Starting phenix.real_space_refine on Sat Aug 23 13:03:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rxk_19577/08_2025/8rxk_19577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rxk_19577/08_2025/8rxk_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_2025/8rxk_19577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rxk_19577/08_2025/8rxk_19577.map" model { file = "/net/cci-nas-00/data/ceres_data/8rxk_19577/08_2025/8rxk_19577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rxk_19577/08_2025/8rxk_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-2.0-5787/lib/python3.9/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: 2.29, 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: 0.69 Conformation dependent library (CDL) restraints added in 343.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.36 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: 1.60 Time building geometry restraints manager: 0.90 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: 17007 3.56 - 7.13: 108 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=" C2' ANP C 601 " pdb=" C1' ANP C 601 " pdb=" N9 ANP C 601 " ideal model delta sigma weight residual 112.01 123.79 -11.78 3.00e+00 1.11e-01 1.54e+01 angle pdb=" N ILE D 123 " pdb=" CA ILE D 123 " pdb=" CB ILE D 123 " ideal model delta sigma weight residual 110.50 112.84 -2.34 6.30e-01 2.52e+00 1.38e+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: 10.470 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.340 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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= 0.220 Angle : 0.771 17.814 17131 Z= 0.371 Chirality : 0.045 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 aren 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 covalent geometry : bond 0.00467 (12491) covalent geometry : angle 0.77105 (17131) hydrogen bonds : bond 0.16511 ( 463) hydrogen bonds : angle 7.04753 ( 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 : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 0.0995 time to fit residues: 16.0625 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 : 0.451 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 202 ASN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 HIS C 340 GLN C 448 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 ASN D 406 GLN D 421 GLN D 500 HIS E 271 HIS E 284 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.090993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.062099 restraints weight = 35894.578| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.10 r_work: 0.2826 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12491 Z= 0.171 Angle : 0.706 9.326 17131 Z= 0.361 Chirality : 0.042 0.208 1977 Planarity : 0.005 0.063 2035 Dihedral : 18.763 135.305 2190 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.41 % Favored : 91.89 % Rotamer: Outliers : 2.55 % Allowed : 18.06 % Favored : 79.39 % 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 aren not related in a simple way. whole: -0.69 (0.24), residues: 1430 helix: 0.37 (0.22), residues: 633 sheet: -1.08 (0.34), residues: 240 loop : -0.99 (0.29), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 253 TYR 0.012 0.002 TYR C 187 PHE 0.021 0.002 PHE D 259 TRP 0.014 0.002 TRP E 191 HIS 0.004 0.001 HIS C 272 Details of bonding type rmsd covalent geometry : bond 0.00395 (12491) covalent geometry : angle 0.70564 (17131) hydrogen bonds : bond 0.04566 ( 463) hydrogen bonds : angle 5.31440 ( 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 144 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8872 (mm-40) REVERT: C 145 GLU cc_start: 0.8479 (mp0) cc_final: 0.8235 (mp0) REVERT: C 256 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8401 (mm) REVERT: C 370 TYR cc_start: 0.8389 (t80) cc_final: 0.8103 (t80) REVERT: C 397 ILE cc_start: 0.9517 (OUTLIER) cc_final: 0.9307 (mp) REVERT: D 213 SER cc_start: 0.9018 (m) cc_final: 0.8289 (p) REVERT: D 345 MET cc_start: 0.8511 (ptm) cc_final: 0.8229 (tmm) REVERT: D 380 ASP cc_start: 0.9416 (OUTLIER) cc_final: 0.9041 (m-30) REVERT: D 417 MET cc_start: 0.9291 (mmm) cc_final: 0.8911 (mmt) REVERT: D 455 MET cc_start: 0.9423 (mmm) cc_final: 0.9015 (tpt) REVERT: E 39 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9036 (mt-10) REVERT: E 151 HIS cc_start: 0.7872 (t70) cc_final: 0.7653 (t70) REVERT: E 227 MET cc_start: 0.9434 (mtp) cc_final: 0.9218 (mpp) REVERT: E 370 TYR cc_start: 0.8324 (t80) cc_final: 0.8068 (t80) REVERT: E 448 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8596 (pp30) outliers start: 31 outliers final: 12 residues processed: 135 average time/residue: 0.0821 time to fit residues: 16.8057 Evaluate side-chains 109 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 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 187 TYR Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 448 GLN 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: 7.9990 chunk 126 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN D 500 HIS E 95 GLN E 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.088633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.059912 restraints weight = 36707.336| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.08 r_work: 0.2779 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12491 Z= 0.248 Angle : 0.719 8.698 17131 Z= 0.365 Chirality : 0.042 0.203 1977 Planarity : 0.005 0.065 2035 Dihedral : 18.726 132.642 2190 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.06 % Favored : 92.31 % Rotamer: Outliers : 3.53 % Allowed : 18.23 % Favored : 78.24 % 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 aren not related in a simple way. whole: -0.70 (0.23), residues: 1430 helix: 0.33 (0.22), residues: 645 sheet: -0.99 (0.36), residues: 204 loop : -1.05 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 230 TYR 0.017 0.002 TYR C 187 PHE 0.028 0.002 PHE D 259 TRP 0.012 0.002 TRP D 191 HIS 0.011 0.001 HIS D 500 Details of bonding type rmsd covalent geometry : bond 0.00562 (12491) covalent geometry : angle 0.71932 (17131) hydrogen bonds : bond 0.04601 ( 463) hydrogen bonds : angle 5.13689 ( 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 141 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8918 (mm-40) REVERT: C 39 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8200 (tm-30) REVERT: C 44 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8487 (pm20) REVERT: C 145 GLU cc_start: 0.8561 (mp0) cc_final: 0.8291 (mp0) REVERT: C 256 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8439 (mm) REVERT: C 310 GLN cc_start: 0.9426 (mm-40) cc_final: 0.9115 (mm-40) REVERT: C 370 TYR cc_start: 0.8457 (t80) cc_final: 0.8222 (t80) REVERT: C 397 ILE cc_start: 0.9522 (OUTLIER) cc_final: 0.9312 (mp) REVERT: C 496 LYS cc_start: 0.8949 (tppp) cc_final: 0.8669 (tppp) REVERT: D 1 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8424 (tpt) REVERT: D 213 SER cc_start: 0.9154 (m) cc_final: 0.8486 (p) REVERT: D 313 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9006 (mm-30) REVERT: D 380 ASP cc_start: 0.9438 (OUTLIER) cc_final: 0.9099 (m-30) REVERT: D 417 MET cc_start: 0.9321 (mmm) cc_final: 0.8746 (mmt) REVERT: D 455 MET cc_start: 0.9372 (mmm) cc_final: 0.9029 (tpt) REVERT: E 39 GLU cc_start: 0.9345 (mt-10) cc_final: 0.9021 (mt-10) REVERT: E 227 MET cc_start: 0.9428 (mtp) cc_final: 0.9208 (mpp) REVERT: E 370 TYR cc_start: 0.8466 (t80) cc_final: 0.8159 (t80) outliers start: 43 outliers final: 20 residues processed: 132 average time/residue: 0.0777 time to fit residues: 15.9931 Evaluate side-chains 117 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 112 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 324 ILE Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 42 VAL 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 500 HIS Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 277 VAL 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: 9.9990 chunk 128 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 HIS 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 = 0.3664 r_free = 0.3664 target = 0.088354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.059258 restraints weight = 36448.765| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 4.11 r_work: 0.2773 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12491 Z= 0.219 Angle : 0.674 8.307 17131 Z= 0.345 Chirality : 0.041 0.166 1977 Planarity : 0.004 0.063 2035 Dihedral : 18.752 134.144 2188 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.48 % Favored : 91.96 % Rotamer: Outliers : 3.53 % Allowed : 18.23 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.23), residues: 1430 helix: 0.42 (0.21), residues: 647 sheet: -0.77 (0.37), residues: 199 loop : -1.08 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 253 TYR 0.011 0.002 TYR C 187 PHE 0.017 0.001 PHE D 259 TRP 0.011 0.002 TRP D 191 HIS 0.010 0.001 HIS D 500 Details of bonding type rmsd covalent geometry : bond 0.00501 (12491) covalent geometry : angle 0.67438 (17131) hydrogen bonds : bond 0.04184 ( 463) hydrogen bonds : angle 4.94867 ( 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 142 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8929 (mm-40) REVERT: C 39 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8194 (tm-30) REVERT: C 145 GLU cc_start: 0.8576 (mp0) cc_final: 0.8271 (mp0) REVERT: C 171 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.9124 (p) REVERT: C 187 TYR cc_start: 0.8329 (m-80) cc_final: 0.7974 (m-80) REVERT: C 256 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8415 (mm) REVERT: C 271 HIS cc_start: 0.8166 (t-90) cc_final: 0.7826 (t70) REVERT: C 310 GLN cc_start: 0.9434 (mm-40) cc_final: 0.9169 (mm-40) REVERT: C 370 TYR cc_start: 0.8469 (t80) cc_final: 0.8187 (t80) REVERT: C 397 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9305 (mp) REVERT: C 449 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9301 (pp) REVERT: C 496 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8778 (tppp) REVERT: D 112 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8770 (mp) REVERT: D 213 SER cc_start: 0.9135 (m) cc_final: 0.8473 (p) REVERT: D 313 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9042 (mm-30) REVERT: D 345 MET cc_start: 0.8571 (ptm) cc_final: 0.8296 (tmm) REVERT: D 380 ASP cc_start: 0.9437 (OUTLIER) cc_final: 0.9105 (m-30) REVERT: D 417 MET cc_start: 0.9454 (mmm) cc_final: 0.8986 (mmt) REVERT: D 455 MET cc_start: 0.9364 (mmm) cc_final: 0.9035 (tpt) REVERT: E 39 GLU cc_start: 0.9363 (mt-10) cc_final: 0.8991 (mt-10) REVERT: E 227 MET cc_start: 0.9413 (mtp) cc_final: 0.9195 (mpp) REVERT: E 370 TYR cc_start: 0.8568 (t80) cc_final: 0.8257 (t80) outliers start: 43 outliers final: 22 residues processed: 133 average time/residue: 0.0809 time to fit residues: 16.6873 Evaluate side-chains 125 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 256 LEU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 496 LYS 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 187 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 415 THR 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: 2.9990 chunk 105 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 421 GLN D 130 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 = 0.3689 r_free = 0.3689 target = 0.089420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.060871 restraints weight = 36637.305| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.11 r_work: 0.2809 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2372 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= 0.145 Angle : 0.640 11.010 17131 Z= 0.326 Chirality : 0.040 0.159 1977 Planarity : 0.004 0.065 2035 Dihedral : 18.705 136.656 2188 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.64 % Favored : 92.80 % Rotamer: Outliers : 3.37 % Allowed : 18.88 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.23), residues: 1430 helix: 0.61 (0.22), residues: 651 sheet: -0.62 (0.37), residues: 199 loop : -1.03 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 253 TYR 0.010 0.001 TYR E 495 PHE 0.014 0.001 PHE D 259 TRP 0.011 0.001 TRP E 191 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00337 (12491) covalent geometry : angle 0.63955 (17131) hydrogen bonds : bond 0.03595 ( 463) hydrogen bonds : angle 4.64325 ( 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 146 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8944 (mm-40) REVERT: C 39 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8217 (tm-30) REVERT: C 44 GLU cc_start: 0.8684 (pm20) cc_final: 0.8367 (pm20) REVERT: C 145 GLU cc_start: 0.8596 (mp0) cc_final: 0.8271 (mp0) REVERT: C 187 TYR cc_start: 0.8348 (m-80) cc_final: 0.8078 (m-80) REVERT: C 255 LYS cc_start: 0.8065 (ptmm) cc_final: 0.7618 (ptmm) REVERT: C 256 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8418 (mm) REVERT: C 271 HIS cc_start: 0.8205 (t-90) cc_final: 0.7781 (t70) REVERT: C 310 GLN cc_start: 0.9454 (mm-40) cc_final: 0.9206 (mm-40) REVERT: C 370 TYR cc_start: 0.8484 (t80) cc_final: 0.8172 (t80) REVERT: C 391 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7543 (tt) REVERT: C 397 ILE cc_start: 0.9517 (OUTLIER) cc_final: 0.9309 (mp) REVERT: C 449 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9323 (pp) REVERT: D 1 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8414 (tpt) REVERT: D 213 SER cc_start: 0.9076 (m) cc_final: 0.8379 (p) REVERT: D 345 MET cc_start: 0.8363 (ptm) cc_final: 0.8160 (tmm) REVERT: D 380 ASP cc_start: 0.9429 (OUTLIER) cc_final: 0.9103 (m-30) REVERT: D 417 MET cc_start: 0.9430 (mmm) cc_final: 0.8997 (mmt) REVERT: D 455 MET cc_start: 0.9386 (mmm) cc_final: 0.9042 (tpt) REVERT: D 478 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8835 (ttm) REVERT: E 39 GLU cc_start: 0.9392 (mt-10) cc_final: 0.9041 (mt-10) REVERT: E 95 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8718 (mt0) REVERT: E 370 TYR cc_start: 0.8638 (t80) cc_final: 0.8329 (t80) outliers start: 41 outliers final: 21 residues processed: 134 average time/residue: 0.0726 time to fit residues: 15.5185 Evaluate side-chains 131 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 D residue 1 MET Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 259 PHE 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 D residue 478 MET 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 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: 6.9990 chunk 127 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 84 optimal weight: 0.0170 chunk 7 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.090515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.061775 restraints weight = 36475.770| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.17 r_work: 0.2836 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2617 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= 0.122 Angle : 0.631 11.104 17131 Z= 0.319 Chirality : 0.040 0.225 1977 Planarity : 0.004 0.064 2035 Dihedral : 18.626 138.911 2188 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.50 % Favored : 92.94 % Rotamer: Outliers : 2.96 % Allowed : 19.62 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.24), residues: 1430 helix: 0.89 (0.22), residues: 631 sheet: -0.70 (0.36), residues: 224 loop : -0.80 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 253 TYR 0.009 0.001 TYR C 187 PHE 0.013 0.001 PHE C 307 TRP 0.015 0.001 TRP E 191 HIS 0.003 0.001 HIS C 272 Details of bonding type rmsd covalent geometry : bond 0.00277 (12491) covalent geometry : angle 0.63108 (17131) hydrogen bonds : bond 0.03306 ( 463) hydrogen bonds : angle 4.38782 ( 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 140 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8948 (mm-40) REVERT: C 39 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8214 (tm-30) REVERT: C 44 GLU cc_start: 0.8716 (pm20) cc_final: 0.8374 (pm20) REVERT: C 145 GLU cc_start: 0.8579 (mp0) cc_final: 0.8229 (mp0) REVERT: C 187 TYR cc_start: 0.8351 (m-80) cc_final: 0.8114 (m-80) REVERT: C 255 LYS cc_start: 0.8081 (ptmm) cc_final: 0.7681 (ptmm) REVERT: C 256 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8498 (mm) REVERT: C 271 HIS cc_start: 0.8268 (t-90) cc_final: 0.7450 (t-90) REVERT: C 310 GLN cc_start: 0.9435 (mm-40) cc_final: 0.9186 (mm-40) REVERT: C 370 TYR cc_start: 0.8472 (t80) cc_final: 0.8164 (t80) REVERT: C 391 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7342 (tt) REVERT: C 397 ILE cc_start: 0.9525 (OUTLIER) cc_final: 0.9314 (mp) REVERT: C 417 MET cc_start: 0.9110 (mmm) cc_final: 0.8639 (mmm) REVERT: C 422 MET cc_start: 0.9374 (mmt) cc_final: 0.9136 (mmp) REVERT: C 449 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9328 (pp) REVERT: C 496 LYS cc_start: 0.8888 (tppt) cc_final: 0.8495 (tppt) REVERT: D 1 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8385 (tpt) REVERT: D 103 ASN cc_start: 0.9343 (OUTLIER) cc_final: 0.8537 (t0) REVERT: D 213 SER cc_start: 0.9055 (m) cc_final: 0.8353 (p) REVERT: D 313 GLU cc_start: 0.9335 (mm-30) cc_final: 0.9070 (mm-30) REVERT: D 380 ASP cc_start: 0.9383 (OUTLIER) cc_final: 0.9091 (m-30) REVERT: D 417 MET cc_start: 0.9396 (mmm) cc_final: 0.8977 (mmt) REVERT: D 455 MET cc_start: 0.9419 (mmm) cc_final: 0.9086 (tpt) REVERT: E 39 GLU cc_start: 0.9403 (mt-10) cc_final: 0.9062 (mt-10) REVERT: E 370 TYR cc_start: 0.8688 (t80) cc_final: 0.8351 (t80) outliers start: 36 outliers final: 20 residues processed: 133 average time/residue: 0.0787 time to fit residues: 16.4557 Evaluate side-chains 131 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 256 LEU Chi-restraints excluded: chain C residue 324 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 D residue 1 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 259 PHE 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 397 ILE 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: 5.9990 chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN E 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.088427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.059238 restraints weight = 36262.419| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.17 r_work: 0.2789 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12491 Z= 0.186 Angle : 0.656 11.870 17131 Z= 0.329 Chirality : 0.040 0.267 1977 Planarity : 0.004 0.059 2035 Dihedral : 18.694 137.673 2188 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.92 % Favored : 92.52 % Rotamer: Outliers : 3.04 % Allowed : 19.13 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.24), residues: 1430 helix: 0.94 (0.22), residues: 636 sheet: -0.67 (0.36), residues: 227 loop : -0.81 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 253 TYR 0.009 0.001 TYR C 187 PHE 0.013 0.001 PHE C 307 TRP 0.011 0.002 TRP D 191 HIS 0.003 0.001 HIS C 272 Details of bonding type rmsd covalent geometry : bond 0.00426 (12491) covalent geometry : angle 0.65557 (17131) hydrogen bonds : bond 0.03728 ( 463) hydrogen bonds : angle 4.51092 ( 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 142 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8962 (mm-40) REVERT: C 39 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8229 (tm-30) REVERT: C 44 GLU cc_start: 0.8727 (pm20) cc_final: 0.8463 (pm20) REVERT: C 145 GLU cc_start: 0.8606 (mp0) cc_final: 0.8236 (mp0) REVERT: C 187 TYR cc_start: 0.8412 (m-80) cc_final: 0.8208 (m-80) REVERT: C 255 LYS cc_start: 0.8167 (ptmm) cc_final: 0.7762 (ptmm) REVERT: C 256 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8452 (mm) REVERT: C 271 HIS cc_start: 0.8292 (t-90) cc_final: 0.7768 (t70) REVERT: C 310 GLN cc_start: 0.9435 (mm-40) cc_final: 0.9201 (mm-40) REVERT: C 370 TYR cc_start: 0.8478 (t80) cc_final: 0.8180 (t80) REVERT: C 391 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7451 (tt) REVERT: C 397 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9282 (mp) REVERT: C 422 MET cc_start: 0.9388 (mmt) cc_final: 0.9140 (mmp) REVERT: C 449 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9334 (pp) REVERT: C 496 LYS cc_start: 0.8979 (tppt) cc_final: 0.8623 (tppt) REVERT: D 1 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8423 (tpt) REVERT: D 103 ASN cc_start: 0.9386 (OUTLIER) cc_final: 0.8580 (t0) REVERT: D 213 SER cc_start: 0.9128 (m) cc_final: 0.8418 (p) REVERT: D 313 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9041 (mm-30) REVERT: D 317 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8631 (tm-30) REVERT: D 380 ASP cc_start: 0.9413 (OUTLIER) cc_final: 0.9129 (m-30) REVERT: D 417 MET cc_start: 0.9421 (mmm) cc_final: 0.9009 (mmt) REVERT: D 455 MET cc_start: 0.9384 (mmm) cc_final: 0.9060 (tpt) REVERT: D 478 MET cc_start: 0.9048 (ttm) cc_final: 0.8782 (mtp) REVERT: E 39 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9038 (mt-10) REVERT: E 44 GLU cc_start: 0.6171 (tt0) cc_final: 0.5846 (tt0) REVERT: E 370 TYR cc_start: 0.8694 (t80) cc_final: 0.8346 (t80) REVERT: E 417 MET cc_start: 0.9626 (mmt) cc_final: 0.9298 (mmt) outliers start: 37 outliers final: 23 residues processed: 133 average time/residue: 0.0825 time to fit residues: 16.9509 Evaluate side-chains 135 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 206 ILE 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 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 D residue 1 MET Chi-restraints excluded: chain D residue 40 THR 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 259 PHE 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 47 ASP 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 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: 2.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 113 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.088813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.059632 restraints weight = 36343.215| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 4.19 r_work: 0.2799 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2830 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= 0.162 Angle : 0.661 13.429 17131 Z= 0.331 Chirality : 0.040 0.221 1977 Planarity : 0.004 0.058 2035 Dihedral : 18.728 136.141 2188 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.99 % Favored : 92.52 % 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 aren not related in a simple way. whole: -0.02 (0.24), residues: 1430 helix: 0.97 (0.22), residues: 636 sheet: -0.61 (0.36), residues: 227 loop : -0.79 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 253 TYR 0.009 0.001 TYR C 187 PHE 0.012 0.001 PHE C 307 TRP 0.013 0.002 TRP E 191 HIS 0.003 0.001 HIS C 272 Details of bonding type rmsd covalent geometry : bond 0.00375 (12491) covalent geometry : angle 0.66073 (17131) hydrogen bonds : bond 0.03429 ( 463) hydrogen bonds : angle 4.43251 ( 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 146 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8948 (mm-40) REVERT: C 44 GLU cc_start: 0.8722 (pm20) cc_final: 0.8466 (pm20) REVERT: C 145 GLU cc_start: 0.8614 (mp0) cc_final: 0.8237 (mp0) REVERT: C 255 LYS cc_start: 0.8203 (ptmm) cc_final: 0.7765 (ptmm) REVERT: C 256 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8434 (mm) REVERT: C 271 HIS cc_start: 0.8331 (t-90) cc_final: 0.7805 (t70) REVERT: C 310 GLN cc_start: 0.9421 (mm-40) cc_final: 0.9190 (mm-40) REVERT: C 370 TYR cc_start: 0.8469 (t80) cc_final: 0.8160 (t80) REVERT: C 391 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7423 (tt) REVERT: C 397 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9284 (mp) REVERT: C 417 MET cc_start: 0.9065 (mmm) cc_final: 0.8652 (mmm) REVERT: C 422 MET cc_start: 0.9392 (mmt) cc_final: 0.9147 (mmp) REVERT: C 449 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9348 (pp) REVERT: C 496 LYS cc_start: 0.8928 (tppt) cc_final: 0.8568 (tppt) REVERT: D 1 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8426 (tpt) REVERT: D 44 GLU cc_start: 0.7738 (mp0) cc_final: 0.7398 (mp0) REVERT: D 103 ASN cc_start: 0.9383 (OUTLIER) cc_final: 0.8589 (t0) REVERT: D 213 SER cc_start: 0.9123 (m) cc_final: 0.8427 (p) REVERT: D 313 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9019 (mm-30) REVERT: D 317 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8633 (tm-30) REVERT: D 380 ASP cc_start: 0.9399 (OUTLIER) cc_final: 0.9132 (m-30) REVERT: D 417 MET cc_start: 0.9406 (mmm) cc_final: 0.8974 (mmt) REVERT: D 455 MET cc_start: 0.9394 (mmm) cc_final: 0.9070 (tpt) REVERT: D 478 MET cc_start: 0.9056 (ttm) cc_final: 0.8738 (mtp) REVERT: E 39 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9039 (mt-10) REVERT: E 370 TYR cc_start: 0.8678 (t80) cc_final: 0.8337 (t80) REVERT: E 417 MET cc_start: 0.9630 (mmt) cc_final: 0.9031 (mmt) outliers start: 44 outliers final: 22 residues processed: 138 average time/residue: 0.0759 time to fit residues: 16.4906 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 : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 206 ILE 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 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 D residue 1 MET Chi-restraints excluded: chain D residue 40 THR 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 259 PHE 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 47 ASP 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 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: 0.9990 chunk 1 optimal weight: 4.9990 chunk 27 optimal weight: 0.0870 chunk 86 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 9 optimal weight: 0.0020 chunk 127 optimal weight: 0.6980 chunk 65 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 overall best weight: 0.3646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 272 HIS ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.090612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.061465 restraints weight = 36170.753| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 4.23 r_work: 0.2847 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3052 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= 0.117 Angle : 0.656 14.545 17131 Z= 0.326 Chirality : 0.039 0.156 1977 Planarity : 0.004 0.060 2035 Dihedral : 18.625 137.002 2188 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.36 % Favored : 93.15 % Rotamer: Outliers : 2.38 % Allowed : 19.62 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.24), residues: 1430 helix: 1.12 (0.22), residues: 630 sheet: -0.49 (0.37), residues: 226 loop : -0.68 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 253 TYR 0.014 0.001 TYR C 187 PHE 0.012 0.001 PHE C 307 TRP 0.010 0.001 TRP E 191 HIS 0.004 0.001 HIS C 272 Details of bonding type rmsd covalent geometry : bond 0.00262 (12491) covalent geometry : angle 0.65611 (17131) hydrogen bonds : bond 0.03072 ( 463) hydrogen bonds : angle 4.25623 ( 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 135 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8950 (mm-40) REVERT: C 44 GLU cc_start: 0.8734 (pm20) cc_final: 0.8339 (pm20) REVERT: C 145 GLU cc_start: 0.8577 (mp0) cc_final: 0.8160 (mp0) REVERT: C 255 LYS cc_start: 0.8138 (ptmm) cc_final: 0.7711 (ptmm) REVERT: C 256 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8407 (mm) REVERT: C 271 HIS cc_start: 0.8313 (t-90) cc_final: 0.7564 (t-90) REVERT: C 310 GLN cc_start: 0.9411 (mm-40) cc_final: 0.9180 (mm-40) REVERT: C 370 TYR cc_start: 0.8439 (t80) cc_final: 0.8147 (t80) REVERT: C 391 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7289 (tt) REVERT: C 397 ILE cc_start: 0.9494 (OUTLIER) cc_final: 0.9284 (mp) REVERT: C 417 MET cc_start: 0.9046 (mmm) cc_final: 0.8628 (mmm) REVERT: C 422 MET cc_start: 0.9407 (mmt) cc_final: 0.9167 (mmp) REVERT: C 449 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9347 (pp) REVERT: C 496 LYS cc_start: 0.8871 (tppt) cc_final: 0.8619 (tppt) REVERT: D 1 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8382 (tpt) REVERT: D 103 ASN cc_start: 0.9346 (OUTLIER) cc_final: 0.8586 (t0) REVERT: D 213 SER cc_start: 0.9057 (m) cc_final: 0.8344 (p) REVERT: D 313 GLU cc_start: 0.9326 (mm-30) cc_final: 0.9037 (mm-30) REVERT: D 317 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8620 (tm-30) REVERT: D 380 ASP cc_start: 0.9318 (OUTLIER) cc_final: 0.9067 (m-30) REVERT: D 417 MET cc_start: 0.9371 (mmm) cc_final: 0.9159 (mmt) REVERT: D 422 MET cc_start: 0.9270 (mmm) cc_final: 0.8990 (mmm) REVERT: D 455 MET cc_start: 0.9394 (mmm) cc_final: 0.9132 (tpt) REVERT: E 39 GLU cc_start: 0.9393 (mt-10) cc_final: 0.9036 (mt-10) REVERT: E 370 TYR cc_start: 0.8664 (t80) cc_final: 0.8455 (t80) REVERT: E 417 MET cc_start: 0.9549 (mmt) cc_final: 0.9086 (tpp) outliers start: 29 outliers final: 18 residues processed: 126 average time/residue: 0.0858 time to fit residues: 16.7910 Evaluate side-chains 127 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 206 ILE 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 391 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 259 PHE 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 47 ASP 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 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: 3.9990 chunk 81 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 39 optimal weight: 9.9990 chunk 63 optimal weight: 0.2980 chunk 104 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.089550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.060852 restraints weight = 36369.016| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.18 r_work: 0.2825 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3117 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= 0.143 Angle : 0.660 14.904 17131 Z= 0.328 Chirality : 0.039 0.168 1977 Planarity : 0.004 0.058 2035 Dihedral : 18.641 136.976 2188 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.85 % Favored : 92.73 % Rotamer: Outliers : 2.30 % Allowed : 20.11 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.24), residues: 1430 helix: 1.11 (0.22), residues: 636 sheet: -0.48 (0.37), residues: 227 loop : -0.74 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 253 TYR 0.013 0.001 TYR C 187 PHE 0.012 0.001 PHE C 307 TRP 0.014 0.002 TRP E 191 HIS 0.006 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00331 (12491) covalent geometry : angle 0.66007 (17131) hydrogen bonds : bond 0.03281 ( 463) hydrogen bonds : angle 4.32666 ( 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 132 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8980 (mm-40) REVERT: C 44 GLU cc_start: 0.8780 (pm20) cc_final: 0.8363 (pm20) REVERT: C 145 GLU cc_start: 0.8571 (mp0) cc_final: 0.8149 (mp0) REVERT: C 271 HIS cc_start: 0.8361 (t-90) cc_final: 0.8024 (t-90) REVERT: C 310 GLN cc_start: 0.9403 (mm-40) cc_final: 0.9174 (mm-40) REVERT: C 370 TYR cc_start: 0.8444 (t80) cc_final: 0.8146 (t80) REVERT: C 391 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7429 (tt) REVERT: C 397 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9308 (mp) REVERT: C 422 MET cc_start: 0.9398 (mmt) cc_final: 0.9159 (mmp) REVERT: C 449 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9346 (pp) REVERT: C 496 LYS cc_start: 0.8868 (tppt) cc_final: 0.8624 (tppt) REVERT: D 1 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8397 (tpt) REVERT: D 103 ASN cc_start: 0.9342 (OUTLIER) cc_final: 0.8557 (t0) REVERT: D 213 SER cc_start: 0.9143 (m) cc_final: 0.8456 (p) REVERT: D 260 ARG cc_start: 0.7667 (tpt170) cc_final: 0.7415 (tpt170) REVERT: D 313 GLU cc_start: 0.9335 (mm-30) cc_final: 0.9037 (mm-30) REVERT: D 380 ASP cc_start: 0.9359 (OUTLIER) cc_final: 0.9120 (m-30) REVERT: D 417 MET cc_start: 0.9370 (mmm) cc_final: 0.9007 (mmt) REVERT: D 455 MET cc_start: 0.9391 (mmm) cc_final: 0.9097 (tpt) REVERT: E 39 GLU cc_start: 0.9408 (mt-10) cc_final: 0.9053 (mt-10) REVERT: E 370 TYR cc_start: 0.8655 (t80) cc_final: 0.8441 (t80) REVERT: E 417 MET cc_start: 0.9563 (mmt) cc_final: 0.9167 (mmt) outliers start: 28 outliers final: 18 residues processed: 124 average time/residue: 0.0730 time to fit residues: 14.1885 Evaluate side-chains 126 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 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 485 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 103 ASN 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 47 ASP 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 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 11 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 120 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.090071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061011 restraints weight = 36242.428| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 4.21 r_work: 0.2836 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3242 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= 0.126 Angle : 0.656 14.875 17131 Z= 0.323 Chirality : 0.039 0.173 1977 Planarity : 0.004 0.058 2035 Dihedral : 18.609 134.559 2188 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.36 % Favored : 93.22 % Rotamer: Outliers : 2.46 % Allowed : 20.03 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.24), residues: 1430 helix: 1.13 (0.22), residues: 630 sheet: -0.40 (0.37), residues: 227 loop : -0.68 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 253 TYR 0.013 0.001 TYR C 187 PHE 0.016 0.001 PHE C 307 TRP 0.011 0.001 TRP E 191 HIS 0.004 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00293 (12491) covalent geometry : angle 0.65617 (17131) hydrogen bonds : bond 0.03061 ( 463) hydrogen bonds : angle 4.25280 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2876.15 seconds wall clock time: 50 minutes 6.39 seconds (3006.39 seconds total)