Starting phenix.real_space_refine on Sat Jan 18 12:07:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rxk_19577/01_2025/8rxk_19577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rxk_19577/01_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_19577/01_2025/8rxk_19577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rxk_19577/01_2025/8rxk_19577.map" model { file = "/net/cci-nas-00/data/ceres_data/8rxk_19577/01_2025/8rxk_19577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rxk_19577/01_2025/8rxk_19577.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 9.06, per 1000 atoms: 0.74 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: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 4.06 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: 4.49 Time building geometry restraints manager: 3.62 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: 20.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.670 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 32.230 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.020 ------------------------------------------------------------------------------- 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= 0.264 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.001 TRP E 262 HIS 0.006 0.001 HIS C 272 PHE 0.017 0.001 PHE D 259 TYR 0.009 0.001 TYR C 187 ARG 0.011 0.000 ARG E 452 *********************** 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 : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 0.2485 time to fit residues: 41.2404 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 : 1.367 ------------------------------------------------------------------------------- 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 124 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 0.0370 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 ASN ** 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 = 0.3708 r_free = 0.3708 target = 0.091386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.062489 restraints weight = 35797.039| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 4.10 r_work: 0.2837 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12491 Z= 0.240 Angle : 0.703 9.443 17131 Z= 0.359 Chirality : 0.042 0.214 1977 Planarity : 0.005 0.064 2035 Dihedral : 18.743 135.680 2190 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.06 % Favored : 92.24 % Rotamer: Outliers : 2.46 % Allowed : 18.23 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1430 helix: 0.39 (0.22), residues: 628 sheet: -1.02 (0.34), residues: 237 loop : -1.01 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 191 HIS 0.005 0.001 HIS C 272 PHE 0.021 0.001 PHE D 259 TYR 0.012 0.002 TYR D 187 ARG 0.007 0.001 ARG E 253 *********************** 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 143 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8871 (mm-40) REVERT: C 256 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8257 (mm) REVERT: C 370 TYR cc_start: 0.8382 (t80) cc_final: 0.8106 (t80) REVERT: C 397 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9286 (mp) REVERT: D 213 SER cc_start: 0.8995 (m) cc_final: 0.8266 (p) REVERT: D 345 MET cc_start: 0.8464 (ptm) cc_final: 0.8203 (tmm) REVERT: D 380 ASP cc_start: 0.9412 (OUTLIER) cc_final: 0.9047 (m-30) REVERT: D 417 MET cc_start: 0.9296 (mmm) cc_final: 0.8915 (mmt) REVERT: D 455 MET cc_start: 0.9427 (mmm) cc_final: 0.9119 (tpt) REVERT: E 39 GLU cc_start: 0.9328 (mt-10) cc_final: 0.9033 (mt-10) REVERT: E 151 HIS cc_start: 0.7819 (t70) cc_final: 0.7601 (t70) REVERT: E 227 MET cc_start: 0.9433 (mtp) cc_final: 0.9208 (mpp) REVERT: E 370 TYR cc_start: 0.8328 (t80) cc_final: 0.8099 (t80) REVERT: E 448 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8596 (pp30) outliers start: 30 outliers final: 12 residues processed: 134 average time/residue: 0.2268 time to fit residues: 45.6260 Evaluate side-chains 108 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 89 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 107 optimal weight: 0.0870 chunk 147 optimal weight: 8.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.088185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.059507 restraints weight = 36669.616| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 4.07 r_work: 0.2770 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12491 Z= 0.399 Angle : 0.735 8.443 17131 Z= 0.373 Chirality : 0.042 0.211 1977 Planarity : 0.005 0.064 2035 Dihedral : 18.740 132.501 2190 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.34 % Favored : 92.03 % Rotamer: Outliers : 3.69 % Allowed : 18.14 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1430 helix: 0.30 (0.22), residues: 645 sheet: -0.99 (0.36), residues: 204 loop : -1.06 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 191 HIS 0.019 0.001 HIS D 500 PHE 0.028 0.002 PHE D 259 TYR 0.018 0.002 TYR C 187 ARG 0.002 0.000 ARG C 366 *********************** 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 140 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8914 (mm-40) REVERT: C 145 GLU cc_start: 0.8552 (mp0) cc_final: 0.8275 (mp0) REVERT: C 256 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8483 (mm) REVERT: C 310 GLN cc_start: 0.9436 (mm-40) cc_final: 0.9133 (mm-40) REVERT: C 370 TYR cc_start: 0.8473 (t80) cc_final: 0.8232 (t80) REVERT: C 397 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9303 (mp) REVERT: D 1 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8415 (tpt) REVERT: D 112 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8811 (mp) REVERT: D 213 SER cc_start: 0.9152 (m) cc_final: 0.8488 (p) REVERT: D 313 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9016 (mm-30) REVERT: D 380 ASP cc_start: 0.9439 (OUTLIER) cc_final: 0.9103 (m-30) REVERT: D 417 MET cc_start: 0.9322 (mmm) cc_final: 0.8720 (mmt) REVERT: D 455 MET cc_start: 0.9357 (mmm) cc_final: 0.9023 (tpt) REVERT: E 39 GLU cc_start: 0.9337 (mt-10) cc_final: 0.9005 (mt-10) REVERT: E 227 MET cc_start: 0.9440 (mtp) cc_final: 0.9209 (mpp) REVERT: E 370 TYR cc_start: 0.8480 (t80) cc_final: 0.8184 (t80) outliers start: 45 outliers final: 20 residues processed: 132 average time/residue: 0.2157 time to fit residues: 44.1921 Evaluate side-chains 114 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.431 ------------------------------------------------------------------------------- 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 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 112 LEU 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 22 optimal weight: 0.0970 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3675 r_free = 0.3675 target = 0.088909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.059901 restraints weight = 36138.357| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.11 r_work: 0.2789 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2124 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= 0.267 Angle : 0.655 8.517 17131 Z= 0.334 Chirality : 0.041 0.175 1977 Planarity : 0.004 0.065 2035 Dihedral : 18.715 134.566 2188 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.92 % Favored : 92.52 % Rotamer: Outliers : 3.28 % Allowed : 18.39 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1430 helix: 0.46 (0.21), residues: 650 sheet: -0.70 (0.38), residues: 199 loop : -1.09 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 191 HIS 0.005 0.001 HIS D 500 PHE 0.015 0.001 PHE D 259 TYR 0.016 0.001 TYR C 187 ARG 0.002 0.000 ARG E 253 *********************** 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: 40 poor density : 102 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8931 (mm-40) REVERT: C 44 GLU cc_start: 0.8708 (pm20) cc_final: 0.8364 (pm20) REVERT: C 145 GLU cc_start: 0.8584 (mp0) cc_final: 0.8280 (mp0) REVERT: C 171 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9146 (p) REVERT: C 187 TYR cc_start: 0.8359 (m-80) cc_final: 0.8081 (m-80) REVERT: C 256 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8398 (mm) REVERT: C 271 HIS cc_start: 0.8115 (t-90) cc_final: 0.7778 (t70) REVERT: C 310 GLN cc_start: 0.9440 (mm-40) cc_final: 0.9173 (mm-40) REVERT: C 370 TYR cc_start: 0.8475 (t80) cc_final: 0.8193 (t80) REVERT: C 397 ILE cc_start: 0.9525 (OUTLIER) cc_final: 0.9316 (mp) REVERT: C 449 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9289 (pp) REVERT: C 496 LYS cc_start: 0.8976 (tppp) cc_final: 0.8676 (tppp) REVERT: D 1 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8399 (tpt) REVERT: D 213 SER cc_start: 0.9117 (m) cc_final: 0.8447 (p) REVERT: D 313 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9031 (mm-30) REVERT: D 345 MET cc_start: 0.8472 (ptm) cc_final: 0.8225 (tmm) REVERT: D 370 TYR cc_start: 0.9104 (t80) cc_final: 0.8799 (t80) REVERT: D 380 ASP cc_start: 0.9439 (OUTLIER) cc_final: 0.9111 (m-30) REVERT: D 417 MET cc_start: 0.9449 (mmm) cc_final: 0.8989 (mmt) REVERT: D 455 MET cc_start: 0.9367 (mmm) cc_final: 0.9031 (tpt) REVERT: D 478 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8804 (ttm) REVERT: E 39 GLU cc_start: 0.9381 (mt-10) cc_final: 0.9043 (mt-10) REVERT: E 227 MET cc_start: 0.9418 (mtp) cc_final: 0.9205 (mpp) REVERT: E 370 TYR cc_start: 0.8572 (t80) cc_final: 0.8255 (t80) outliers start: 40 outliers final: 19 residues processed: 133 average time/residue: 0.2153 time to fit residues: 43.7421 Evaluate side-chains 122 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 374 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 371 LEU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 468 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 D 400 ASN E 95 GLN E 198 GLN E 272 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.086612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.058099 restraints weight = 36731.721| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 4.06 r_work: 0.2743 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 12491 Z= 0.458 Angle : 0.736 8.961 17131 Z= 0.374 Chirality : 0.043 0.154 1977 Planarity : 0.005 0.060 2035 Dihedral : 18.898 135.409 2188 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.11 % Favored : 91.33 % Rotamer: Outliers : 4.27 % Allowed : 18.47 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.23), residues: 1430 helix: 0.34 (0.21), residues: 654 sheet: -0.77 (0.37), residues: 200 loop : -1.12 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 191 HIS 0.007 0.001 HIS D 130 PHE 0.018 0.002 PHE D 259 TYR 0.016 0.002 TYR C 187 ARG 0.003 0.000 ARG C 467 *********************** 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 144 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 92 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8979 (mm-40) REVERT: C 145 GLU cc_start: 0.8623 (mp0) cc_final: 0.8283 (mp0) REVERT: C 256 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8445 (mm) REVERT: C 271 HIS cc_start: 0.8332 (t70) cc_final: 0.8109 (t-90) REVERT: C 310 GLN cc_start: 0.9444 (mm-40) cc_final: 0.9193 (mm-40) REVERT: C 370 TYR cc_start: 0.8506 (t80) cc_final: 0.8186 (t80) REVERT: C 391 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7498 (tt) REVERT: C 449 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9318 (pp) REVERT: D 1 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8467 (tpt) REVERT: D 103 ASN cc_start: 0.9401 (OUTLIER) cc_final: 0.8517 (t0) REVERT: D 112 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8876 (mp) REVERT: D 313 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9044 (mm-30) REVERT: D 380 ASP cc_start: 0.9436 (OUTLIER) cc_final: 0.9111 (m-30) REVERT: D 417 MET cc_start: 0.9448 (mmm) cc_final: 0.8999 (mmt) REVERT: D 478 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8819 (ttm) REVERT: E 370 TYR cc_start: 0.8629 (t80) cc_final: 0.8345 (t80) outliers start: 52 outliers final: 26 residues processed: 136 average time/residue: 0.2055 time to fit residues: 43.2679 Evaluate side-chains 121 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ILE 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 374 LEU Chi-restraints excluded: chain C residue 391 LEU 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 1 MET Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 119 VAL 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 232 SER 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 277 VAL 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 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 91 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.088437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.059380 restraints weight = 36472.468| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.14 r_work: 0.2795 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12491 Z= 0.220 Angle : 0.656 13.081 17131 Z= 0.331 Chirality : 0.041 0.289 1977 Planarity : 0.004 0.062 2035 Dihedral : 18.821 137.993 2188 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.71 % Favored : 92.73 % Rotamer: Outliers : 3.12 % Allowed : 19.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1430 helix: 0.62 (0.21), residues: 651 sheet: -0.81 (0.36), residues: 227 loop : -1.03 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 191 HIS 0.003 0.001 HIS C 272 PHE 0.014 0.001 PHE D 259 TYR 0.010 0.001 TYR C 187 ARG 0.003 0.000 ARG E 253 *********************** 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 138 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8972 (mm-40) REVERT: C 44 GLU cc_start: 0.8715 (pm20) cc_final: 0.8423 (pm20) REVERT: C 145 GLU cc_start: 0.8603 (mp0) cc_final: 0.8253 (mp0) REVERT: C 255 LYS cc_start: 0.8056 (ptmm) cc_final: 0.7635 (ptmm) REVERT: C 256 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8436 (mm) REVERT: C 271 HIS cc_start: 0.8250 (t70) cc_final: 0.7982 (t-90) REVERT: C 310 GLN cc_start: 0.9422 (mm-40) cc_final: 0.9175 (mm-40) REVERT: C 370 TYR cc_start: 0.8490 (t80) cc_final: 0.8160 (t80) REVERT: C 449 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9334 (pp) REVERT: D 1 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8448 (tpt) REVERT: D 112 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8707 (mp) REVERT: D 213 SER cc_start: 0.9102 (m) cc_final: 0.8419 (p) REVERT: D 313 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9042 (mm-30) REVERT: D 317 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8593 (tm-30) REVERT: D 345 MET cc_start: 0.8511 (ptm) cc_final: 0.8271 (tmm) REVERT: D 380 ASP cc_start: 0.9455 (OUTLIER) cc_final: 0.9115 (m-30) REVERT: D 417 MET cc_start: 0.9413 (mmm) cc_final: 0.8964 (mmt) REVERT: D 455 MET cc_start: 0.9397 (mmm) cc_final: 0.9108 (tpt) REVERT: D 478 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8771 (ttm) REVERT: E 39 GLU cc_start: 0.9383 (mt-10) cc_final: 0.9016 (mt-10) REVERT: E 370 TYR cc_start: 0.8684 (t80) cc_final: 0.8385 (t80) outliers start: 38 outliers final: 19 residues processed: 130 average time/residue: 0.2201 time to fit residues: 43.7566 Evaluate side-chains 123 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 374 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 112 LEU 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 D residue 478 MET Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 232 SER 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 415 THR Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 474 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.086686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.058220 restraints weight = 36714.381| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 4.07 r_work: 0.2750 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 12491 Z= 0.405 Angle : 0.717 12.876 17131 Z= 0.360 Chirality : 0.042 0.258 1977 Planarity : 0.005 0.056 2035 Dihedral : 18.969 138.386 2188 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.18 % Favored : 91.26 % Rotamer: Outliers : 3.45 % Allowed : 19.62 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.23), residues: 1430 helix: 0.54 (0.21), residues: 653 sheet: -0.69 (0.37), residues: 212 loop : -1.13 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 191 HIS 0.004 0.001 HIS C 488 PHE 0.015 0.001 PHE D 259 TYR 0.012 0.002 TYR C 187 ARG 0.007 0.000 ARG C 467 *********************** 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 137 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 95 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9255 (mm-40) cc_final: 0.8995 (mm-40) REVERT: C 44 GLU cc_start: 0.8730 (pm20) cc_final: 0.8529 (pm20) REVERT: C 145 GLU cc_start: 0.8658 (mp0) cc_final: 0.8269 (mp0) REVERT: C 187 TYR cc_start: 0.8429 (m-80) cc_final: 0.8222 (m-80) REVERT: C 255 LYS cc_start: 0.8128 (ptmm) cc_final: 0.7734 (ptmm) REVERT: C 256 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8482 (mm) REVERT: C 271 HIS cc_start: 0.8393 (t70) cc_final: 0.7920 (t-90) REVERT: C 310 GLN cc_start: 0.9410 (mm-40) cc_final: 0.9175 (mm-40) REVERT: C 370 TYR cc_start: 0.8542 (t80) cc_final: 0.8201 (t80) REVERT: C 449 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9340 (pp) REVERT: D 1 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8474 (tpt) REVERT: D 103 ASN cc_start: 0.9399 (OUTLIER) cc_final: 0.8530 (t0) REVERT: D 112 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8863 (mp) REVERT: D 345 MET cc_start: 0.8707 (ptm) cc_final: 0.8277 (tmm) REVERT: D 380 ASP cc_start: 0.9445 (OUTLIER) cc_final: 0.9106 (m-30) REVERT: D 417 MET cc_start: 0.9432 (mmm) cc_final: 0.9015 (mmt) REVERT: D 455 MET cc_start: 0.9393 (mmm) cc_final: 0.9077 (tpt) REVERT: D 478 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8798 (ttm) REVERT: E 95 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8799 (mt0) REVERT: E 370 TYR cc_start: 0.8689 (t80) cc_final: 0.8446 (t80) REVERT: E 417 MET cc_start: 0.9386 (mmp) cc_final: 0.9123 (mmp) outliers start: 42 outliers final: 23 residues processed: 128 average time/residue: 0.2097 time to fit residues: 41.9422 Evaluate side-chains 125 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 GLN 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 374 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 96 ILE Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 112 LEU 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 35 VAL Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 391 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 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 89 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 55 optimal weight: 0.0970 chunk 125 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 130 optimal weight: 0.3980 chunk 135 optimal weight: 3.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.088553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.059400 restraints weight = 36692.159| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 4.20 r_work: 0.2799 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2907 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= 0.210 Angle : 0.661 13.824 17131 Z= 0.329 Chirality : 0.040 0.196 1977 Planarity : 0.004 0.060 2035 Dihedral : 18.887 139.203 2188 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.08 % Favored : 93.36 % Rotamer: Outliers : 3.04 % Allowed : 20.53 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1430 helix: 0.87 (0.22), residues: 638 sheet: -0.66 (0.37), residues: 226 loop : -0.92 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 191 HIS 0.003 0.001 HIS E 130 PHE 0.012 0.001 PHE C 307 TYR 0.009 0.001 TYR C 187 ARG 0.004 0.000 ARG E 253 *********************** 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 141 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 1.406 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9248 (mm-40) cc_final: 0.9012 (mm-40) REVERT: C 44 GLU cc_start: 0.8753 (pm20) cc_final: 0.8480 (pm20) REVERT: C 145 GLU cc_start: 0.8649 (mp0) cc_final: 0.8273 (mp0) REVERT: C 187 TYR cc_start: 0.8388 (m-80) cc_final: 0.8181 (m-80) REVERT: C 255 LYS cc_start: 0.8110 (ptmm) cc_final: 0.7675 (ptmm) REVERT: C 256 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8411 (mm) REVERT: C 271 HIS cc_start: 0.8357 (t70) cc_final: 0.8036 (t-90) REVERT: C 310 GLN cc_start: 0.9399 (mm-40) cc_final: 0.9173 (mm-40) REVERT: C 370 TYR cc_start: 0.8533 (t80) cc_final: 0.8185 (t80) REVERT: C 417 MET cc_start: 0.9053 (mmm) cc_final: 0.8653 (mmm) REVERT: C 449 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9354 (pp) REVERT: C 467 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7858 (ptp90) REVERT: D 1 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8482 (tpt) REVERT: D 112 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8810 (mp) REVERT: D 213 SER cc_start: 0.9151 (m) cc_final: 0.8482 (p) REVERT: D 313 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9049 (mm-30) REVERT: D 345 MET cc_start: 0.8492 (ptm) cc_final: 0.8249 (tmm) REVERT: D 380 ASP cc_start: 0.9460 (OUTLIER) cc_final: 0.9123 (m-30) REVERT: D 417 MET cc_start: 0.9387 (mmm) cc_final: 0.8982 (mmt) REVERT: D 455 MET cc_start: 0.9429 (mmm) cc_final: 0.9119 (tpt) REVERT: D 478 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8792 (ttm) REVERT: E 39 GLU cc_start: 0.9403 (mt-10) cc_final: 0.9049 (mt-10) REVERT: E 417 MET cc_start: 0.9358 (mmp) cc_final: 0.9113 (mmp) outliers start: 37 outliers final: 21 residues processed: 134 average time/residue: 0.2164 time to fit residues: 44.7731 Evaluate side-chains 125 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 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 449 LEU Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 319 LEU 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 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 415 THR 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 8 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 130 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3663 r_free = 0.3663 target = 0.088423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.059413 restraints weight = 36356.936| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.18 r_work: 0.2802 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12491 Z= 0.223 Angle : 0.688 14.744 17131 Z= 0.339 Chirality : 0.040 0.182 1977 Planarity : 0.005 0.088 2035 Dihedral : 18.843 139.559 2188 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.41 % Favored : 92.10 % Rotamer: Outliers : 2.71 % Allowed : 20.85 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1430 helix: 0.96 (0.22), residues: 638 sheet: -0.55 (0.37), residues: 227 loop : -0.87 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 191 HIS 0.003 0.001 HIS E 151 PHE 0.012 0.001 PHE C 307 TYR 0.009 0.001 TYR C 187 ARG 0.009 0.000 ARG C 467 *********************** 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 136 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9249 (mm-40) cc_final: 0.9019 (mm-40) REVERT: C 44 GLU cc_start: 0.8779 (pm20) cc_final: 0.8492 (pm20) REVERT: C 145 GLU cc_start: 0.8632 (mp0) cc_final: 0.8240 (mp0) REVERT: C 255 LYS cc_start: 0.8115 (ptmm) cc_final: 0.7641 (ptmm) REVERT: C 256 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8399 (mm) REVERT: C 271 HIS cc_start: 0.8372 (t70) cc_final: 0.8051 (t-90) REVERT: C 310 GLN cc_start: 0.9403 (mm-40) cc_final: 0.9186 (mm-40) REVERT: C 370 TYR cc_start: 0.8531 (t80) cc_final: 0.8173 (t80) REVERT: C 449 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9349 (pp) REVERT: D 1 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8466 (tpt) REVERT: D 103 ASN cc_start: 0.9351 (OUTLIER) cc_final: 0.8582 (t0) REVERT: D 112 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8789 (mp) REVERT: D 213 SER cc_start: 0.9170 (m) cc_final: 0.8503 (p) REVERT: D 313 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9040 (mm-30) REVERT: D 345 MET cc_start: 0.8410 (ptm) cc_final: 0.8161 (tmm) REVERT: D 380 ASP cc_start: 0.9455 (OUTLIER) cc_final: 0.9098 (m-30) REVERT: D 417 MET cc_start: 0.9391 (mmm) cc_final: 0.8998 (mmt) REVERT: D 455 MET cc_start: 0.9415 (mmm) cc_final: 0.9092 (tpt) REVERT: D 478 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8819 (ttm) REVERT: E 39 GLU cc_start: 0.9400 (mt-10) cc_final: 0.9042 (mt-10) REVERT: E 370 TYR cc_start: 0.8266 (t80) cc_final: 0.7944 (t80) REVERT: E 417 MET cc_start: 0.9363 (mmp) cc_final: 0.9102 (mmp) outliers start: 33 outliers final: 22 residues processed: 128 average time/residue: 0.2110 time to fit residues: 41.3734 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 : 1.327 ------------------------------------------------------------------------------- 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 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 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 112 LEU 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 163 VAL 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 391 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 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 100 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 84 optimal weight: 0.0020 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3659 r_free = 0.3659 target = 0.088169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.059373 restraints weight = 36223.849| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.15 r_work: 0.2797 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3101 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= 0.250 Angle : 0.691 15.035 17131 Z= 0.340 Chirality : 0.040 0.191 1977 Planarity : 0.004 0.056 2035 Dihedral : 18.869 138.243 2188 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.99 % Favored : 92.59 % Rotamer: Outliers : 2.55 % Allowed : 21.02 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1430 helix: 0.97 (0.22), residues: 638 sheet: -0.51 (0.37), residues: 227 loop : -0.86 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 191 HIS 0.003 0.001 HIS E 151 PHE 0.012 0.001 PHE D 259 TYR 0.011 0.001 TYR C 187 ARG 0.003 0.000 ARG E 253 ********************** 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 137 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 17 GLN cc_start: 0.9253 (mm-40) cc_final: 0.9017 (mm-40) REVERT: C 44 GLU cc_start: 0.8763 (pm20) cc_final: 0.8484 (pm20) REVERT: C 145 GLU cc_start: 0.8621 (mp0) cc_final: 0.8215 (mp0) REVERT: C 255 LYS cc_start: 0.8130 (ptmm) cc_final: 0.7786 (ptmm) REVERT: C 256 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8566 (mm) REVERT: C 271 HIS cc_start: 0.8374 (t70) cc_final: 0.8045 (t-90) REVERT: C 310 GLN cc_start: 0.9403 (mm-40) cc_final: 0.9190 (mm-40) REVERT: C 370 TYR cc_start: 0.8517 (t80) cc_final: 0.8147 (t80) REVERT: C 417 MET cc_start: 0.9052 (mmm) cc_final: 0.8588 (mmm) REVERT: C 422 MET cc_start: 0.9332 (mmm) cc_final: 0.8993 (mmm) REVERT: C 449 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9350 (pp) REVERT: D 1 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8486 (tpt) REVERT: D 103 ASN cc_start: 0.9357 (OUTLIER) cc_final: 0.8583 (t0) REVERT: D 112 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8808 (mp) REVERT: D 213 SER cc_start: 0.9168 (m) cc_final: 0.8487 (p) REVERT: D 313 GLU cc_start: 0.9333 (mm-30) cc_final: 0.9051 (mm-30) REVERT: D 345 MET cc_start: 0.8420 (ptm) cc_final: 0.8160 (tmm) REVERT: D 380 ASP cc_start: 0.9452 (OUTLIER) cc_final: 0.9107 (m-30) REVERT: D 417 MET cc_start: 0.9400 (mmm) cc_final: 0.9008 (mmt) REVERT: D 455 MET cc_start: 0.9391 (mmm) cc_final: 0.9094 (tpt) REVERT: D 478 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8812 (ttm) REVERT: E 39 GLU cc_start: 0.9389 (mt-10) cc_final: 0.9032 (mt-10) REVERT: E 370 TYR cc_start: 0.8325 (t80) cc_final: 0.8020 (t80) REVERT: E 417 MET cc_start: 0.9383 (mmp) cc_final: 0.9130 (mmp) outliers start: 31 outliers final: 22 residues processed: 130 average time/residue: 0.2141 time to fit residues: 42.7117 Evaluate side-chains 130 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 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 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 112 LEU Chi-restraints excluded: chain D residue 319 LEU 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 163 VAL 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 391 LEU Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 474 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 121 optimal weight: 0.0570 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.089080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.060339 restraints weight = 36228.018| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.18 r_work: 0.2819 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3252 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= 0.200 Angle : 0.675 15.135 17131 Z= 0.331 Chirality : 0.040 0.196 1977 Planarity : 0.004 0.058 2035 Dihedral : 18.782 137.915 2188 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.85 % Favored : 92.73 % Rotamer: Outliers : 2.46 % Allowed : 20.69 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1430 helix: 1.05 (0.22), residues: 638 sheet: -0.45 (0.37), residues: 227 loop : -0.82 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 191 HIS 0.003 0.001 HIS E 151 PHE 0.015 0.001 PHE C 307 TYR 0.011 0.001 TYR C 495 ARG 0.003 0.000 ARG E 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6873.37 seconds wall clock time: 123 minutes 24.72 seconds (7404.72 seconds total)