Starting phenix.real_space_refine on Thu Jul 31 23:48:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ogr_12886/07_2025/7ogr_12886.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ogr_12886/07_2025/7ogr_12886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ogr_12886/07_2025/7ogr_12886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ogr_12886/07_2025/7ogr_12886.map" model { file = "/net/cci-nas-00/data/ceres_data/7ogr_12886/07_2025/7ogr_12886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ogr_12886/07_2025/7ogr_12886.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 73 5.16 5 C 9010 2.51 5 N 2432 2.21 5 O 2619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 14135 Number of models: 1 Model: "" Number of chains: 7 Chain: "X" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 160 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "A" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1527 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 11, 'TRANS': 178} Chain breaks: 1 Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1565 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 9, 'TRANS': 187} Chain breaks: 1 Chain: "C" Number of atoms: 4875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4875 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 35, 'TRANS': 576} Chain breaks: 1 Chain: "D" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3023 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 14, 'TRANS': 358} Chain breaks: 2 Chain: "E" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2984 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 16, 'TRANS': 354} Chain breaks: 2 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10491 SG CYS D 288 16.948 82.058 18.253 1.00 82.42 S ATOM 10896 SG CYS D 341 17.363 79.547 21.885 1.00 84.63 S ATOM 10918 SG CYS D 350 19.774 82.408 19.784 1.00 76.18 S ATOM 10939 SG CYS D 353 17.808 83.449 21.085 1.00 67.76 S Time building chain proxies: 8.08, per 1000 atoms: 0.57 Number of scatterers: 14135 At special positions: 0 Unit cell: (107.1, 135.15, 114.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 73 16.00 O 2619 8.00 N 2432 7.00 C 9010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 288 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 341 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 353 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 350 " Number of angles added : 6 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 17 sheets defined 41.5% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'X' and resid 4 through 12 Processing helix chain 'X' and resid 18 through 25 Processing helix chain 'A' and resid 313 through 321 removed outlier: 3.670A pdb=" N GLN A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.664A pdb=" N ASN A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.657A pdb=" N ASN A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 365 Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.604A pdb=" N THR A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.902A pdb=" N ILE A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.604A pdb=" N LEU A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 322 removed outlier: 3.673A pdb=" N ALA B 322 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 337 through 346 removed outlier: 3.544A pdb=" N ILE B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 353 removed outlier: 3.532A pdb=" N THR B 351 " --> pdb=" O CYS B 347 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 367 removed outlier: 3.504A pdb=" N ILE B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 removed outlier: 3.551A pdb=" N PHE B 377 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 378 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 380 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 removed outlier: 3.617A pdb=" N HIS B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.809A pdb=" N MET B 408 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 442 removed outlier: 3.733A pdb=" N GLU B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 4.114A pdb=" N ALA B 465 " --> pdb=" O ILE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 504 through 520 Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.647A pdb=" N MET C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.651A pdb=" N GLU C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.664A pdb=" N LYS C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 193' Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.676A pdb=" N ARG C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 327 removed outlier: 3.629A pdb=" N TYR C 305 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 312 " --> pdb=" O HIS C 308 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 317 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 348 removed outlier: 3.604A pdb=" N ARG C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 422 No H-bonds generated for 'chain 'C' and resid 420 through 422' Processing helix chain 'C' and resid 423 through 428 Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.592A pdb=" N TYR C 434 " --> pdb=" O TYR C 430 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 removed outlier: 3.630A pdb=" N ASN C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER C 468 " --> pdb=" O GLN C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 491 removed outlier: 3.696A pdb=" N VAL C 476 " --> pdb=" O ASN C 472 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR C 478 " --> pdb=" O GLN C 474 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE C 489 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE C 490 " --> pdb=" O PHE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 498 Processing helix chain 'C' and resid 504 through 512 removed outlier: 3.581A pdb=" N VAL C 508 " --> pdb=" O PRO C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 538 Processing helix chain 'C' and resid 634 through 640 Processing helix chain 'C' and resid 643 through 656 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 40 through 49 removed outlier: 3.858A pdb=" N LEU D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 51 No H-bonds generated for 'chain 'D' and resid 50 through 51' Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.658A pdb=" N HIS D 56 " --> pdb=" O PRO D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 67 removed outlier: 3.564A pdb=" N HIS D 66 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS D 67 " --> pdb=" O SER D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 67' Processing helix chain 'D' and resid 92 through 109 removed outlier: 3.536A pdb=" N HIS D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 98 " --> pdb=" O MET D 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 137 removed outlier: 3.665A pdb=" N LEU D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 153 removed outlier: 4.011A pdb=" N ILE D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 150 " --> pdb=" O MET D 146 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 151 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.538A pdb=" N ALA D 161 " --> pdb=" O LYS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.778A pdb=" N VAL D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.515A pdb=" N LEU D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 212 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 261 removed outlier: 4.240A pdb=" N THR D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU D 256 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR D 258 " --> pdb=" O LYS D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 277 removed outlier: 4.170A pdb=" N ASN D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER D 273 " --> pdb=" O PHE D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 removed outlier: 3.606A pdb=" N LYS D 307 " --> pdb=" O LYS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.631A pdb=" N ILE D 359 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 381 removed outlier: 3.828A pdb=" N LYS D 378 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE D 379 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 40 through 53 removed outlier: 3.784A pdb=" N ILE E 52 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 70 through 79 Processing helix chain 'E' and resid 323 through 337 removed outlier: 4.233A pdb=" N ASN E 327 " --> pdb=" O LYS E 323 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS E 331 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN E 337 " --> pdb=" O HIS E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 366 removed outlier: 3.804A pdb=" N LEU E 361 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 removed outlier: 3.523A pdb=" N HIS E 371 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 372 " --> pdb=" O ALA E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 368 through 372' Processing helix chain 'E' and resid 394 through 410 Processing helix chain 'E' and resid 417 through 429 Processing helix chain 'E' and resid 488 through 493 Processing helix chain 'E' and resid 518 through 522 removed outlier: 3.574A pdb=" N GLY E 521 " --> pdb=" O GLY E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 540 Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 300 removed outlier: 7.591A pdb=" N ILE A 404 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 297 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET A 406 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR A 299 " --> pdb=" O MET A 406 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 312 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 395 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 388 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 372 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 296 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 410 through 412 removed outlier: 3.961A pdb=" N TRP B 478 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA4, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'C' and resid 67 through 68 removed outlier: 3.667A pdb=" N VAL C 67 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 111 through 116 removed outlier: 6.672A pdb=" N THR C 98 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL C 78 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE C 100 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 119 through 123 removed outlier: 4.614A pdb=" N HIS C 122 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N PHE C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 188 removed outlier: 6.915A pdb=" N PHE C 185 " --> pdb=" O CYS C 398 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL C 400 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 187 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS C 386 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 198 through 206 removed outlier: 6.374A pdb=" N ARG C 370 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 283 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU C 372 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE C 281 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 374 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 211 through 213 removed outlier: 3.566A pdb=" N VAL C 270 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA C 241 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG C 268 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AB3, first strand: chain 'C' and resid 550 through 552 Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.005A pdb=" N ASN D 4 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLU D 30 " --> pdb=" O ASN D 4 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR D 6 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 39 " --> pdb=" O HIS D 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 294 through 297 removed outlier: 3.517A pdb=" N ALA D 294 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 67 through 68 removed outlier: 3.756A pdb=" N TYR E 96 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AB8, first strand: chain 'E' and resid 144 through 145 removed outlier: 4.199A pdb=" N ILE E 152 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU E 159 " --> pdb=" O ILE E 152 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1275 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: 4.18 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4599 1.34 - 1.46: 3122 1.46 - 1.58: 6606 1.58 - 1.70: 0 1.70 - 1.81: 130 Bond restraints: 14457 Sorted by residual: bond pdb=" N ARG E 541 " pdb=" CA ARG E 541 " ideal model delta sigma weight residual 1.466 1.501 -0.035 1.36e-02 5.41e+03 6.47e+00 bond pdb=" C ASN C 290 " pdb=" N PRO C 291 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.15e+00 bond pdb=" C PHE E 540 " pdb=" N ARG E 541 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.58e-02 4.01e+03 4.08e+00 bond pdb=" C ALA C 141 " pdb=" N PRO C 142 " ideal model delta sigma weight residual 1.337 1.353 -0.016 9.80e-03 1.04e+04 2.67e+00 bond pdb=" CA ASP C 125 " pdb=" CB ASP C 125 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.54e-02 4.22e+03 1.81e+00 ... (remaining 14452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 19180 2.07 - 4.13: 371 4.13 - 6.20: 39 6.20 - 8.26: 10 8.26 - 10.33: 2 Bond angle restraints: 19602 Sorted by residual: angle pdb=" C GLN D 281 " pdb=" N ARG D 282 " pdb=" CA ARG D 282 " ideal model delta sigma weight residual 120.82 127.00 -6.18 1.47e+00 4.63e-01 1.77e+01 angle pdb=" N VAL B 367 " pdb=" CA VAL B 367 " pdb=" C VAL B 367 " ideal model delta sigma weight residual 110.21 105.81 4.40 1.13e+00 7.83e-01 1.52e+01 angle pdb=" CA GLN C 3 " pdb=" CB GLN C 3 " pdb=" CG GLN C 3 " ideal model delta sigma weight residual 114.10 121.62 -7.52 2.00e+00 2.50e-01 1.41e+01 angle pdb=" C ILE C 239 " pdb=" N PHE C 240 " pdb=" CA PHE C 240 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C VAL B 367 " pdb=" N MET B 368 " pdb=" CA MET B 368 " ideal model delta sigma weight residual 122.36 127.57 -5.21 1.42e+00 4.96e-01 1.35e+01 ... (remaining 19597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7854 17.85 - 35.71: 714 35.71 - 53.56: 96 53.56 - 71.41: 12 71.41 - 89.26: 10 Dihedral angle restraints: 8686 sinusoidal: 3500 harmonic: 5186 Sorted by residual: dihedral pdb=" CA ALA A 413 " pdb=" C ALA A 413 " pdb=" N PRO A 414 " pdb=" CA PRO A 414 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PHE E 540 " pdb=" C PHE E 540 " pdb=" N ARG E 541 " pdb=" CA ARG E 541 " ideal model delta harmonic sigma weight residual 180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ARG E 510 " pdb=" C ARG E 510 " pdb=" N LEU E 511 " pdb=" CA LEU E 511 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 8683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1571 0.046 - 0.092: 442 0.092 - 0.137: 141 0.137 - 0.183: 20 0.183 - 0.229: 3 Chirality restraints: 2177 Sorted by residual: chirality pdb=" CA PHE C 240 " pdb=" N PHE C 240 " pdb=" C PHE C 240 " pdb=" CB PHE C 240 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ASN C 290 " pdb=" N ASN C 290 " pdb=" C ASN C 290 " pdb=" CB ASN C 290 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASP C 125 " pdb=" N ASP C 125 " pdb=" C ASP C 125 " pdb=" CB ASP C 125 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 2174 not shown) Planarity restraints: 2515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 540 " -0.037 2.00e-02 2.50e+03 7.19e-02 5.16e+01 pdb=" C PHE E 540 " 0.124 2.00e-02 2.50e+03 pdb=" O PHE E 540 " -0.047 2.00e-02 2.50e+03 pdb=" N ARG E 541 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 141 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO C 142 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 255 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO C 256 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 256 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 256 " 0.033 5.00e-02 4.00e+02 ... (remaining 2512 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4292 2.83 - 3.35: 11704 3.35 - 3.86: 22749 3.86 - 4.38: 26495 4.38 - 4.90: 45733 Nonbonded interactions: 110973 Sorted by model distance: nonbonded pdb=" OE1 GLU D 166 " pdb=" OG1 THR D 168 " model vdw 2.309 3.040 nonbonded pdb=" O ALA D 161 " pdb=" OG SER D 176 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR C 434 " pdb=" O ILE D 236 " model vdw 2.343 3.040 nonbonded pdb=" OH TYR C 82 " pdb=" O ILE C 281 " model vdw 2.347 3.040 nonbonded pdb=" OH TYR B 480 " pdb=" O PRO B 483 " model vdw 2.355 3.040 ... (remaining 110968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.580 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 0.110 14461 Z= 0.165 Angle : 0.841 44.328 19608 Z= 0.403 Chirality : 0.048 0.229 2177 Planarity : 0.006 0.072 2515 Dihedral : 13.646 89.265 5340 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.14), residues: 1749 helix: -3.84 (0.10), residues: 700 sheet: -1.71 (0.40), residues: 146 loop : -2.72 (0.16), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 445 HIS 0.011 0.001 HIS C 436 PHE 0.028 0.002 PHE E 151 TYR 0.015 0.001 TYR D 311 ARG 0.005 0.000 ARG D 159 Details of bonding type rmsd hydrogen bonds : bond 0.21425 ( 451) hydrogen bonds : angle 7.30919 ( 1275) metal coordination : bond 0.05565 ( 4) metal coordination : angle 27.50888 ( 6) covalent geometry : bond 0.00306 (14457) covalent geometry : angle 0.68971 (19602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.7738 (t0) cc_final: 0.7409 (t0) REVERT: B 467 GLN cc_start: 0.7808 (tp40) cc_final: 0.7448 (mt0) REVERT: B 476 SER cc_start: 0.8637 (t) cc_final: 0.8317 (t) REVERT: B 498 VAL cc_start: 0.8232 (t) cc_final: 0.7958 (p) REVERT: C 504 PRO cc_start: 0.6326 (Cg_endo) cc_final: 0.5943 (Cg_exo) REVERT: D 237 ASP cc_start: 0.7688 (p0) cc_final: 0.7180 (p0) REVERT: D 312 GLN cc_start: 0.6001 (tm-30) cc_final: 0.5329 (tp40) REVERT: D 351 MET cc_start: 0.8276 (tpp) cc_final: 0.8073 (mmm) REVERT: D 375 MET cc_start: 0.8259 (ttm) cc_final: 0.7993 (ttp) REVERT: D 377 ASP cc_start: 0.7689 (m-30) cc_final: 0.7331 (m-30) outliers start: 0 outliers final: 1 residues processed: 318 average time/residue: 1.4728 time to fit residues: 507.1295 Evaluate side-chains 194 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 502 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 5.9990 chunk 133 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.0770 chunk 89 optimal weight: 0.0070 chunk 71 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 159 optimal weight: 30.0000 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS A 319 GLN A 453 HIS A 471 ASN B 342 GLN B 369 HIS ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 65 HIS C 245 HIS C 345 GLN C 436 HIS C 474 GLN C 534 ASN D 66 HIS D 71 ASN D 83 ASN D 104 ASN D 127 ASN D 154 ASN D 155 HIS D 189 GLN D 208 GLN D 274 GLN D 278 GLN E 66 ASN E 123 ASN ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130165 restraints weight = 16609.742| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.85 r_work: 0.3392 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14461 Z= 0.096 Angle : 0.530 13.387 19608 Z= 0.272 Chirality : 0.041 0.149 2177 Planarity : 0.004 0.051 2515 Dihedral : 4.765 22.701 1933 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.03 % Allowed : 12.51 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.17), residues: 1749 helix: -2.00 (0.16), residues: 681 sheet: -1.05 (0.41), residues: 146 loop : -2.16 (0.18), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 314 HIS 0.004 0.001 HIS C 436 PHE 0.021 0.001 PHE C 240 TYR 0.018 0.001 TYR C 104 ARG 0.005 0.000 ARG D 216 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 451) hydrogen bonds : angle 4.78471 ( 1275) metal coordination : bond 0.00909 ( 4) metal coordination : angle 5.17954 ( 6) covalent geometry : bond 0.00210 (14457) covalent geometry : angle 0.52244 (19602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8028 (t0) cc_final: 0.7771 (t0) REVERT: A 361 GLU cc_start: 0.8132 (tt0) cc_final: 0.7710 (mt-10) REVERT: B 467 GLN cc_start: 0.8182 (tp40) cc_final: 0.7496 (mt0) REVERT: B 472 SER cc_start: 0.8452 (p) cc_final: 0.8210 (m) REVERT: B 476 SER cc_start: 0.8572 (t) cc_final: 0.8285 (t) REVERT: B 492 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.5883 (tt0) REVERT: B 498 VAL cc_start: 0.8111 (t) cc_final: 0.7747 (p) REVERT: C 498 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.6379 (ptp) REVERT: D 237 ASP cc_start: 0.7982 (p0) cc_final: 0.7656 (p0) REVERT: D 302 THR cc_start: 0.7046 (p) cc_final: 0.6657 (t) REVERT: D 312 GLN cc_start: 0.5938 (tm-30) cc_final: 0.5219 (tp40) REVERT: D 351 MET cc_start: 0.8130 (tpp) cc_final: 0.7779 (mmm) REVERT: D 375 MET cc_start: 0.8272 (ttm) cc_final: 0.7989 (ttp) REVERT: E 101 MET cc_start: 0.7758 (mmp) cc_final: 0.7453 (mmm) outliers start: 31 outliers final: 9 residues processed: 231 average time/residue: 1.5640 time to fit residues: 393.0506 Evaluate side-chains 197 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 492 GLN Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 418 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 156 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 121 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 319 GLN A 347 ASN A 471 ASN B 342 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 474 GLN C 643 ASN D 13 ASN D 71 ASN D 97 HIS D 104 ASN D 208 GLN D 274 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.150450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119806 restraints weight = 16712.121| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.90 r_work: 0.3269 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14461 Z= 0.133 Angle : 0.557 11.608 19608 Z= 0.284 Chirality : 0.043 0.152 2177 Planarity : 0.004 0.053 2515 Dihedral : 4.802 23.097 1929 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.62 % Allowed : 14.01 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.18), residues: 1749 helix: -1.11 (0.18), residues: 703 sheet: -0.86 (0.42), residues: 148 loop : -1.93 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 240 HIS 0.007 0.001 HIS C 436 PHE 0.021 0.001 PHE C 240 TYR 0.014 0.001 TYR C 487 ARG 0.006 0.000 ARG E 427 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 451) hydrogen bonds : angle 4.42564 ( 1275) metal coordination : bond 0.00552 ( 4) metal coordination : angle 3.65115 ( 6) covalent geometry : bond 0.00313 (14457) covalent geometry : angle 0.55330 (19602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8473 (mm) REVERT: A 327 ASN cc_start: 0.8383 (t0) cc_final: 0.8110 (t0) REVERT: B 467 GLN cc_start: 0.8151 (tp40) cc_final: 0.7387 (mt0) REVERT: B 476 SER cc_start: 0.8655 (t) cc_final: 0.8368 (t) REVERT: B 492 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6275 (tt0) REVERT: B 498 VAL cc_start: 0.8151 (t) cc_final: 0.7729 (p) REVERT: C 107 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8428 (tttm) REVERT: C 268 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7953 (mtp180) REVERT: C 406 MET cc_start: 0.8589 (mmm) cc_final: 0.8323 (mmt) REVERT: C 498 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.6532 (ptp) REVERT: D 25 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5427 (pm20) REVERT: D 312 GLN cc_start: 0.6107 (tm-30) cc_final: 0.5395 (tp40) REVERT: D 351 MET cc_start: 0.7940 (tpp) cc_final: 0.7694 (mmm) REVERT: D 375 MET cc_start: 0.8356 (ttm) cc_final: 0.8085 (ttp) REVERT: E 441 ASP cc_start: 0.7753 (p0) cc_final: 0.7307 (p0) REVERT: E 530 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.5081 (tpt90) outliers start: 40 outliers final: 13 residues processed: 209 average time/residue: 1.4921 time to fit residues: 340.1554 Evaluate side-chains 192 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 492 GLN Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 530 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 152 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 174 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 471 ASN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 GLN C 94 ASN C 463 GLN C 474 GLN D 71 ASN D 104 ASN D 208 GLN D 274 GLN D 327 HIS E 18 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118823 restraints weight = 16670.216| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.80 r_work: 0.3240 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14461 Z= 0.134 Angle : 0.559 10.129 19608 Z= 0.286 Chirality : 0.043 0.164 2177 Planarity : 0.004 0.053 2515 Dihedral : 4.811 23.640 1929 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.01 % Allowed : 15.39 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.19), residues: 1749 helix: -0.60 (0.19), residues: 699 sheet: -0.74 (0.43), residues: 141 loop : -1.79 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 445 HIS 0.006 0.001 HIS C 436 PHE 0.027 0.001 PHE C 240 TYR 0.014 0.001 TYR D 311 ARG 0.005 0.000 ARG C 234 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 451) hydrogen bonds : angle 4.31641 ( 1275) metal coordination : bond 0.00490 ( 4) metal coordination : angle 3.25262 ( 6) covalent geometry : bond 0.00321 (14457) covalent geometry : angle 0.55622 (19602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 5.046 Fit side-chains revert: symmetry clash REVERT: A 298 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8417 (mm) REVERT: B 476 SER cc_start: 0.8646 (t) cc_final: 0.8370 (t) REVERT: B 492 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6496 (tt0) REVERT: B 498 VAL cc_start: 0.8143 (t) cc_final: 0.7709 (p) REVERT: C 68 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6880 (ttt90) REVERT: C 107 LYS cc_start: 0.8724 (ttmt) cc_final: 0.8464 (tttm) REVERT: C 160 LYS cc_start: 0.8431 (mtpt) cc_final: 0.7651 (ttpp) REVERT: C 217 TYR cc_start: 0.7923 (m-80) cc_final: 0.7629 (m-80) REVERT: C 268 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7951 (mtp180) REVERT: C 363 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7429 (mt) REVERT: C 368 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: C 456 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7408 (t70) REVERT: C 498 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.6650 (ptp) REVERT: D 25 GLU cc_start: 0.6258 (pm20) cc_final: 0.5759 (pm20) REVERT: D 225 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: D 237 ASP cc_start: 0.8127 (p0) cc_final: 0.7489 (p0) REVERT: D 304 LYS cc_start: 0.7168 (mmtt) cc_final: 0.6540 (mtpt) REVERT: D 312 GLN cc_start: 0.6293 (tm-30) cc_final: 0.5616 (tp40) REVERT: D 334 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7233 (ttmm) REVERT: D 351 MET cc_start: 0.7942 (tpp) cc_final: 0.7689 (mmm) REVERT: D 375 MET cc_start: 0.8375 (ttm) cc_final: 0.8090 (ttp) REVERT: D 377 ASP cc_start: 0.7550 (m-30) cc_final: 0.7255 (m-30) REVERT: E 107 GLU cc_start: 0.7564 (tt0) cc_final: 0.7228 (tp30) outliers start: 46 outliers final: 16 residues processed: 207 average time/residue: 2.0420 time to fit residues: 459.1118 Evaluate side-chains 193 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 492 GLN Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 389 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 388 GLN A 471 ASN B 342 GLN B 369 HIS B 467 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS C 115 HIS C 332 HIS C 474 GLN D 71 ASN D 208 GLN D 274 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.144581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114807 restraints weight = 16797.484| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.77 r_work: 0.3189 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14461 Z= 0.190 Angle : 0.625 10.175 19608 Z= 0.319 Chirality : 0.046 0.174 2177 Planarity : 0.004 0.050 2515 Dihedral : 5.141 24.690 1929 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.47 % Allowed : 15.85 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.19), residues: 1749 helix: -0.66 (0.19), residues: 712 sheet: -0.70 (0.42), residues: 143 loop : -1.79 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 240 HIS 0.009 0.001 HIS C 436 PHE 0.030 0.002 PHE C 240 TYR 0.017 0.002 TYR D 311 ARG 0.006 0.001 ARG C 234 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 451) hydrogen bonds : angle 4.41846 ( 1275) metal coordination : bond 0.00599 ( 4) metal coordination : angle 3.65759 ( 6) covalent geometry : bond 0.00463 (14457) covalent geometry : angle 0.62185 (19602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8589 (mm) REVERT: B 476 SER cc_start: 0.8763 (t) cc_final: 0.8515 (t) REVERT: B 498 VAL cc_start: 0.8125 (t) cc_final: 0.7781 (p) REVERT: C 107 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8561 (tttm) REVERT: C 160 LYS cc_start: 0.8510 (mtpt) cc_final: 0.7726 (ttpp) REVERT: C 268 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7949 (mtp180) REVERT: C 363 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7476 (mt) REVERT: C 368 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: C 406 MET cc_start: 0.8598 (mmm) cc_final: 0.8280 (mmt) REVERT: C 498 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.6776 (ptp) REVERT: D 25 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6155 (pm20) REVERT: D 304 LYS cc_start: 0.7253 (mmtt) cc_final: 0.6630 (mtpt) REVERT: D 334 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7166 (ttmm) REVERT: D 351 MET cc_start: 0.7918 (tpp) cc_final: 0.7701 (mmm) REVERT: D 375 MET cc_start: 0.8380 (ttm) cc_final: 0.8092 (ttp) REVERT: E 107 GLU cc_start: 0.7551 (tt0) cc_final: 0.7235 (tp30) outliers start: 53 outliers final: 23 residues processed: 197 average time/residue: 1.4063 time to fit residues: 302.6172 Evaluate side-chains 190 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 435 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 144 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 471 ASN B 467 GLN B 492 GLN C 94 ASN D 71 ASN D 208 GLN D 274 GLN ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115231 restraints weight = 16884.984| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.76 r_work: 0.3199 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14461 Z= 0.142 Angle : 0.570 9.042 19608 Z= 0.292 Chirality : 0.044 0.168 2177 Planarity : 0.004 0.051 2515 Dihedral : 4.942 24.085 1929 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.21 % Allowed : 17.03 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.19), residues: 1749 helix: -0.37 (0.19), residues: 708 sheet: -0.83 (0.41), residues: 152 loop : -1.71 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 26 HIS 0.007 0.001 HIS C 436 PHE 0.027 0.001 PHE C 240 TYR 0.016 0.001 TYR D 311 ARG 0.006 0.000 ARG C 543 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 451) hydrogen bonds : angle 4.28067 ( 1275) metal coordination : bond 0.00465 ( 4) metal coordination : angle 3.49558 ( 6) covalent geometry : bond 0.00341 (14457) covalent geometry : angle 0.56642 (19602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 163 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 415 ASN cc_start: 0.6662 (OUTLIER) cc_final: 0.6189 (t0) REVERT: B 476 SER cc_start: 0.8736 (t) cc_final: 0.8445 (t) REVERT: B 498 VAL cc_start: 0.7997 (t) cc_final: 0.7512 (p) REVERT: C 107 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8540 (tttm) REVERT: C 160 LYS cc_start: 0.8501 (mtpt) cc_final: 0.7711 (ttpp) REVERT: C 217 TYR cc_start: 0.7909 (m-80) cc_final: 0.7668 (m-80) REVERT: C 268 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7937 (mtp180) REVERT: C 288 ARG cc_start: 0.7888 (mmm-85) cc_final: 0.7602 (tpp80) REVERT: C 368 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: C 456 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7495 (t70) REVERT: C 498 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7557 (mtp) REVERT: C 573 MET cc_start: 0.8379 (ptt) cc_final: 0.8166 (ptt) REVERT: D 25 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6295 (pm20) REVERT: D 237 ASP cc_start: 0.8238 (p0) cc_final: 0.7650 (p0) REVERT: D 304 LYS cc_start: 0.7229 (mmtt) cc_final: 0.6598 (mtpt) REVERT: D 334 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7053 (ttmm) REVERT: D 375 MET cc_start: 0.8316 (ttm) cc_final: 0.8018 (ttp) REVERT: E 107 GLU cc_start: 0.7625 (tt0) cc_final: 0.7274 (tp30) outliers start: 49 outliers final: 22 residues processed: 195 average time/residue: 1.3346 time to fit residues: 284.8414 Evaluate side-chains 185 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 435 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 136 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 47 optimal weight: 0.0980 chunk 161 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 101 optimal weight: 0.0770 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 471 ASN B 467 GLN B 492 GLN C 474 GLN D 71 ASN D 208 GLN D 274 GLN ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.145925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115120 restraints weight = 16656.347| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.77 r_work: 0.3206 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14461 Z= 0.136 Angle : 0.565 8.780 19608 Z= 0.290 Chirality : 0.044 0.165 2177 Planarity : 0.004 0.051 2515 Dihedral : 4.872 23.511 1929 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.27 % Allowed : 17.03 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.19), residues: 1749 helix: -0.22 (0.20), residues: 708 sheet: -0.55 (0.42), residues: 146 loop : -1.69 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 26 HIS 0.007 0.001 HIS C 436 PHE 0.026 0.001 PHE C 240 TYR 0.016 0.001 TYR D 311 ARG 0.007 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 451) hydrogen bonds : angle 4.23197 ( 1275) metal coordination : bond 0.00388 ( 4) metal coordination : angle 3.34653 ( 6) covalent geometry : bond 0.00326 (14457) covalent geometry : angle 0.56196 (19602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 415 ASN cc_start: 0.6487 (OUTLIER) cc_final: 0.6092 (t0) REVERT: B 476 SER cc_start: 0.8711 (t) cc_final: 0.8410 (t) REVERT: B 498 VAL cc_start: 0.8060 (t) cc_final: 0.7574 (p) REVERT: C 107 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8540 (tttm) REVERT: C 160 LYS cc_start: 0.8465 (mtpt) cc_final: 0.7685 (ttpp) REVERT: C 217 TYR cc_start: 0.7948 (m-80) cc_final: 0.7680 (m-80) REVERT: C 268 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7942 (mtp180) REVERT: C 288 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7623 (tpp80) REVERT: C 368 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: C 406 MET cc_start: 0.8816 (mmm) cc_final: 0.8287 (mmt) REVERT: C 456 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7543 (t70) REVERT: C 463 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: C 498 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7636 (mtp) REVERT: D 25 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6319 (pm20) REVERT: D 225 ASP cc_start: 0.6924 (OUTLIER) cc_final: 0.6718 (m-30) REVERT: D 237 ASP cc_start: 0.8207 (p0) cc_final: 0.7588 (p0) REVERT: D 284 HIS cc_start: 0.5333 (OUTLIER) cc_final: 0.4858 (m90) REVERT: D 304 LYS cc_start: 0.7239 (mmtt) cc_final: 0.6605 (mtpt) REVERT: D 334 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.7024 (ttmm) REVERT: D 375 MET cc_start: 0.8310 (ttm) cc_final: 0.8006 (ttp) REVERT: E 107 GLU cc_start: 0.7660 (tt0) cc_final: 0.7339 (tp30) outliers start: 50 outliers final: 27 residues processed: 194 average time/residue: 1.3178 time to fit residues: 279.9694 Evaluate side-chains 192 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 492 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 435 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 46 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 18 optimal weight: 0.0670 chunk 119 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 471 ASN B 492 GLN C 495 HIS D 71 ASN D 208 GLN D 274 GLN ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.149401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118400 restraints weight = 16641.993| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.64 r_work: 0.3274 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14461 Z= 0.097 Angle : 0.521 8.614 19608 Z= 0.268 Chirality : 0.042 0.157 2177 Planarity : 0.004 0.053 2515 Dihedral : 4.577 22.108 1929 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.16 % Allowed : 18.53 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.20), residues: 1749 helix: 0.13 (0.20), residues: 703 sheet: -0.56 (0.42), residues: 148 loop : -1.59 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 26 HIS 0.005 0.001 HIS B 470 PHE 0.023 0.001 PHE C 240 TYR 0.014 0.001 TYR D 311 ARG 0.006 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.02902 ( 451) hydrogen bonds : angle 4.05652 ( 1275) metal coordination : bond 0.00272 ( 4) metal coordination : angle 2.63007 ( 6) covalent geometry : bond 0.00221 (14457) covalent geometry : angle 0.51895 (19602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8285 (t0) cc_final: 0.7992 (t0) REVERT: A 415 ASN cc_start: 0.6292 (OUTLIER) cc_final: 0.5984 (t0) REVERT: B 476 SER cc_start: 0.8704 (t) cc_final: 0.8433 (t) REVERT: B 498 VAL cc_start: 0.8034 (t) cc_final: 0.7548 (p) REVERT: C 107 LYS cc_start: 0.8814 (ttmt) cc_final: 0.8560 (tttm) REVERT: C 160 LYS cc_start: 0.8416 (mtpt) cc_final: 0.7598 (ttpp) REVERT: C 217 TYR cc_start: 0.7824 (m-80) cc_final: 0.7559 (m-80) REVERT: C 268 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7884 (mtp180) REVERT: C 368 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: C 406 MET cc_start: 0.8847 (mmm) cc_final: 0.8191 (mmt) REVERT: C 456 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7425 (t70) REVERT: C 463 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6887 (mp10) REVERT: D 25 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6244 (pm20) REVERT: D 225 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6682 (m-30) REVERT: D 237 ASP cc_start: 0.8063 (p0) cc_final: 0.7475 (p0) REVERT: D 284 HIS cc_start: 0.5319 (OUTLIER) cc_final: 0.4834 (m90) REVERT: D 304 LYS cc_start: 0.7211 (mmtt) cc_final: 0.6593 (mtpt) REVERT: D 334 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6959 (ttmm) REVERT: D 375 MET cc_start: 0.8278 (ttm) cc_final: 0.7986 (ttp) REVERT: E 107 GLU cc_start: 0.7559 (tt0) cc_final: 0.7335 (tp30) REVERT: E 342 MET cc_start: 0.5670 (mpp) cc_final: 0.5058 (mpp) outliers start: 33 outliers final: 11 residues processed: 197 average time/residue: 1.3411 time to fit residues: 288.9098 Evaluate side-chains 182 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 389 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 0.0370 chunk 115 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 157 optimal weight: 0.0470 chunk 47 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 471 ASN B 342 GLN B 467 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 104 ASN D 208 GLN D 274 GLN ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121279 restraints weight = 16616.314| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.67 r_work: 0.3303 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14461 Z= 0.090 Angle : 0.512 9.099 19608 Z= 0.260 Chirality : 0.041 0.155 2177 Planarity : 0.004 0.055 2515 Dihedral : 4.300 20.675 1929 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.70 % Allowed : 19.25 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.20), residues: 1749 helix: 0.32 (0.20), residues: 704 sheet: -0.65 (0.40), residues: 167 loop : -1.53 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 366 HIS 0.005 0.001 HIS C 436 PHE 0.021 0.001 PHE C 240 TYR 0.018 0.001 TYR C 478 ARG 0.007 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.02692 ( 451) hydrogen bonds : angle 3.95402 ( 1275) metal coordination : bond 0.00249 ( 4) metal coordination : angle 2.19924 ( 6) covalent geometry : bond 0.00205 (14457) covalent geometry : angle 0.51043 (19602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8189 (t0) cc_final: 0.7901 (t0) REVERT: A 415 ASN cc_start: 0.6111 (OUTLIER) cc_final: 0.5445 (t0) REVERT: B 467 GLN cc_start: 0.8159 (tp40) cc_final: 0.7583 (mt0) REVERT: B 476 SER cc_start: 0.8554 (t) cc_final: 0.8239 (t) REVERT: B 498 VAL cc_start: 0.8060 (t) cc_final: 0.7579 (p) REVERT: C 107 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8559 (tttm) REVERT: C 160 LYS cc_start: 0.8399 (mtpt) cc_final: 0.7549 (ttpp) REVERT: C 455 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7657 (mt) REVERT: C 456 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7338 (t0) REVERT: C 463 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6828 (mp10) REVERT: D 25 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5962 (pm20) REVERT: D 237 ASP cc_start: 0.7801 (p0) cc_final: 0.7244 (p0) REVERT: D 284 HIS cc_start: 0.5330 (OUTLIER) cc_final: 0.4892 (m90) REVERT: D 304 LYS cc_start: 0.7204 (mmtt) cc_final: 0.6585 (mtpt) REVERT: D 375 MET cc_start: 0.8158 (ttm) cc_final: 0.7873 (ttp) REVERT: E 107 GLU cc_start: 0.7494 (tt0) cc_final: 0.7286 (tp30) outliers start: 26 outliers final: 11 residues processed: 195 average time/residue: 1.3067 time to fit residues: 279.7272 Evaluate side-chains 181 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 168 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 62 optimal weight: 0.0470 chunk 11 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 122 optimal weight: 0.0980 chunk 60 optimal weight: 0.9980 overall best weight: 2.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 471 ASN B 342 GLN B 492 GLN C 474 GLN D 71 ASN D 208 GLN D 274 GLN ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.145513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115444 restraints weight = 16751.782| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.87 r_work: 0.3222 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14461 Z= 0.162 Angle : 0.609 11.131 19608 Z= 0.308 Chirality : 0.045 0.165 2177 Planarity : 0.004 0.051 2515 Dihedral : 4.798 23.598 1929 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.64 % Allowed : 20.10 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1749 helix: -0.01 (0.20), residues: 712 sheet: -0.60 (0.40), residues: 166 loop : -1.61 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 103 HIS 0.008 0.001 HIS C 436 PHE 0.024 0.002 PHE C 240 TYR 0.017 0.001 TYR C 487 ARG 0.009 0.000 ARG D 250 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 451) hydrogen bonds : angle 4.20427 ( 1275) metal coordination : bond 0.00378 ( 4) metal coordination : angle 3.11507 ( 6) covalent geometry : bond 0.00397 (14457) covalent geometry : angle 0.60651 (19602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 415 ASN cc_start: 0.6338 (OUTLIER) cc_final: 0.6094 (t0) REVERT: B 476 SER cc_start: 0.8716 (t) cc_final: 0.8450 (t) REVERT: B 498 VAL cc_start: 0.8088 (t) cc_final: 0.7606 (p) REVERT: C 107 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8594 (tttm) REVERT: C 160 LYS cc_start: 0.8435 (mtpt) cc_final: 0.7617 (ttpp) REVERT: C 456 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7436 (t70) REVERT: C 463 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: D 25 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6334 (pm20) REVERT: D 284 HIS cc_start: 0.5282 (OUTLIER) cc_final: 0.4746 (m90) REVERT: D 304 LYS cc_start: 0.7319 (mmtt) cc_final: 0.6675 (mtpt) REVERT: D 375 MET cc_start: 0.8328 (ttm) cc_final: 0.8045 (ttp) REVERT: E 502 LYS cc_start: 0.8296 (tttm) cc_final: 0.7891 (mptp) outliers start: 25 outliers final: 13 residues processed: 183 average time/residue: 1.6842 time to fit residues: 337.7560 Evaluate side-chains 183 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 51 optimal weight: 0.0770 chunk 95 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 471 ASN B 342 GLN B 492 GLN D 71 ASN D 208 GLN D 274 GLN ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117991 restraints weight = 16766.491| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.66 r_work: 0.3271 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14461 Z= 0.106 Angle : 0.552 12.079 19608 Z= 0.278 Chirality : 0.042 0.155 2177 Planarity : 0.004 0.052 2515 Dihedral : 4.518 22.013 1929 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.51 % Allowed : 20.56 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.20), residues: 1749 helix: 0.29 (0.20), residues: 705 sheet: -0.68 (0.40), residues: 167 loop : -1.51 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 26 HIS 0.005 0.001 HIS C 436 PHE 0.024 0.001 PHE C 240 TYR 0.015 0.001 TYR C 487 ARG 0.010 0.000 ARG D 250 Details of bonding type rmsd hydrogen bonds : bond 0.03023 ( 451) hydrogen bonds : angle 4.05090 ( 1275) metal coordination : bond 0.00358 ( 4) metal coordination : angle 2.78141 ( 6) covalent geometry : bond 0.00249 (14457) covalent geometry : angle 0.55010 (19602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11517.81 seconds wall clock time: 207 minutes 13.43 seconds (12433.43 seconds total)