16.7125 Evaluate side-chains 127 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 474 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.089288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.060616 restraints weight = 36314.703| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.10 r_work: 0.2797 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12491 Z= 0.177 Angle : 0.679 15.401 17131 Z= 0.341 Chirality : 0.042 0.363 1977 Planarity : 0.004 0.057 2035 Dihedral : 18.881 136.620 2188 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.13 % Favored : 92.31 % Rotamer: Outliers : 3.61 % Allowed : 19.21 % Favored : 77.18 % 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 are not related in a simple way. whole: -0.46 (0.23), residues: 1430 helix: 0.54 (0.22), residues: 648 sheet: -0.66 (0.37), residues: 211 loop : -1.04 (0.28), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 253 TYR 0.018 0.002 TYR C 187 PHE 0.011 0.001 PHE C 307 TRP 0.010 0.001 TRP D 191 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (12491) covalent geometry : angle 0.67865 / 0.34 (17131) hydrogen bonds : bond 0.03913 / 2.37 ( 463) hydrogen bonds : angle 4.69641 / 3.35 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 94 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8916 (mm-40) REVERT: C 44 GLU cc_start: 0.8733 (pm20) cc_final: 0.8472 (pm20) REVERT: C 145 GLU cc_start: 0.8540 (mp0) cc_final: 0.8214 (mp0) REVERT: C 171 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9152 (p) REVERT: C 187 TYR cc_start: 0.8302 (m-80) cc_final: 0.7965 (m-80) REVERT: C 271 HIS cc_start: 0.8263 (t-90) cc_final: 0.7569 (t-90) REVERT: C 310 GLN cc_start: 0.9448 (mm-40) cc_final: 0.9186 (mm-40) REVERT: C 370 TYR cc_start: 0.8474 (t80) cc_final: 0.8172 (t80) REVERT: C 391 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7419 (tt) REVERT: C 397 ILE cc_start: 0.9502 (OUTLIER) cc_final: 0.9295 (mp) REVERT: C 449 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9293 (pp) REVERT: C 455 MET cc_start: 0.8712 (tpt) cc_final: 0.8457 (ttt) REVERT: D 213 SER cc_start: 0.9115 (m) cc_final: 0.8402 (p) REVERT: D 259 PHE cc_start: 0.7820 (t80) cc_final: 0.7541 (t80) REVERT: D 313 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9112 (mm-30) REVERT: D 317 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8607 (tm-30) REVERT: D 380 ASP cc_start: 0.9428 (OUTLIER) cc_final: 0.9128 (m-30) REVERT: D 417 MET cc_start: 0.9458 (mmm) cc_final: 0.8775 (mmt) REVERT: D 455 MET cc_start: 0.9358 (mmm) cc_final: 0.9035 (tpt) REVERT: E 39 GLU cc_start: 0.9394 (mt-10) cc_final: 0.9028 (mt-10) REVERT: E 95 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8812 (mt0) REVERT: E 227 MET cc_start: 0.9400 (mtp) cc_final: 0.9195 (mpp) outliers start: 44 outliers final: 29 residues processed: 131 average time/residue: 0.0829 time to fit residues: 16.6985 Evaluate side-chains 131 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 474 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 130 HIS E 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.089441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.060486 restraints weight = 36338.576| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.12 r_work: 0.2804 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12491 Z= 0.150 Angle : 0.668 15.281 17131 Z= 0.335 Chirality : 0.041 0.187 1977 Planarity : 0.004 0.057 2035 Dihedral : 18.890 136.815 2188 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.06 % Favored : 92.45 % Rotamer: Outliers : 3.28 % Allowed : 19.62 % Favored : 77.09 % 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 are not related in a simple way. whole: -0.42 (0.24), residues: 1430 helix: 0.55 (0.22), residues: 649 sheet: -0.77 (0.36), residues: 225 loop : -0.93 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 253 TYR 0.018 0.002 TYR E 370 PHE 0.012 0.001 PHE C 307 TRP 0.009 0.001 TRP D 191 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (12491) covalent geometry : angle 0.66843 / 0.34 (17131) hydrogen bonds : bond 0.03739 / 2.26 ( 463) hydrogen bonds : angle 4.63396 / 3.31 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8935 (mm-40) REVERT: C 44 GLU cc_start: 0.8743 (pm20) cc_final: 0.8471 (pm20) REVERT: C 145 GLU cc_start: 0.8574 (mp0) cc_final: 0.8237 (mp0) REVERT: C 187 TYR cc_start: 0.8331 (m-80) cc_final: 0.7997 (m-80) REVERT: C 271 HIS cc_start: 0.8267 (t-90) cc_final: 0.7573 (t-90) REVERT: C 310 GLN cc_start: 0.9455 (mm-40) cc_final: 0.9198 (mm-40) REVERT: C 370 TYR cc_start: 0.8473 (t80) cc_final: 0.8167 (t80) REVERT: C 391 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7371 (tt) REVERT: C 397 ILE cc_start: 0.9501 (OUTLIER) cc_final: 0.9292 (mp) REVERT: C 417 MET cc_start: 0.9145 (mmm) cc_final: 0.8566 (mmm) REVERT: C 449 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9301 (pp) REVERT: C 455 MET cc_start: 0.8698 (tpt) cc_final: 0.8429 (ttt) REVERT: D 103 ASN cc_start: 0.9361 (OUTLIER) cc_final: 0.8529 (t0) REVERT: D 213 SER cc_start: 0.9105 (m) cc_final: 0.8392 (p) REVERT: D 259 PHE cc_start: 0.7793 (t80) cc_final: 0.7526 (t80) REVERT: D 313 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9074 (mm-30) REVERT: D 317 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8607 (tm-30) REVERT: D 345 MET cc_start: 0.8508 (ptm) cc_final: 0.8123 (tmm) REVERT: D 370 TYR cc_start: 0.8917 (t80) cc_final: 0.8709 (t80) REVERT: D 380 ASP cc_start: 0.9420 (OUTLIER) cc_final: 0.9136 (m-30) REVERT: D 417 MET cc_start: 0.9456 (mmm) cc_final: 0.8968 (mmt) REVERT: D 455 MET cc_start: 0.9374 (mmm) cc_final: 0.9051 (tpt) REVERT: E 39 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9014 (mt-10) REVERT: E 227 MET cc_start: 0.9397 (mtp) cc_final: 0.9195 (mpp) outliers start: 40 outliers final: 24 residues processed: 129 average time/residue: 0.0850 time to fit residues: 17.0518 Evaluate side-chains 130 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 474 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 7 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 0.0170 chunk 86 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 127 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 overall best weight: 1.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 418 HIS E 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.089477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.060577 restraints weight = 36239.698| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.11 r_work: 0.2807 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12491 Z= 0.149 Angle : 0.672 14.551 17131 Z= 0.335 Chirality : 0.041 0.300 1977 Planarity : 0.004 0.057 2035 Dihedral : 18.893 137.533 2188 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.34 % Favored : 92.17 % Rotamer: Outliers : 2.96 % Allowed : 20.03 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.35 (0.24), residues: 1430 helix: 0.61 (0.22), residues: 648 sheet: -0.72 (0.36), residues: 225 loop : -0.90 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 253 TYR 0.021 0.002 TYR E 370 PHE 0.012 0.001 PHE C 307 TRP 0.009 0.001 TRP D 191 HIS 0.004 0.001 HIS E 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (12491) covalent geometry : angle 0.67197 / 0.33 (17131) hydrogen bonds : bond 0.03639 / 2.22 ( 463) hydrogen bonds : angle 4.58220 / 3.27 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8947 (mm-40) REVERT: C 44 GLU cc_start: 0.8754 (pm20) cc_final: 0.8458 (pm20) REVERT: C 145 GLU cc_start: 0.8590 (mp0) cc_final: 0.8238 (mp0) REVERT: C 187 TYR cc_start: 0.8358 (m-80) cc_final: 0.8136 (m-80) REVERT: C 271 HIS cc_start: 0.8278 (t-90) cc_final: 0.7595 (t-90) REVERT: C 310 GLN cc_start: 0.9454 (mm-40) cc_final: 0.9209 (mm-40) REVERT: C 370 TYR cc_start: 0.8482 (t80) cc_final: 0.8180 (t80) REVERT: C 391 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7343 (tt) REVERT: C 397 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9286 (mp) REVERT: C 417 MET cc_start: 0.9081 (mmm) cc_final: 0.8536 (mmm) REVERT: C 449 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9307 (pp) REVERT: C 455 MET cc_start: 0.8619 (tpt) cc_final: 0.8359 (ttt) REVERT: D 103 ASN cc_start: 0.9361 (OUTLIER) cc_final: 0.8557 (t0) REVERT: D 213 SER cc_start: 0.9107 (m) cc_final: 0.8401 (p) REVERT: D 259 PHE cc_start: 0.7765 (t80) cc_final: 0.7511 (t80) REVERT: D 313 GLU cc_start: 0.9334 (mm-30) cc_final: 0.9104 (mm-30) REVERT: D 345 MET cc_start: 0.8470 (ptm) cc_final: 0.8127 (tmm) REVERT: D 370 TYR cc_start: 0.8907 (t80) cc_final: 0.8699 (t80) REVERT: D 380 ASP cc_start: 0.9404 (OUTLIER) cc_final: 0.9128 (m-30) REVERT: D 417 MET cc_start: 0.9450 (mmm) cc_final: 0.9012 (mmt) REVERT: D 455 MET cc_start: 0.9387 (mmm) cc_final: 0.9069 (tpt) REVERT: E 39 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9037 (mt-10) outliers start: 36 outliers final: 25 residues processed: 130 average time/residue: 0.0906 time to fit residues: 18.4083 Evaluate side-chains 128 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 474 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 62 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 30 optimal weight: 0.0270 chunk 10 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.089628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.061036 restraints weight = 36279.238| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 4.11 r_work: 0.2817 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12491 Z= 0.138 Angle : 0.685 15.627 17131 Z= 0.342 Chirality : 0.041 0.215 1977 Planarity : 0.004 0.056 2035 Dihedral : 18.882 137.621 2188 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.85 % Favored : 92.66 % Rotamer: Outliers : 2.55 % Allowed : 20.77 % Favored : 76.68 % 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 are not related in a simple way. whole: -0.24 (0.24), residues: 1430 helix: 0.69 (0.22), residues: 644 sheet: -0.66 (0.36), residues: 225 loop : -0.82 (0.29), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 260 TYR 0.022 0.002 TYR E 370 PHE 0.012 0.001 PHE C 307 TRP 0.009 0.002 TRP E 191 HIS 0.003 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (12491) covalent geometry : angle 0.68535 / 0.34 (17131) hydrogen bonds : bond 0.03529 / 2.15 ( 463) hydrogen bonds : angle 4.55087 / 3.25 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8943 (mm-40) REVERT: C 44 GLU cc_start: 0.8754 (pm20) cc_final: 0.8437 (pm20) REVERT: C 145 GLU cc_start: 0.8588 (mp0) cc_final: 0.8226 (mp0) REVERT: C 187 TYR cc_start: 0.8321 (m-80) cc_final: 0.8107 (m-80) REVERT: C 271 HIS cc_start: 0.8277 (t-90) cc_final: 0.7559 (t-90) REVERT: C 310 GLN cc_start: 0.9455 (mm-40) cc_final: 0.9208 (mm-40) REVERT: C 370 TYR cc_start: 0.8471 (t80) cc_final: 0.8170 (t80) REVERT: C 391 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7350 (tt) REVERT: C 397 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9288 (mp) REVERT: C 417 MET cc_start: 0.9049 (mmm) cc_final: 0.8530 (mmm) REVERT: C 449 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9300 (pp) REVERT: C 455 MET cc_start: 0.8603 (tpt) cc_final: 0.8357 (ttt) REVERT: D 103 ASN cc_start: 0.9354 (OUTLIER) cc_final: 0.8566 (t0) REVERT: D 213 SER cc_start: 0.9092 (m) cc_final: 0.8370 (p) REVERT: D 259 PHE cc_start: 0.7733 (t80) cc_final: 0.7493 (t80) REVERT: D 313 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9121 (mm-30) REVERT: D 317 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8580 (tm-30) REVERT: D 345 MET cc_start: 0.8430 (ptm) cc_final: 0.8109 (tmm) REVERT: D 380 ASP cc_start: 0.9386 (OUTLIER) cc_final: 0.9124 (m-30) REVERT: D 417 MET cc_start: 0.9456 (mmm) cc_final: 0.9022 (mmt) REVERT: D 455 MET cc_start: 0.9402 (mmm) cc_final: 0.9084 (tpt) REVERT: E 39 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9045 (mt-10) REVERT: E 478 MET cc_start: 0.8837 (ttm) cc_final: 0.8350 (mtp) outliers start: 31 outliers final: 25 residues processed: 126 average time/residue: 0.0883 time to fit residues: 17.3289 Evaluate side-chains 127 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 11 optimal weight: 0.2980 chunk 124 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.0040 chunk 120 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.089778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.060908 restraints weight = 36073.231| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.12 r_work: 0.2816 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 12491 Z= 0.236 Angle : 0.919 59.200 17131 Z= 0.508 Chirality : 0.041 0.181 1977 Planarity : 0.004 0.056 2035 Dihedral : 18.889 137.624 2188 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.99 % Favored : 92.52 % Rotamer: Outliers : 2.96 % Allowed : 20.61 % Favored : 76.44 % Cbeta Deviations : 0.07 % 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 are not related in a simple way. whole: -0.24 (0.24), residues: 1430 helix: 0.70 (0.22), residues: 644 sheet: -0.66 (0.36), residues: 225 loop : -0.84 (0.29), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 260 TYR 0.018 0.002 TYR E 370 PHE 0.012 0.001 PHE C 307 TRP 0.009 0.001 TRP E 191 HIS 0.002 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.24 (12491) covalent geometry : angle 0.91935 / 0.51 (17131) hydrogen bonds : bond 0.03525 / 2.15 ( 463) hydrogen bonds : angle 4.54825 / 3.25 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3000.16 seconds wall clock time: 52 minutes 9.65 seconds (3129.65 seconds total)