Starting phenix.real_space_refine on Sun Apr 5 18:51:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u9j_63966/04_2026/9u9j_63966.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u9j_63966/04_2026/9u9j_63966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u9j_63966/04_2026/9u9j_63966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u9j_63966/04_2026/9u9j_63966.map" model { file = "/net/cci-nas-00/data/ceres_data/9u9j_63966/04_2026/9u9j_63966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u9j_63966/04_2026/9u9j_63966.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.052 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: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 7856 2.51 5 N 2074 2.21 5 O 2240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12243 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4128 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 497} Chain breaks: 6 Chain: "E" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 4014 Classifications: {'peptide': 498} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 479} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2993 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 358} Chain breaks: 5 Chain: "S" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1108 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 4 Time building chain proxies: 2.82, per 1000 atoms: 0.23 Number of scatterers: 12243 At special positions: 0 Unit cell: (95.68, 125.84, 118.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 2240 8.00 N 2074 7.00 C 7856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 442.1 milliseconds 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2916 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 6 sheets defined 58.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 28 through 42 removed outlier: 4.035A pdb=" N GLN B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 55 removed outlier: 4.014A pdb=" N MET B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 54 " --> pdb=" O PHE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 76 removed outlier: 3.987A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Proline residue: B 80 - end of helix removed outlier: 3.761A pdb=" N LEU B 84 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.663A pdb=" N GLY B 103 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 removed outlier: 4.207A pdb=" N ASN B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.592A pdb=" N VAL B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 145 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 removed outlier: 3.817A pdb=" N ASN B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 removed outlier: 4.180A pdb=" N VAL B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 183 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 Processing helix chain 'B' and resid 211 through 223 Processing helix chain 'B' and resid 229 through 241 Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 248 through 263 removed outlier: 3.912A pdb=" N VAL B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 286 removed outlier: 4.047A pdb=" N GLY B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Proline residue: B 280 - end of helix removed outlier: 3.694A pdb=" N SER B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 304 Processing helix chain 'B' and resid 308 through 319 removed outlier: 4.142A pdb=" N PHE B 311 " --> pdb=" O PRO B 308 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER B 313 " --> pdb=" O HIS B 310 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 314 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR B 315 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS B 316 " --> pdb=" O SER B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 344 through 357 removed outlier: 4.075A pdb=" N VAL B 348 " --> pdb=" O ASN B 344 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 376 Processing helix chain 'B' and resid 380 through 393 removed outlier: 3.932A pdb=" N LEU B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 412 removed outlier: 3.943A pdb=" N GLN B 403 " --> pdb=" O THR B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 423 Processing helix chain 'B' and resid 424 through 430 removed outlier: 4.785A pdb=" N GLU B 427 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLU B 428 " --> pdb=" O GLY B 425 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 430 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.861A pdb=" N GLN B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 462 Processing helix chain 'B' and resid 470 through 486 Processing helix chain 'B' and resid 491 through 505 removed outlier: 3.764A pdb=" N GLU B 504 " --> pdb=" O TYR B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 523 Processing helix chain 'B' and resid 526 through 532 Processing helix chain 'B' and resid 552 through 558 removed outlier: 4.372A pdb=" N TRP B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER B 558 " --> pdb=" O ASN B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 568 Processing helix chain 'E' and resid 116 through 124 removed outlier: 3.943A pdb=" N SER E 121 " --> pdb=" O TYR E 117 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 164 through 174 Proline residue: E 171 - end of helix removed outlier: 3.615A pdb=" N GLU E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 removed outlier: 4.012A pdb=" N ARG E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 206 Processing helix chain 'E' and resid 219 through 234 Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.857A pdb=" N LYS E 241 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP E 242 " --> pdb=" O GLY E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 256 Processing helix chain 'E' and resid 274 through 285 Processing helix chain 'E' and resid 288 through 305 removed outlier: 3.949A pdb=" N SER E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ASP E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG E 305 " --> pdb=" O GLU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 325 removed outlier: 3.601A pdb=" N TYR E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 336 Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.592A pdb=" N PHE E 344 " --> pdb=" O CYS E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 367 removed outlier: 3.860A pdb=" N TYR E 362 " --> pdb=" O LYS E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 380 removed outlier: 6.152A pdb=" N MET E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N THR E 377 " --> pdb=" O GLN E 373 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 400 removed outlier: 4.344A pdb=" N LYS E 390 " --> pdb=" O ASP E 386 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG E 391 " --> pdb=" O PRO E 387 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLU E 392 " --> pdb=" O ILE E 388 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E 397 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG E 399 " --> pdb=" O GLU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 420 Processing helix chain 'E' and resid 424 through 439 removed outlier: 3.854A pdb=" N ASN E 428 " --> pdb=" O TYR E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 457 removed outlier: 3.526A pdb=" N THR E 450 " --> pdb=" O TRP E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 476 Processing helix chain 'E' and resid 482 through 500 removed outlier: 3.553A pdb=" N GLN E 486 " --> pdb=" O THR E 482 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP E 500 " --> pdb=" O LEU E 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 522 Processing helix chain 'E' and resid 523 through 525 No H-bonds generated for 'chain 'E' and resid 523 through 525' Processing helix chain 'E' and resid 530 through 543 removed outlier: 3.773A pdb=" N LEU E 540 " --> pdb=" O LYS E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 565 removed outlier: 3.918A pdb=" N GLN E 564 " --> pdb=" O LYS E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 578 removed outlier: 3.887A pdb=" N GLU E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 599 removed outlier: 3.668A pdb=" N HIS E 589 " --> pdb=" O CYS E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 607 Processing helix chain 'M' and resid 27 through 32 removed outlier: 4.028A pdb=" N GLU M 31 " --> pdb=" O ARG M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 40 removed outlier: 4.064A pdb=" N THR M 38 " --> pdb=" O TYR M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 93 removed outlier: 3.565A pdb=" N TYR M 93 " --> pdb=" O LEU M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 106 Processing helix chain 'M' and resid 106 through 117 removed outlier: 3.925A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU M 117 " --> pdb=" O LEU M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 131 removed outlier: 3.655A pdb=" N LEU M 130 " --> pdb=" O SER M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 268 Processing helix chain 'S' and resid 26 through 42 Processing helix chain 'S' and resid 76 through 95 Processing helix chain 'S' and resid 99 through 106 removed outlier: 3.833A pdb=" N ASN S 106 " --> pdb=" O ASP S 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 118 removed outlier: 4.333A pdb=" N VAL S 110 " --> pdb=" O ASN S 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 144 Processing sheet with id=AA1, first strand: chain 'M' and resid 55 through 58 Processing sheet with id=AA2, first strand: chain 'M' and resid 252 through 255 removed outlier: 6.317A pdb=" N THR M 280 " --> pdb=" O LEU M 216 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU M 216 " --> pdb=" O THR M 280 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N MET M 282 " --> pdb=" O ILE M 214 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE M 188 " --> pdb=" O LYS M 217 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N VAL M 187 " --> pdb=" O VAL M 440 " (cutoff:3.500A) removed outlier: 11.173A pdb=" N HIS M 442 " --> pdb=" O VAL M 187 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N LEU M 189 " --> pdb=" O HIS M 442 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N SER M 444 " --> pdb=" O LEU M 189 " (cutoff:3.500A) removed outlier: 10.087A pdb=" N VAL M 191 " --> pdb=" O SER M 444 " (cutoff:3.500A) removed outlier: 10.443A pdb=" N SER M 446 " --> pdb=" O VAL M 191 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N GLU M 193 " --> pdb=" O SER M 446 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ALA M 448 " --> pdb=" O GLU M 193 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU M 195 " --> pdb=" O ALA M 448 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL M 450 " --> pdb=" O LEU M 195 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL M 197 " --> pdb=" O VAL M 450 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N HIS M 445 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU M 411 " --> pdb=" O HIS M 445 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP M 447 " --> pdb=" O PHE M 409 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE M 409 " --> pdb=" O ASP M 447 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER M 406 " --> pdb=" O LEU M 332 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU M 332 " --> pdb=" O SER M 406 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER M 408 " --> pdb=" O VAL M 330 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL M 330 " --> pdb=" O SER M 408 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLN M 326 " --> pdb=" O PRO M 412 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 260 through 263 removed outlier: 5.687A pdb=" N LEU M 261 " --> pdb=" O ARG M 271 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG M 271 " --> pdb=" O LEU M 261 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU M 263 " --> pdb=" O ILE M 269 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE M 269 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU M 272 " --> pdb=" O MET M 226 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET M 226 " --> pdb=" O LEU M 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 297 through 299 Processing sheet with id=AA5, first strand: chain 'M' and resid 302 through 303 removed outlier: 3.893A pdb=" N GLU M 346 " --> pdb=" O LEU M 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 14 through 17 removed outlier: 6.142A pdb=" N MET S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER S 17 " --> pdb=" O PHE S 5 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE S 5 " --> pdb=" O SER S 17 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE S 4 " --> pdb=" O GLY S 70 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL S 8 " --> pdb=" O PHE S 66 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3983 1.35 - 1.46: 2695 1.46 - 1.58: 5678 1.58 - 1.70: 0 1.70 - 1.82: 113 Bond restraints: 12469 Sorted by residual: bond pdb=" N PRO E 442 " pdb=" CD PRO E 442 " ideal model delta sigma weight residual 1.473 1.550 -0.077 1.40e-02 5.10e+03 3.02e+01 bond pdb=" N PRO B 124 " pdb=" CD PRO B 124 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.18e+01 bond pdb=" C GLN B 123 " pdb=" N PRO B 124 " ideal model delta sigma weight residual 1.332 1.363 -0.030 8.90e-03 1.26e+04 1.15e+01 bond pdb=" N ARG B 35 " pdb=" CA ARG B 35 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.19e-02 7.06e+03 6.12e+00 bond pdb=" N ARG E 231 " pdb=" CA ARG E 231 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.20e-02 6.94e+03 4.55e+00 ... (remaining 12464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 16646 2.78 - 5.56: 190 5.56 - 8.35: 25 8.35 - 11.13: 7 11.13 - 13.91: 2 Bond angle restraints: 16870 Sorted by residual: angle pdb=" N ASP M 43 " pdb=" CA ASP M 43 " pdb=" C ASP M 43 " ideal model delta sigma weight residual 113.28 127.19 -13.91 1.22e+00 6.72e-01 1.30e+02 angle pdb=" N ASP M 43 " pdb=" CA ASP M 43 " pdb=" CB ASP M 43 " ideal model delta sigma weight residual 110.46 99.75 10.71 1.57e+00 4.06e-01 4.65e+01 angle pdb=" N PRO B 124 " pdb=" CA PRO B 124 " pdb=" C PRO B 124 " ideal model delta sigma weight residual 114.80 106.52 8.28 1.42e+00 4.96e-01 3.40e+01 angle pdb=" C ALA E 441 " pdb=" CA ALA E 441 " pdb=" CB ALA E 441 " ideal model delta sigma weight residual 110.17 120.93 -10.76 1.97e+00 2.58e-01 2.98e+01 angle pdb=" C GLN B 123 " pdb=" CA GLN B 123 " pdb=" CB GLN B 123 " ideal model delta sigma weight residual 110.17 101.02 9.15 1.97e+00 2.58e-01 2.16e+01 ... (remaining 16865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6756 17.94 - 35.88: 658 35.88 - 53.82: 124 53.82 - 71.76: 29 71.76 - 89.70: 10 Dihedral angle restraints: 7577 sinusoidal: 3094 harmonic: 4483 Sorted by residual: dihedral pdb=" CD ARG B 35 " pdb=" NE ARG B 35 " pdb=" CZ ARG B 35 " pdb=" NH1 ARG B 35 " ideal model delta sinusoidal sigma weight residual 0.00 -53.40 53.40 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CD ARG E 231 " pdb=" NE ARG E 231 " pdb=" CZ ARG E 231 " pdb=" NH1 ARG E 231 " ideal model delta sinusoidal sigma weight residual 0.00 51.27 -51.27 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" C ALA E 441 " pdb=" N ALA E 441 " pdb=" CA ALA E 441 " pdb=" CB ALA E 441 " ideal model delta harmonic sigma weight residual -122.60 -135.91 13.31 0 2.50e+00 1.60e-01 2.83e+01 ... (remaining 7574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1796 0.078 - 0.156: 155 0.156 - 0.234: 5 0.234 - 0.312: 3 0.312 - 0.390: 2 Chirality restraints: 1961 Sorted by residual: chirality pdb=" CA ALA E 441 " pdb=" N ALA E 441 " pdb=" C ALA E 441 " pdb=" CB ALA E 441 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA GLU S 125 " pdb=" N GLU S 125 " pdb=" C GLU S 125 " pdb=" CB GLU S 125 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA SER B 433 " pdb=" N SER B 433 " pdb=" C SER B 433 " pdb=" CB SER B 433 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1958 not shown) Planarity restraints: 2134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 35 " -0.877 9.50e-02 1.11e+02 3.93e-01 9.37e+01 pdb=" NE ARG B 35 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG B 35 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 35 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 35 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 231 " -0.865 9.50e-02 1.11e+02 3.88e-01 9.12e+01 pdb=" NE ARG E 231 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG E 231 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG E 231 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 231 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 441 " -0.103 5.00e-02 4.00e+02 1.52e-01 3.69e+01 pdb=" N PRO E 442 " 0.262 5.00e-02 4.00e+02 pdb=" CA PRO E 442 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO E 442 " -0.074 5.00e-02 4.00e+02 ... (remaining 2131 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 774 2.73 - 3.27: 14241 3.27 - 3.81: 20475 3.81 - 4.36: 24989 4.36 - 4.90: 38625 Nonbonded interactions: 99104 Sorted by model distance: nonbonded pdb=" O LYS E 358 " pdb=" OG1 THR E 361 " model vdw 2.185 3.040 nonbonded pdb=" O ARG B 38 " pdb=" OG1 THR B 41 " model vdw 2.188 3.040 nonbonded pdb=" OD1 ASP B 342 " pdb=" OH TYR B 378 " model vdw 2.201 3.040 nonbonded pdb=" NZ LYS M 18 " pdb=" OD1 ASP M 114 " model vdw 2.226 3.120 nonbonded pdb=" OE2 GLU M 193 " pdb=" OH TYR M 284 " model vdw 2.230 3.040 ... (remaining 99099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.170 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.003 0.077 12469 Z= 0.160 Angle : 0.772 13.911 16870 Z= 0.408 Chirality : 0.046 0.390 1961 Planarity : 0.013 0.393 2134 Dihedral : 14.995 89.697 4661 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.89 % Favored : 87.58 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.22), residues: 1489 helix: -0.50 (0.19), residues: 766 sheet: -0.82 (0.51), residues: 119 loop : -2.45 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 130 TYR 0.015 0.001 TYR E 265 PHE 0.027 0.002 PHE M 77 TRP 0.010 0.001 TRP E 272 HIS 0.006 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00304 (12469) covalent geometry : angle 0.77189 (16870) hydrogen bonds : bond 0.18057 ( 567) hydrogen bonds : angle 7.19811 ( 1656) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 459 ASP cc_start: 0.8993 (m-30) cc_final: 0.8743 (m-30) REVERT: E 146 ASN cc_start: 0.8364 (m-40) cc_final: 0.7974 (m-40) REVERT: E 294 LEU cc_start: 0.8746 (mt) cc_final: 0.8469 (mt) REVERT: E 295 MET cc_start: 0.9064 (mmp) cc_final: 0.8742 (mmm) REVERT: E 426 ILE cc_start: 0.8967 (pt) cc_final: 0.8656 (pt) REVERT: E 466 ILE cc_start: 0.8357 (mp) cc_final: 0.8106 (mp) REVERT: M 13 ASP cc_start: 0.8269 (p0) cc_final: 0.8045 (p0) REVERT: M 16 ILE cc_start: 0.8265 (mm) cc_final: 0.8060 (mm) REVERT: M 110 TYR cc_start: 0.7981 (m-80) cc_final: 0.7702 (m-80) REVERT: M 328 LEU cc_start: 0.9054 (tt) cc_final: 0.8706 (tt) REVERT: M 329 ASN cc_start: 0.9193 (m110) cc_final: 0.8976 (m110) REVERT: S 117 MET cc_start: 0.8735 (mmp) cc_final: 0.8487 (tpp) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1025 time to fit residues: 44.1316 Evaluate side-chains 229 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.0670 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.0370 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.116032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.083084 restraints weight = 38702.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.085650 restraints weight = 24641.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.087402 restraints weight = 17919.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.088587 restraints weight = 14288.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.089483 restraints weight = 12139.676| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12469 Z= 0.145 Angle : 0.659 8.223 16870 Z= 0.339 Chirality : 0.043 0.220 1961 Planarity : 0.005 0.076 2134 Dihedral : 5.126 74.225 1654 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.28 % Favored : 88.31 % Rotamer: Outliers : 0.22 % Allowed : 6.10 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.22), residues: 1489 helix: -0.24 (0.19), residues: 786 sheet: -0.91 (0.51), residues: 117 loop : -2.43 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 130 TYR 0.016 0.001 TYR B 69 PHE 0.018 0.002 PHE E 578 TRP 0.006 0.001 TRP M 363 HIS 0.007 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00313 (12469) covalent geometry : angle 0.65855 (16870) hydrogen bonds : bond 0.04275 ( 567) hydrogen bonds : angle 5.65084 ( 1656) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 287 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.9361 (ppp) cc_final: 0.9121 (ppp) REVERT: B 330 LEU cc_start: 0.9524 (tt) cc_final: 0.8902 (tt) REVERT: B 334 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8036 (pm20) REVERT: B 355 TYR cc_start: 0.6471 (t80) cc_final: 0.6149 (t80) REVERT: E 146 ASN cc_start: 0.8378 (m-40) cc_final: 0.8004 (m-40) REVERT: E 294 LEU cc_start: 0.8865 (mt) cc_final: 0.8612 (mt) REVERT: E 295 MET cc_start: 0.8979 (mmp) cc_final: 0.8750 (mmm) REVERT: E 415 GLU cc_start: 0.8898 (mp0) cc_final: 0.8645 (mp0) REVERT: E 426 ILE cc_start: 0.8989 (pt) cc_final: 0.8744 (pt) REVERT: M 13 ASP cc_start: 0.8268 (p0) cc_final: 0.8008 (p0) REVERT: M 36 LYS cc_start: 0.8889 (tptp) cc_final: 0.8681 (tppt) REVERT: M 77 PHE cc_start: 0.8329 (m-80) cc_final: 0.8039 (m-80) REVERT: M 303 GLN cc_start: 0.7786 (mp10) cc_final: 0.7413 (mp10) REVERT: M 328 LEU cc_start: 0.9125 (tt) cc_final: 0.8708 (tt) REVERT: M 329 ASN cc_start: 0.9201 (m110) cc_final: 0.8977 (m110) REVERT: S 105 PHE cc_start: 0.8213 (m-80) cc_final: 0.7884 (m-80) REVERT: S 130 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8109 (mmm160) outliers start: 3 outliers final: 0 residues processed: 288 average time/residue: 0.0959 time to fit residues: 41.2834 Evaluate side-chains 225 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 129 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.0170 chunk 10 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 0.0980 overall best weight: 0.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 HIS E 374 HIS E 384 HIS E 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.117619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084550 restraints weight = 38957.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.087261 restraints weight = 24618.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.089060 restraints weight = 17657.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.090327 restraints weight = 13997.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.091155 restraints weight = 11820.397| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12469 Z= 0.123 Angle : 0.657 9.048 16870 Z= 0.331 Chirality : 0.042 0.244 1961 Planarity : 0.005 0.068 2134 Dihedral : 5.031 70.899 1654 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.01 % Favored : 88.58 % Rotamer: Outliers : 0.15 % Allowed : 5.16 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.22), residues: 1489 helix: -0.14 (0.19), residues: 779 sheet: -1.08 (0.47), residues: 134 loop : -2.37 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 399 TYR 0.020 0.001 TYR S 81 PHE 0.018 0.001 PHE M 6 TRP 0.006 0.001 TRP E 553 HIS 0.005 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00262 (12469) covalent geometry : angle 0.65706 (16870) hydrogen bonds : bond 0.03878 ( 567) hydrogen bonds : angle 5.44196 ( 1656) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 303 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9561 (tmt170) cc_final: 0.9242 (tpt90) REVERT: B 104 LEU cc_start: 0.9075 (mt) cc_final: 0.8850 (mt) REVERT: B 253 MET cc_start: 0.8364 (ptp) cc_final: 0.8164 (mtm) REVERT: B 355 TYR cc_start: 0.6336 (t80) cc_final: 0.5906 (t80) REVERT: E 146 ASN cc_start: 0.8411 (m-40) cc_final: 0.8039 (m-40) REVERT: E 294 LEU cc_start: 0.8841 (mt) cc_final: 0.8589 (mt) REVERT: E 295 MET cc_start: 0.8932 (mmp) cc_final: 0.8648 (mmm) REVERT: E 466 ILE cc_start: 0.8346 (mp) cc_final: 0.8064 (mp) REVERT: M 13 ASP cc_start: 0.8281 (p0) cc_final: 0.7929 (p0) REVERT: M 16 ILE cc_start: 0.8018 (mm) cc_final: 0.7813 (mm) REVERT: M 36 LYS cc_start: 0.8879 (tptp) cc_final: 0.8649 (tppt) REVERT: M 77 PHE cc_start: 0.8165 (m-80) cc_final: 0.7870 (m-80) REVERT: M 110 TYR cc_start: 0.8115 (m-80) cc_final: 0.7892 (m-80) REVERT: M 303 GLN cc_start: 0.7740 (mp10) cc_final: 0.7479 (mp10) REVERT: S 130 ARG cc_start: 0.8893 (mmm160) cc_final: 0.7995 (mmm160) outliers start: 2 outliers final: 1 residues processed: 303 average time/residue: 0.1003 time to fit residues: 44.9659 Evaluate side-chains 228 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 120 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 62 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.116976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.083554 restraints weight = 39536.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.086179 restraints weight = 24730.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.088009 restraints weight = 17875.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.089274 restraints weight = 14172.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.090137 restraints weight = 11968.717| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12469 Z= 0.129 Angle : 0.655 8.178 16870 Z= 0.332 Chirality : 0.042 0.221 1961 Planarity : 0.004 0.052 2134 Dihedral : 4.985 70.908 1654 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.62 % Favored : 87.98 % Rotamer: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.22), residues: 1489 helix: -0.10 (0.19), residues: 778 sheet: -1.08 (0.48), residues: 126 loop : -2.35 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 399 TYR 0.014 0.001 TYR B 69 PHE 0.024 0.001 PHE S 87 TRP 0.007 0.001 TRP M 363 HIS 0.016 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00282 (12469) covalent geometry : angle 0.65468 (16870) hydrogen bonds : bond 0.03678 ( 567) hydrogen bonds : angle 5.36253 ( 1656) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9587 (tmt170) cc_final: 0.9258 (tpt90) REVERT: B 104 LEU cc_start: 0.9125 (mt) cc_final: 0.8880 (mt) REVERT: B 355 TYR cc_start: 0.6724 (t80) cc_final: 0.6375 (t80) REVERT: E 145 THR cc_start: 0.8512 (t) cc_final: 0.8202 (t) REVERT: E 146 ASN cc_start: 0.8210 (m-40) cc_final: 0.7837 (m-40) REVERT: E 151 CYS cc_start: 0.7756 (t) cc_final: 0.7249 (t) REVERT: E 294 LEU cc_start: 0.8906 (mt) cc_final: 0.8649 (mt) REVERT: E 295 MET cc_start: 0.8977 (mmp) cc_final: 0.8707 (mmm) REVERT: E 466 ILE cc_start: 0.8425 (mp) cc_final: 0.8160 (mp) REVERT: M 13 ASP cc_start: 0.8283 (p0) cc_final: 0.7926 (p0) REVERT: M 18 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8204 (mtpt) REVERT: M 72 GLU cc_start: 0.5751 (pm20) cc_final: 0.5442 (pm20) REVERT: M 77 PHE cc_start: 0.8290 (m-80) cc_final: 0.7927 (m-80) REVERT: M 303 GLN cc_start: 0.7804 (mp10) cc_final: 0.7515 (mp10) REVERT: M 328 LEU cc_start: 0.9249 (tt) cc_final: 0.8783 (tt) REVERT: M 329 ASN cc_start: 0.9320 (m110) cc_final: 0.9108 (m110) REVERT: S 17 SER cc_start: 0.8468 (p) cc_final: 0.8172 (t) REVERT: S 130 ARG cc_start: 0.8925 (mmm160) cc_final: 0.8026 (mmm160) outliers start: 1 outliers final: 0 residues processed: 295 average time/residue: 0.1002 time to fit residues: 43.9967 Evaluate side-chains 231 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 1 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 111 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.117494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.084610 restraints weight = 39420.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.087277 restraints weight = 24912.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.089071 restraints weight = 17961.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.090263 restraints weight = 14237.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.091213 restraints weight = 12075.835| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12469 Z= 0.124 Angle : 0.669 9.296 16870 Z= 0.334 Chirality : 0.042 0.225 1961 Planarity : 0.004 0.053 2134 Dihedral : 4.938 69.497 1654 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.55 % Favored : 88.05 % Rotamer: Outliers : 0.15 % Allowed : 3.56 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.22), residues: 1489 helix: -0.06 (0.19), residues: 776 sheet: -1.21 (0.45), residues: 136 loop : -2.31 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 399 TYR 0.013 0.001 TYR B 69 PHE 0.041 0.002 PHE B 405 TRP 0.007 0.001 TRP M 363 HIS 0.010 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00270 (12469) covalent geometry : angle 0.66926 (16870) hydrogen bonds : bond 0.03480 ( 567) hydrogen bonds : angle 5.27062 ( 1656) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9565 (tmt170) cc_final: 0.9238 (tpt90) REVERT: B 104 LEU cc_start: 0.9071 (mt) cc_final: 0.8823 (mt) REVERT: B 355 TYR cc_start: 0.6631 (t80) cc_final: 0.6417 (t80) REVERT: E 145 THR cc_start: 0.8510 (t) cc_final: 0.8184 (t) REVERT: E 146 ASN cc_start: 0.8294 (m-40) cc_final: 0.7936 (m-40) REVERT: E 193 TYR cc_start: 0.8463 (t80) cc_final: 0.7760 (t80) REVERT: E 283 LEU cc_start: 0.9367 (tt) cc_final: 0.8968 (mt) REVERT: E 294 LEU cc_start: 0.8881 (mt) cc_final: 0.8590 (mt) REVERT: E 295 MET cc_start: 0.8928 (mmp) cc_final: 0.8669 (mmm) REVERT: E 466 ILE cc_start: 0.8328 (mp) cc_final: 0.8127 (mp) REVERT: M 13 ASP cc_start: 0.8243 (p0) cc_final: 0.7880 (p0) REVERT: M 18 LYS cc_start: 0.8676 (ttmt) cc_final: 0.8235 (mtpp) REVERT: M 72 GLU cc_start: 0.5931 (pm20) cc_final: 0.5553 (pm20) REVERT: M 303 GLN cc_start: 0.7850 (mp10) cc_final: 0.7545 (mp10) REVERT: M 328 LEU cc_start: 0.9220 (tt) cc_final: 0.8719 (tt) REVERT: M 329 ASN cc_start: 0.9320 (m110) cc_final: 0.9114 (m110) REVERT: S 17 SER cc_start: 0.8513 (p) cc_final: 0.8228 (t) outliers start: 2 outliers final: 0 residues processed: 299 average time/residue: 0.0916 time to fit residues: 40.9421 Evaluate side-chains 232 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 60 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.116957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.083553 restraints weight = 39583.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086131 restraints weight = 25391.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.087915 restraints weight = 18564.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.089153 restraints weight = 14782.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.089893 restraints weight = 12557.413| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12469 Z= 0.139 Angle : 0.677 10.009 16870 Z= 0.342 Chirality : 0.043 0.235 1961 Planarity : 0.005 0.053 2134 Dihedral : 4.977 70.477 1654 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.35 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.22), residues: 1489 helix: -0.17 (0.19), residues: 779 sheet: -1.21 (0.45), residues: 136 loop : -2.30 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 130 TYR 0.013 0.001 TYR E 416 PHE 0.029 0.002 PHE E 123 TRP 0.007 0.001 TRP M 363 HIS 0.007 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00308 (12469) covalent geometry : angle 0.67678 (16870) hydrogen bonds : bond 0.03673 ( 567) hydrogen bonds : angle 5.30750 ( 1656) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9579 (tmt170) cc_final: 0.9268 (tpt90) REVERT: B 104 LEU cc_start: 0.9095 (mt) cc_final: 0.8843 (mt) REVERT: B 334 GLU cc_start: 0.8930 (tt0) cc_final: 0.8065 (tm-30) REVERT: E 146 ASN cc_start: 0.8238 (m-40) cc_final: 0.7797 (m110) REVERT: E 151 CYS cc_start: 0.7775 (t) cc_final: 0.7320 (t) REVERT: E 283 LEU cc_start: 0.9333 (tt) cc_final: 0.8980 (mt) REVERT: E 294 LEU cc_start: 0.8892 (mt) cc_final: 0.8592 (mt) REVERT: E 295 MET cc_start: 0.9009 (mmp) cc_final: 0.8751 (mmm) REVERT: M 13 ASP cc_start: 0.8317 (p0) cc_final: 0.7934 (p0) REVERT: M 18 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8493 (mtpt) REVERT: M 72 GLU cc_start: 0.6072 (pm20) cc_final: 0.5616 (pm20) REVERT: M 110 TYR cc_start: 0.8171 (m-80) cc_final: 0.7928 (m-80) REVERT: M 303 GLN cc_start: 0.7907 (mp10) cc_final: 0.7603 (mp10) REVERT: M 328 LEU cc_start: 0.9230 (tt) cc_final: 0.8740 (tt) REVERT: S 17 SER cc_start: 0.8423 (p) cc_final: 0.8165 (t) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.0920 time to fit residues: 40.1215 Evaluate side-chains 229 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 84 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 0.0570 chunk 59 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 6 optimal weight: 0.0470 chunk 85 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.119257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085681 restraints weight = 39076.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.088455 restraints weight = 24809.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090281 restraints weight = 17886.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.091639 restraints weight = 14187.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.092460 restraints weight = 11973.820| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12469 Z= 0.124 Angle : 0.693 10.995 16870 Z= 0.341 Chirality : 0.043 0.231 1961 Planarity : 0.005 0.056 2134 Dihedral : 4.950 66.430 1654 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.01 % Favored : 88.58 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.22), residues: 1489 helix: -0.12 (0.19), residues: 776 sheet: -0.97 (0.47), residues: 129 loop : -2.31 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 206 TYR 0.015 0.001 TYR B 355 PHE 0.030 0.002 PHE S 87 TRP 0.008 0.001 TRP E 553 HIS 0.005 0.001 HIS M 61 Details of bonding type rmsd covalent geometry : bond 0.00267 (12469) covalent geometry : angle 0.69334 (16870) hydrogen bonds : bond 0.03540 ( 567) hydrogen bonds : angle 5.23182 ( 1656) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9552 (tmt170) cc_final: 0.9238 (tpt90) REVERT: B 104 LEU cc_start: 0.9098 (mt) cc_final: 0.8827 (mt) REVERT: B 334 GLU cc_start: 0.9008 (tt0) cc_final: 0.8131 (tm-30) REVERT: E 146 ASN cc_start: 0.8305 (m-40) cc_final: 0.7868 (m110) REVERT: E 283 LEU cc_start: 0.9336 (tt) cc_final: 0.8970 (mt) REVERT: E 294 LEU cc_start: 0.8871 (mt) cc_final: 0.8562 (mt) REVERT: E 295 MET cc_start: 0.8924 (mmp) cc_final: 0.8686 (mmm) REVERT: M 13 ASP cc_start: 0.8258 (p0) cc_final: 0.7899 (p0) REVERT: M 18 LYS cc_start: 0.8860 (ttmm) cc_final: 0.8578 (mtpt) REVERT: M 72 GLU cc_start: 0.5923 (pm20) cc_final: 0.5473 (pm20) REVERT: M 110 TYR cc_start: 0.8135 (m-80) cc_final: 0.7911 (m-80) REVERT: M 303 GLN cc_start: 0.7889 (mp10) cc_final: 0.7553 (mp10) REVERT: S 13 GLN cc_start: 0.7126 (mt0) cc_final: 0.6868 (tm-30) REVERT: S 17 SER cc_start: 0.8363 (p) cc_final: 0.8088 (t) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.0928 time to fit residues: 41.5784 Evaluate side-chains 229 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 40 optimal weight: 0.6980 chunk 129 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 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 = 0.4028 r_free = 0.4028 target = 0.117399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.083652 restraints weight = 39999.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.086312 restraints weight = 25469.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.088136 restraints weight = 18557.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.089432 restraints weight = 14805.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.090251 restraints weight = 12531.758| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12469 Z= 0.141 Angle : 0.703 10.673 16870 Z= 0.350 Chirality : 0.044 0.218 1961 Planarity : 0.004 0.055 2134 Dihedral : 4.963 68.460 1654 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.42 % Favored : 88.18 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.22), residues: 1489 helix: -0.21 (0.19), residues: 785 sheet: -1.15 (0.45), residues: 136 loop : -2.31 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 130 TYR 0.017 0.001 TYR E 416 PHE 0.019 0.002 PHE S 83 TRP 0.008 0.001 TRP M 363 HIS 0.006 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00314 (12469) covalent geometry : angle 0.70251 (16870) hydrogen bonds : bond 0.03526 ( 567) hydrogen bonds : angle 5.33820 ( 1656) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9581 (tmt170) cc_final: 0.9279 (tpt90) REVERT: B 204 LEU cc_start: 0.9762 (mm) cc_final: 0.9536 (pp) REVERT: B 222 LEU cc_start: 0.9452 (mt) cc_final: 0.9244 (mm) REVERT: B 334 GLU cc_start: 0.9014 (tt0) cc_final: 0.8175 (tm-30) REVERT: E 146 ASN cc_start: 0.8324 (m-40) cc_final: 0.7921 (m110) REVERT: E 272 TRP cc_start: 0.3245 (m-10) cc_final: 0.1807 (m-10) REVERT: E 283 LEU cc_start: 0.9340 (tt) cc_final: 0.8986 (mt) REVERT: E 294 LEU cc_start: 0.8876 (mt) cc_final: 0.8580 (mt) REVERT: E 295 MET cc_start: 0.9006 (mmp) cc_final: 0.8568 (mmm) REVERT: E 415 GLU cc_start: 0.8681 (pm20) cc_final: 0.8421 (mp0) REVERT: E 462 MET cc_start: 0.7302 (ptt) cc_final: 0.6871 (ptt) REVERT: E 466 ILE cc_start: 0.8334 (mp) cc_final: 0.8125 (mp) REVERT: E 514 MET cc_start: 0.8273 (mmp) cc_final: 0.8019 (mmp) REVERT: M 13 ASP cc_start: 0.8324 (p0) cc_final: 0.7939 (p0) REVERT: M 18 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8603 (mtpt) REVERT: M 72 GLU cc_start: 0.6252 (pm20) cc_final: 0.5765 (pm20) REVERT: M 110 TYR cc_start: 0.8183 (m-80) cc_final: 0.7933 (m-80) REVERT: M 328 LEU cc_start: 0.9238 (tt) cc_final: 0.8997 (tt) REVERT: S 13 GLN cc_start: 0.7087 (mt0) cc_final: 0.6744 (tm-30) REVERT: S 17 SER cc_start: 0.8382 (p) cc_final: 0.8117 (t) REVERT: S 105 PHE cc_start: 0.7722 (m-10) cc_final: 0.7351 (m-80) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.0979 time to fit residues: 42.6531 Evaluate side-chains 232 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 112 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.117722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.083829 restraints weight = 39708.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.086508 restraints weight = 25224.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.088318 restraints weight = 18394.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.089537 restraints weight = 14681.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.090485 restraints weight = 12535.703| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12469 Z= 0.138 Angle : 0.718 11.657 16870 Z= 0.354 Chirality : 0.043 0.229 1961 Planarity : 0.005 0.055 2134 Dihedral : 5.025 69.136 1654 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.89 % Favored : 87.78 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.22), residues: 1489 helix: -0.21 (0.19), residues: 778 sheet: -0.92 (0.47), residues: 129 loop : -2.33 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 206 TYR 0.020 0.001 TYR M 93 PHE 0.026 0.002 PHE S 87 TRP 0.006 0.001 TRP E 553 HIS 0.011 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00308 (12469) covalent geometry : angle 0.71763 (16870) hydrogen bonds : bond 0.03559 ( 567) hydrogen bonds : angle 5.32788 ( 1656) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9577 (tmt170) cc_final: 0.9267 (tpt90) REVERT: B 204 LEU cc_start: 0.9749 (mm) cc_final: 0.9528 (pp) REVERT: B 334 GLU cc_start: 0.9005 (tt0) cc_final: 0.8196 (tm-30) REVERT: E 146 ASN cc_start: 0.8330 (m-40) cc_final: 0.8006 (m-40) REVERT: E 151 CYS cc_start: 0.7733 (t) cc_final: 0.7293 (t) REVERT: E 272 TRP cc_start: 0.3294 (m-10) cc_final: 0.1833 (m-10) REVERT: E 283 LEU cc_start: 0.9332 (tt) cc_final: 0.8967 (mt) REVERT: E 294 LEU cc_start: 0.8862 (mt) cc_final: 0.8563 (mt) REVERT: E 295 MET cc_start: 0.8981 (mmp) cc_final: 0.8536 (mmm) REVERT: E 396 LEU cc_start: 0.9546 (mm) cc_final: 0.8779 (mm) REVERT: E 399 ARG cc_start: 0.9229 (mpp-170) cc_final: 0.8918 (mpp80) REVERT: E 415 GLU cc_start: 0.8666 (pm20) cc_final: 0.8444 (pm20) REVERT: M 13 ASP cc_start: 0.8344 (p0) cc_final: 0.7957 (p0) REVERT: M 18 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8556 (mtpt) REVERT: M 72 GLU cc_start: 0.6318 (pm20) cc_final: 0.5838 (pm20) REVERT: M 110 TYR cc_start: 0.8147 (m-80) cc_final: 0.7936 (m-80) REVERT: M 328 LEU cc_start: 0.9253 (tt) cc_final: 0.9015 (tt) REVERT: S 13 GLN cc_start: 0.7132 (mt0) cc_final: 0.6782 (tm-30) REVERT: S 17 SER cc_start: 0.8393 (p) cc_final: 0.8125 (t) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.0942 time to fit residues: 41.9026 Evaluate side-chains 233 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.117875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.084015 restraints weight = 40069.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.086602 restraints weight = 25365.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.088507 restraints weight = 18536.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.089850 restraints weight = 14646.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.090786 restraints weight = 12346.689| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12469 Z= 0.134 Angle : 0.724 11.983 16870 Z= 0.358 Chirality : 0.044 0.177 1961 Planarity : 0.005 0.059 2134 Dihedral : 5.003 67.927 1654 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.55 % Favored : 88.11 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.22), residues: 1489 helix: -0.24 (0.19), residues: 779 sheet: -0.87 (0.49), residues: 120 loop : -2.33 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG S 130 TYR 0.016 0.001 TYR E 416 PHE 0.020 0.002 PHE S 83 TRP 0.006 0.001 TRP M 363 HIS 0.012 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00300 (12469) covalent geometry : angle 0.72386 (16870) hydrogen bonds : bond 0.03558 ( 567) hydrogen bonds : angle 5.33245 ( 1656) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9574 (tmt170) cc_final: 0.9263 (tpt90) REVERT: B 104 LEU cc_start: 0.9160 (mt) cc_final: 0.8909 (mt) REVERT: B 334 GLU cc_start: 0.9058 (tt0) cc_final: 0.8236 (tm-30) REVERT: E 146 ASN cc_start: 0.8325 (m-40) cc_final: 0.7998 (m-40) REVERT: E 272 TRP cc_start: 0.3222 (m-10) cc_final: 0.2288 (m-10) REVERT: E 283 LEU cc_start: 0.9329 (tt) cc_final: 0.8966 (mt) REVERT: E 294 LEU cc_start: 0.8891 (mt) cc_final: 0.8591 (mt) REVERT: E 295 MET cc_start: 0.8985 (mmp) cc_final: 0.8533 (mmm) REVERT: E 415 GLU cc_start: 0.8652 (pm20) cc_final: 0.8406 (mp0) REVERT: E 426 ILE cc_start: 0.9015 (pt) cc_final: 0.8811 (pt) REVERT: E 432 LYS cc_start: 0.9119 (tptp) cc_final: 0.8836 (tptt) REVERT: M 13 ASP cc_start: 0.8353 (p0) cc_final: 0.7962 (p0) REVERT: M 18 LYS cc_start: 0.8887 (ttmm) cc_final: 0.8579 (mtpt) REVERT: M 72 GLU cc_start: 0.6191 (pm20) cc_final: 0.5713 (pm20) REVERT: M 110 TYR cc_start: 0.8117 (m-80) cc_final: 0.7906 (m-80) REVERT: M 328 LEU cc_start: 0.9233 (tt) cc_final: 0.8987 (tt) REVERT: S 13 GLN cc_start: 0.7142 (mt0) cc_final: 0.6785 (tm-30) REVERT: S 17 SER cc_start: 0.8385 (p) cc_final: 0.8121 (t) REVERT: S 141 MET cc_start: 0.2261 (ptt) cc_final: 0.0317 (mmt) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.0955 time to fit residues: 40.2095 Evaluate side-chains 232 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 38 optimal weight: 9.9990 chunk 140 optimal weight: 0.0870 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 129 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 125 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** 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 = 0.4052 r_free = 0.4052 target = 0.119009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.085778 restraints weight = 38935.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.088372 restraints weight = 24807.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.090201 restraints weight = 18088.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.091424 restraints weight = 14375.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.092367 restraints weight = 12237.611| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12469 Z= 0.127 Angle : 0.736 12.236 16870 Z= 0.358 Chirality : 0.044 0.183 1961 Planarity : 0.005 0.058 2134 Dihedral : 4.960 65.206 1654 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.28 % Favored : 88.38 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.22), residues: 1489 helix: -0.27 (0.19), residues: 778 sheet: -0.85 (0.49), residues: 120 loop : -2.33 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 206 TYR 0.017 0.001 TYR S 59 PHE 0.029 0.002 PHE S 87 TRP 0.007 0.001 TRP E 272 HIS 0.010 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00282 (12469) covalent geometry : angle 0.73571 (16870) hydrogen bonds : bond 0.03512 ( 567) hydrogen bonds : angle 5.29667 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2275.33 seconds wall clock time: 40 minutes 1.65 seconds (2401.65 seconds total)