Starting phenix.real_space_refine on Fri Oct 30 15:45:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36bm_77359/10_2026/36bm_77359.cif Found real_map, /net/cci-nas-00/data/ceres_data/36bm_77359/10_2026/36bm_77359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/36bm_77359/10_2026/36bm_77359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36bm_77359/10_2026/36bm_77359.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/36bm_77359/10_2026/36bm_77359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36bm_77359/10_2026/36bm_77359.map" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 153 5.16 5 C 23046 2.51 5 N 6179 2.21 5 O 7056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36449 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3042 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 21, 'TRANS': 369} Chain breaks: 1 Chain: "B" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3020 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 365} Chain: "C" Number of atoms: 6569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6569 Classifications: {'peptide': 846} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 816} Chain breaks: 2 Chain: "D" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3832 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 455} Chain: "K" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3106 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 372} Chain: "P" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3030 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 371} Chain breaks: 1 Chain: "I" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 939 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 111} Chain: "J" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2935 Classifications: {'peptide': 372} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 354} Chain: "Z" Number of atoms: 6952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 6952 Classifications: {'peptide': 901} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 873} Chain breaks: 1 Chain: "L" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1061 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 9, 'TRANS': 121} Chain: "N" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1808 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.66, per 1000 atoms: 0.21 Number of scatterers: 36449 At special positions: 0 Unit cell: (175.016, 203.312, 208.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 153 16.00 P 15 15.00 O 7056 8.00 N 6179 7.00 C 23046 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: 3.21 Conformation dependent library (CDL) restraints added in 1.7 seconds 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8676 Finding SS restraints... Secondary structure from input PDB file: 242 helices and 15 sheets defined 63.4% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 30 through 40 removed outlier: 3.906A pdb=" N SER A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 68 removed outlier: 3.563A pdb=" N LYS A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 214 through 226 removed outlier: 4.040A pdb=" N VAL A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 231 through 239 removed outlier: 4.179A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 removed outlier: 4.044A pdb=" N VAL A 263 " --> pdb=" O CYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.860A pdb=" N VAL A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 4.022A pdb=" N MET A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 327 through 343 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 415 through 433 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'B' and resid 55 through 83 Processing helix chain 'B' and resid 86 through 101 removed outlier: 3.664A pdb=" N GLU B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.663A pdb=" N ILE B 184 " --> pdb=" O TYR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 204 through 212 removed outlier: 4.047A pdb=" N TYR B 208 " --> pdb=" O HIS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 240 Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.557A pdb=" N LYS B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 292 removed outlier: 3.682A pdb=" N GLY B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 299 removed outlier: 3.739A pdb=" N GLU B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 300 through 314 Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 335 through 339 Processing helix chain 'B' and resid 354 through 367 Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 60 through 62 No H-bonds generated for 'chain 'C' and resid 60 through 62' Processing helix chain 'C' and resid 63 through 80 Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 95 through 106 Processing helix chain 'C' and resid 108 through 123 removed outlier: 3.702A pdb=" N ILE C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 146 through 149 Processing helix chain 'C' and resid 150 through 177 Processing helix chain 'C' and resid 196 through 214 Proline residue: C 209 - end of helix Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 229 through 237 Proline residue: C 234 - end of helix Processing helix chain 'C' and resid 241 through 252 removed outlier: 3.527A pdb=" N CYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 259 through 275 Processing helix chain 'C' and resid 277 through 289 Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.618A pdb=" N VAL C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 317 removed outlier: 3.601A pdb=" N GLN C 317 " --> pdb=" O ILE C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 334 through 346 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 360 through 363 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.563A pdb=" N PHE C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 391 Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.242A pdb=" N VAL C 407 " --> pdb=" O ASN C 403 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 408' Processing helix chain 'C' and resid 409 through 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'C' and resid 412 through 426 removed outlier: 3.939A pdb=" N THR C 416 " --> pdb=" O GLY C 412 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY C 423 " --> pdb=" O VAL C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 441 removed outlier: 4.143A pdb=" N GLN C 434 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS C 438 " --> pdb=" O GLN C 434 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR C 439 " --> pdb=" O GLN C 435 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR C 441 " --> pdb=" O ASP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 459 Processing helix chain 'C' and resid 468 through 479 removed outlier: 4.623A pdb=" N ASP C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 497 Processing helix chain 'C' and resid 502 through 515 Proline residue: C 511 - end of helix Processing helix chain 'C' and resid 519 through 534 Processing helix chain 'C' and resid 539 through 553 removed outlier: 3.527A pdb=" N MET C 547 " --> pdb=" O THR C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 560 Processing helix chain 'C' and resid 561 through 574 removed outlier: 4.067A pdb=" N PHE C 565 " --> pdb=" O ASP C 561 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 580 Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 608 Processing helix chain 'C' and resid 613 through 624 Processing helix chain 'C' and resid 724 through 748 removed outlier: 3.636A pdb=" N ALA C 744 " --> pdb=" O VAL C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 768 removed outlier: 3.506A pdb=" N ARG C 759 " --> pdb=" O GLU C 755 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET C 765 " --> pdb=" O PHE C 761 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS C 766 " --> pdb=" O GLY C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 784 removed outlier: 3.538A pdb=" N MET C 775 " --> pdb=" O HIS C 771 " (cutoff:3.500A) Proline residue: C 777 - end of helix Processing helix chain 'C' and resid 789 through 798 removed outlier: 3.538A pdb=" N PHE C 793 " --> pdb=" O GLN C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 819 removed outlier: 3.560A pdb=" N GLY C 816 " --> pdb=" O ILE C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 838 Processing helix chain 'C' and resid 841 through 856 Processing helix chain 'C' and resid 857 through 860 Processing helix chain 'C' and resid 874 through 888 Processing helix chain 'C' and resid 890 through 895 Processing helix chain 'C' and resid 896 through 908 removed outlier: 5.786A pdb=" N GLN C 899 " --> pdb=" O LYS C 896 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET C 903 " --> pdb=" O LEU C 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 22 Processing helix chain 'D' and resid 28 through 43 removed outlier: 4.377A pdb=" N THR D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 65 removed outlier: 3.573A pdb=" N LEU D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 84 Processing helix chain 'D' and resid 88 through 96 Processing helix chain 'D' and resid 97 through 106 Processing helix chain 'D' and resid 109 through 122 Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 166 through 176 removed outlier: 3.735A pdb=" N ARG D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 188 Processing helix chain 'D' and resid 189 through 207 removed outlier: 3.538A pdb=" N PHE D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE D 206 " --> pdb=" O ILE D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 220 through 228 Processing helix chain 'D' and resid 230 through 252 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 262 removed outlier: 3.957A pdb=" N VAL D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 273 removed outlier: 4.041A pdb=" N ALA D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 284 through 297 removed outlier: 3.774A pdb=" N ARG D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 removed outlier: 3.981A pdb=" N ASP D 312 " --> pdb=" O THR D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 330 Processing helix chain 'D' and resid 331 through 338 Processing helix chain 'D' and resid 339 through 347 removed outlier: 3.523A pdb=" N PHE D 347 " --> pdb=" O VAL D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.501A pdb=" N ASN D 359 " --> pdb=" O GLY D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'D' and resid 375 through 382 removed outlier: 4.100A pdb=" N LEU D 382 " --> pdb=" O ILE D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 395 Processing helix chain 'D' and resid 397 through 408 removed outlier: 3.637A pdb=" N MET D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 417 removed outlier: 3.524A pdb=" N MET D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 424 removed outlier: 3.754A pdb=" N ILE D 424 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 442 Processing helix chain 'D' and resid 444 through 449 Processing helix chain 'D' and resid 451 through 464 Processing helix chain 'K' and resid 48 through 100 Processing helix chain 'K' and resid 166 through 172 Processing helix chain 'K' and resid 179 through 183 Processing helix chain 'K' and resid 186 through 197 Processing helix chain 'K' and resid 197 through 203 removed outlier: 3.582A pdb=" N LEU K 201 " --> pdb=" O ILE K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 211 Processing helix chain 'K' and resid 227 through 240 Processing helix chain 'K' and resid 247 through 252 removed outlier: 3.581A pdb=" N ILE K 251 " --> pdb=" O PRO K 247 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL K 252 " --> pdb=" O ALA K 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 247 through 252' Processing helix chain 'K' and resid 257 through 273 Processing helix chain 'K' and resid 283 through 286 Processing helix chain 'K' and resid 295 through 314 removed outlier: 3.530A pdb=" N ASP K 313 " --> pdb=" O LEU K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 339 Processing helix chain 'K' and resid 353 through 367 removed outlier: 4.457A pdb=" N LYS K 367 " --> pdb=" O ILE K 363 " (cutoff:3.500A) Processing helix chain 'K' and resid 375 through 383 removed outlier: 3.642A pdb=" N ALA K 379 " --> pdb=" O ASP K 375 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 405 removed outlier: 3.583A pdb=" N ILE K 391 " --> pdb=" O ASN K 387 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG K 392 " --> pdb=" O GLY K 388 " (cutoff:3.500A) Processing helix chain 'K' and resid 411 through 427 removed outlier: 3.587A pdb=" N LEU K 415 " --> pdb=" O ASN K 411 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET K 416 " --> pdb=" O PRO K 412 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS K 417 " --> pdb=" O ASP K 413 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS K 427 " --> pdb=" O ALA K 423 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 24 Processing helix chain 'P' and resid 26 through 73 Processing helix chain 'P' and resid 164 through 171 removed outlier: 3.562A pdb=" N GLU P 171 " --> pdb=" O VAL P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 183 removed outlier: 3.506A pdb=" N VAL P 183 " --> pdb=" O TYR P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 186 through 197 Processing helix chain 'P' and resid 197 through 203 Processing helix chain 'P' and resid 203 through 210 removed outlier: 3.956A pdb=" N PHE P 207 " --> pdb=" O ARG P 203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET P 210 " --> pdb=" O LYS P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 238 Processing helix chain 'P' and resid 248 through 252 Processing helix chain 'P' and resid 257 through 273 Processing helix chain 'P' and resid 283 through 288 removed outlier: 3.579A pdb=" N THR P 288 " --> pdb=" O ASP P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 313 Processing helix chain 'P' and resid 334 through 339 Processing helix chain 'P' and resid 353 through 366 Processing helix chain 'P' and resid 375 through 383 Processing helix chain 'P' and resid 387 through 405 Processing helix chain 'P' and resid 411 through 425 removed outlier: 3.579A pdb=" N PHE P 415 " --> pdb=" O LYS P 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 67 removed outlier: 3.646A pdb=" N GLN I 66 " --> pdb=" O LEU I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 91 Processing helix chain 'J' and resid 127 through 131 Processing helix chain 'J' and resid 170 through 174 removed outlier: 3.804A pdb=" N VAL J 174 " --> pdb=" O TYR J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 188 Processing helix chain 'J' and resid 188 through 194 removed outlier: 3.712A pdb=" N LEU J 192 " --> pdb=" O VAL J 188 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL J 193 " --> pdb=" O GLU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 202 removed outlier: 4.086A pdb=" N TYR J 198 " --> pdb=" O GLN J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 230 Processing helix chain 'J' and resid 240 through 242 No H-bonds generated for 'chain 'J' and resid 240 through 242' Processing helix chain 'J' and resid 248 through 264 Processing helix chain 'J' and resid 273 through 277 Processing helix chain 'J' and resid 286 through 303 removed outlier: 3.592A pdb=" N ARG J 290 " --> pdb=" O THR J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 324 Processing helix chain 'J' and resid 346 through 359 removed outlier: 3.894A pdb=" N ARG J 350 " --> pdb=" O ARG J 346 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU J 351 " --> pdb=" O ARG J 347 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS J 359 " --> pdb=" O THR J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 379 through 397 removed outlier: 3.527A pdb=" N GLY J 391 " --> pdb=" O MET J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 403 through 416 Processing helix chain 'Z' and resid 6 through 14 removed outlier: 3.562A pdb=" N LEU Z 13 " --> pdb=" O LEU Z 9 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG Z 14 " --> pdb=" O LEU Z 10 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 40 removed outlier: 3.574A pdb=" N VAL Z 31 " --> pdb=" O SER Z 27 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASP Z 33 " --> pdb=" O ASN Z 29 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN Z 34 " --> pdb=" O ASN Z 30 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N SER Z 37 " --> pdb=" O ASP Z 33 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU Z 38 " --> pdb=" O GLN Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 52 Processing helix chain 'Z' and resid 57 through 73 removed outlier: 3.666A pdb=" N ALA Z 61 " --> pdb=" O ASP Z 57 " (cutoff:3.500A) Processing helix chain 'Z' and resid 74 through 85 Processing helix chain 'Z' and resid 86 through 89 Processing helix chain 'Z' and resid 95 through 120 removed outlier: 3.781A pdb=" N LYS Z 119 " --> pdb=" O LYS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 122 through 127 removed outlier: 3.819A pdb=" N ASP Z 127 " --> pdb=" O TYR Z 124 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 147 removed outlier: 3.505A pdb=" N ALA Z 147 " --> pdb=" O LYS Z 143 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 160 Processing helix chain 'Z' and resid 162 through 175 Processing helix chain 'Z' and resid 178 through 197 Processing helix chain 'Z' and resid 199 through 216 Processing helix chain 'Z' and resid 221 through 233 Processing helix chain 'Z' and resid 234 through 249 Processing helix chain 'Z' and resid 250 through 265 Processing helix chain 'Z' and resid 266 through 280 Processing helix chain 'Z' and resid 283 through 291 Processing helix chain 'Z' and resid 292 through 306 Processing helix chain 'Z' and resid 310 through 321 removed outlier: 3.736A pdb=" N LEU Z 314 " --> pdb=" O ASP Z 310 " (cutoff:3.500A) Processing helix chain 'Z' and resid 325 through 340 removed outlier: 3.521A pdb=" N PHE Z 338 " --> pdb=" O VAL Z 334 " (cutoff:3.500A) Processing helix chain 'Z' and resid 346 through 352 Processing helix chain 'Z' and resid 352 through 358 Processing helix chain 'Z' and resid 361 through 375 removed outlier: 3.958A pdb=" N LEU Z 371 " --> pdb=" O ALA Z 367 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY Z 372 " --> pdb=" O THR Z 368 " (cutoff:3.500A) Processing helix chain 'Z' and resid 381 through 387 Processing helix chain 'Z' and resid 388 through 390 No H-bonds generated for 'chain 'Z' and resid 388 through 390' Processing helix chain 'Z' and resid 397 through 412 removed outlier: 3.530A pdb=" N LEU Z 410 " --> pdb=" O TYR Z 406 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE Z 411 " --> pdb=" O GLY Z 407 " (cutoff:3.500A) Processing helix chain 'Z' and resid 418 through 432 removed outlier: 4.188A pdb=" N TYR Z 422 " --> pdb=" O ASP Z 418 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE Z 426 " --> pdb=" O TYR Z 422 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY Z 432 " --> pdb=" O VAL Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 436 through 454 Processing helix chain 'Z' and resid 459 through 471 removed outlier: 3.508A pdb=" N TYR Z 463 " --> pdb=" O ASN Z 459 " (cutoff:3.500A) Processing helix chain 'Z' and resid 474 through 489 removed outlier: 4.012A pdb=" N GLU Z 479 " --> pdb=" O ALA Z 475 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA Z 480 " --> pdb=" O THR Z 476 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY Z 486 " --> pdb=" O ALA Z 482 " (cutoff:3.500A) Processing helix chain 'Z' and resid 494 through 508 removed outlier: 3.535A pdb=" N GLN Z 506 " --> pdb=" O PHE Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 510 through 525 removed outlier: 3.662A pdb=" N ALA Z 522 " --> pdb=" O ALA Z 518 " (cutoff:3.500A) Processing helix chain 'Z' and resid 528 through 531 Processing helix chain 'Z' and resid 532 through 542 removed outlier: 3.683A pdb=" N LYS Z 538 " --> pdb=" O ASP Z 534 " (cutoff:3.500A) Processing helix chain 'Z' and resid 544 through 559 removed outlier: 3.521A pdb=" N PHE Z 553 " --> pdb=" O TYR Z 549 " (cutoff:3.500A) Processing helix chain 'Z' and resid 564 through 578 Processing helix chain 'Z' and resid 580 through 595 removed outlier: 3.594A pdb=" N LEU Z 591 " --> pdb=" O ALA Z 587 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY Z 592 " --> pdb=" O VAL Z 588 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE Z 593 " --> pdb=" O ILE Z 589 " (cutoff:3.500A) Processing helix chain 'Z' and resid 596 through 600 removed outlier: 3.974A pdb=" N TYR Z 599 " --> pdb=" O LEU Z 596 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N THR Z 600 " --> pdb=" O ARG Z 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 596 through 600' Processing helix chain 'Z' and resid 601 through 611 removed outlier: 4.606A pdb=" N LEU Z 608 " --> pdb=" O ARG Z 604 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU Z 609 " --> pdb=" O ILE Z 605 " (cutoff:3.500A) Processing helix chain 'Z' and resid 614 through 629 Processing helix chain 'Z' and resid 634 through 646 removed outlier: 4.037A pdb=" N VAL Z 640 " --> pdb=" O SER Z 636 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU Z 641 " --> pdb=" O ALA Z 637 " (cutoff:3.500A) Proline residue: Z 643 - end of helix removed outlier: 3.766A pdb=" N LYS Z 646 " --> pdb=" O ASP Z 642 " (cutoff:3.500A) Processing helix chain 'Z' and resid 649 through 664 removed outlier: 3.806A pdb=" N ILE Z 658 " --> pdb=" O GLN Z 654 " (cutoff:3.500A) Processing helix chain 'Z' and resid 673 through 688 removed outlier: 4.084A pdb=" N ASP Z 677 " --> pdb=" O PRO Z 673 " (cutoff:3.500A) Processing helix chain 'Z' and resid 692 through 707 Processing helix chain 'Z' and resid 726 through 737 Processing helix chain 'Z' and resid 738 through 741 Processing helix chain 'Z' and resid 742 through 747 removed outlier: 3.727A pdb=" N HIS Z 747 " --> pdb=" O PRO Z 744 " (cutoff:3.500A) Processing helix chain 'Z' and resid 748 through 752 removed outlier: 4.102A pdb=" N SER Z 752 " --> pdb=" O PHE Z 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 748 through 752' Processing helix chain 'Z' and resid 806 through 819 Processing helix chain 'Z' and resid 875 through 880 removed outlier: 4.138A pdb=" N ARG Z 880 " --> pdb=" O PRO Z 876 " (cutoff:3.500A) Processing helix chain 'Z' and resid 919 through 925 removed outlier: 3.623A pdb=" N LYS Z 924 " --> pdb=" O VAL Z 920 " (cutoff:3.500A) Processing helix chain 'Z' and resid 937 through 942 Processing helix chain 'L' and resid 40 through 44 Processing helix chain 'L' and resid 115 through 129 Processing helix chain 'N' and resid 4 through 12 removed outlier: 3.596A pdb=" N GLN N 8 " --> pdb=" O TYR N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 25 Processing helix chain 'N' and resid 26 through 30 removed outlier: 3.714A pdb=" N LEU N 30 " --> pdb=" O SER N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 46 removed outlier: 3.764A pdb=" N TRP N 42 " --> pdb=" O ILE N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 57 removed outlier: 3.540A pdb=" N SER N 57 " --> pdb=" O SER N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 67 removed outlier: 3.519A pdb=" N TYR N 67 " --> pdb=" O LEU N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 83 removed outlier: 3.709A pdb=" N ILE N 78 " --> pdb=" O THR N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 93 Processing helix chain 'N' and resid 109 through 117 removed outlier: 3.932A pdb=" N LEU N 113 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA N 114 " --> pdb=" O CYS N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 129 removed outlier: 3.519A pdb=" N PHE N 125 " --> pdb=" O GLU N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 151 removed outlier: 3.686A pdb=" N ARG N 146 " --> pdb=" O ILE N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 162 Processing helix chain 'N' and resid 176 through 184 removed outlier: 3.690A pdb=" N HIS N 180 " --> pdb=" O THR N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 198 Processing helix chain 'N' and resid 217 through 228 removed outlier: 3.558A pdb=" N ASN N 227 " --> pdb=" O PHE N 223 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 106 removed outlier: 5.708A pdb=" N CYS A 102 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASN A 148 " --> pdb=" O CYS A 102 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 154 through 157 current: chain 'A' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 183 through 186 current: chain 'B' and resid 117 through 121 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 128 through 131 current: chain 'B' and resid 156 through 159 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 156 through 159 current: chain 'K' and resid 117 through 121 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 126 through 129 current: chain 'K' and resid 155 through 158 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 155 through 158 current: chain 'P' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 126 through 129 current: chain 'P' and resid 155 through 158 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 155 through 158 current: chain 'I' and resid 83 through 88 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 92 through 97 current: chain 'I' and resid 122 through 125 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 122 through 125 current: chain 'J' and resid 107 through 112 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 117 through 121 current: chain 'J' and resid 146 through 149 Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 201 removed outlier: 6.319A pdb=" N CYS A 304 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N MET A 352 " --> pdb=" O CYS A 304 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE A 306 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ALA A 354 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE A 308 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY A 245 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N VAL A 375 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 247 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 174 removed outlier: 6.353A pdb=" N THR B 243 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE B 280 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B 245 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ASP B 282 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE B 247 " --> pdb=" O ASP B 282 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER B 277 " --> pdb=" O LYS B 323 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE B 325 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL B 279 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA B 327 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE B 281 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 219 " --> pdb=" O MET B 326 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N THR B 328 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 221 " --> pdb=" O THR B 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 862 through 863 removed outlier: 3.617A pdb=" N ARG C 909 " --> pdb=" O THR C 863 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 912 through 916 removed outlier: 4.298A pdb=" N ALA C 915 " --> pdb=" O ILE C 923 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 922 through 923 current: chain 'C' and resid 979 through 985 Processing sheet with id=AA6, first strand: chain 'C' and resid 945 through 952 removed outlier: 5.835A pdb=" N GLY C 947 " --> pdb=" O GLN C 931 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLN C 931 " --> pdb=" O GLY C 947 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 217 through 221 removed outlier: 6.107A pdb=" N CYS K 276 " --> pdb=" O LYS K 322 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE K 324 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE K 278 " --> pdb=" O ILE K 324 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA K 326 " --> pdb=" O ILE K 278 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N MET K 280 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN K 242 " --> pdb=" O ILE K 277 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE K 279 " --> pdb=" O ASN K 242 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE K 244 " --> pdb=" O PHE K 279 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP K 281 " --> pdb=" O ILE K 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 242 through 247 removed outlier: 6.583A pdb=" N THR P 242 " --> pdb=" O ILE P 277 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE P 279 " --> pdb=" O THR P 242 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU P 244 " --> pdb=" O PHE P 279 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASP P 281 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU P 246 " --> pdb=" O ASP P 281 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR P 276 " --> pdb=" O LYS P 322 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU P 324 " --> pdb=" O THR P 276 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE P 278 " --> pdb=" O LEU P 324 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ALA P 326 " --> pdb=" O ILE P 278 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE P 280 " --> pdb=" O ALA P 326 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA P 218 " --> pdb=" O ALA P 325 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N THR P 327 " --> pdb=" O ALA P 218 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N MET P 220 " --> pdb=" O THR P 327 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ILE P 347 " --> pdb=" O GLY P 217 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU P 219 " --> pdb=" O ILE P 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'J' and resid 233 through 238 removed outlier: 6.330A pdb=" N ALA J 233 " --> pdb=" O ILE J 268 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE J 270 " --> pdb=" O ALA J 233 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE J 235 " --> pdb=" O PHE J 270 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ASP J 272 " --> pdb=" O ILE J 235 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL J 237 " --> pdb=" O ASP J 272 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER J 267 " --> pdb=" O LYS J 313 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE J 315 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE J 269 " --> pdb=" O ILE J 315 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA J 317 " --> pdb=" O ILE J 269 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE J 271 " --> pdb=" O ALA J 317 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL J 209 " --> pdb=" O MET J 316 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY J 208 " --> pdb=" O ARG J 336 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE J 338 " --> pdb=" O GLY J 208 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU J 210 " --> pdb=" O ILE J 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'Z' and resid 713 through 715 Processing sheet with id=AB2, first strand: chain 'Z' and resid 758 through 762 removed outlier: 6.100A pdb=" N ILE Z 759 " --> pdb=" O VAL Z 903 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU Z 905 " --> pdb=" O ILE Z 759 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE Z 761 " --> pdb=" O LEU Z 905 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ASP Z 907 " --> pdb=" O ILE Z 761 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Z' and resid 768 through 769 removed outlier: 4.181A pdb=" N ILE Z 768 " --> pdb=" O ILE Z 917 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Z' and resid 866 through 869 Processing sheet with id=AB5, first strand: chain 'Z' and resid 934 through 935 removed outlier: 4.624A pdb=" N PHE L 98 " --> pdb=" O CYS L 15 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 8 through 10 1940 hydrogen bonds defined for protein. 5619 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: 8.15 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12127 1.34 - 1.46: 7202 1.46 - 1.58: 17443 1.58 - 1.70: 12 1.70 - 1.82: 265 Bond restraints: 37049 Sorted by residual: bond pdb=" CA GLN P 238 " pdb=" C GLN P 238 " ideal model delta sigma weight residual 1.523 1.491 0.031 1.41e-02 5.03e+03 4.89e+00 bond pdb=" CA MET Z 489 " pdb=" C MET Z 489 " ideal model delta sigma weight residual 1.524 1.545 -0.021 1.40e-02 5.10e+03 2.21e+00 bond pdb=" O3B ATP K 501 " pdb=" PB ATP K 501 " ideal model delta sigma weight residual 1.592 1.550 0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CG LEU Z 490 " pdb=" CD2 LEU Z 490 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.86e+00 bond pdb=" SD MET Z 539 " pdb=" CE MET Z 539 " ideal model delta sigma weight residual 1.791 1.757 0.034 2.50e-02 1.60e+03 1.83e+00 ... (remaining 37044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 49383 2.32 - 4.64: 580 4.64 - 6.96: 95 6.96 - 9.28: 35 9.28 - 11.60: 6 Bond angle restraints: 50099 Sorted by residual: angle pdb=" C LEU B 82 " pdb=" N LYS B 83 " pdb=" CA LYS B 83 " ideal model delta sigma weight residual 123.16 116.88 6.28 1.23e+00 6.61e-01 2.61e+01 angle pdb=" CA LYS N 117 " pdb=" CB LYS N 117 " pdb=" CG LYS N 117 " ideal model delta sigma weight residual 114.10 123.49 -9.39 2.00e+00 2.50e-01 2.20e+01 angle pdb=" CA MET Z 489 " pdb=" CB MET Z 489 " pdb=" CG MET Z 489 " ideal model delta sigma weight residual 114.10 123.47 -9.37 2.00e+00 2.50e-01 2.20e+01 angle pdb=" C PRO J 133 " pdb=" N SER J 134 " pdb=" CA SER J 134 " ideal model delta sigma weight residual 122.34 127.88 -5.54 1.39e+00 5.18e-01 1.59e+01 angle pdb=" CB MET B 326 " pdb=" CG MET B 326 " pdb=" SD MET B 326 " ideal model delta sigma weight residual 112.70 123.84 -11.14 3.00e+00 1.11e-01 1.38e+01 ... (remaining 50094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 20377 18.02 - 36.03: 1979 36.03 - 54.05: 403 54.05 - 72.07: 63 72.07 - 90.08: 36 Dihedral angle restraints: 22858 sinusoidal: 9444 harmonic: 13414 Sorted by residual: dihedral pdb=" CA ASP B 165 " pdb=" C ASP B 165 " pdb=" N PRO B 166 " pdb=" CA PRO B 166 " ideal model delta harmonic sigma weight residual 180.00 143.34 36.66 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CA PRO A 193 " pdb=" C PRO A 193 " pdb=" N SER A 194 " pdb=" CA SER A 194 " ideal model delta harmonic sigma weight residual -180.00 -153.67 -26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA PRO K 165 " pdb=" C PRO K 165 " pdb=" N LEU K 166 " pdb=" CA LEU K 166 " ideal model delta harmonic sigma weight residual 180.00 154.76 25.24 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 22855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3841 0.035 - 0.070: 1356 0.070 - 0.104: 425 0.104 - 0.139: 110 0.139 - 0.174: 17 Chirality restraints: 5749 Sorted by residual: chirality pdb=" CG LEU Z 535 " pdb=" CB LEU Z 535 " pdb=" CD1 LEU Z 535 " pdb=" CD2 LEU Z 535 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CB ILE A 183 " pdb=" CA ILE A 183 " pdb=" CG1 ILE A 183 " pdb=" CG2 ILE A 183 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA ILE N 142 " pdb=" N ILE N 142 " pdb=" C ILE N 142 " pdb=" CB ILE N 142 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.78e-01 ... (remaining 5746 not shown) Planarity restraints: 6452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 901 " -0.022 2.00e-02 2.50e+03 2.13e-02 7.90e+00 pdb=" CG PHE C 901 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE C 901 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE C 901 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 901 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 901 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 901 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 165 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO B 166 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 894 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C MET C 894 " -0.045 2.00e-02 2.50e+03 pdb=" O MET C 894 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU C 895 " 0.015 2.00e-02 2.50e+03 ... (remaining 6449 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 18670 2.98 - 3.46: 41434 3.46 - 3.94: 62822 3.94 - 4.42: 73619 4.42 - 4.90: 111746 Nonbonded interactions: 308291 Sorted by model distance: nonbonded pdb=" N GLN N 34 " pdb=" OE1 GLN N 34 " model vdw 2.496 3.120 nonbonded pdb=" N GLU K 205 " pdb=" OE1 GLU K 205 " model vdw 2.500 3.120 nonbonded pdb=" OD1 ASP D 273 " pdb=" OE1 GLU D 275 " model vdw 2.511 3.040 nonbonded pdb=" N ASP J 168 " pdb=" OD1 ASP J 168 " model vdw 2.512 3.120 nonbonded pdb=" N ASP N 202 " pdb=" OD1 ASP N 202 " model vdw 2.519 3.120 ... (remaining 308286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.140 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: 0.040 Extract box with map and model: 0.730 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.490 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 0.045 37049 Z= 0.157 Angle : 0.676 11.600 50099 Z= 0.359 Chirality : 0.041 0.174 5749 Planarity : 0.004 0.098 6452 Dihedral : 14.915 90.085 14182 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.30 % Allowed : 15.86 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.63 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.13), residues: 4585 helix: 0.81 (0.10), residues: 2596 sheet: -0.51 (0.26), residues: 366 loop : 0.68 (0.17), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 161 TYR 0.027 0.001 TYR A 145 PHE 0.047 0.002 PHE C 901 TRP 0.040 0.002 TRP L 100 HIS 0.010 0.001 HIS C 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (37049) covalent geometry : angle 0.67647 / 0.36 (50099) hydrogen bonds : bond 0.19833 / 13.37 ( 1940) hydrogen bonds : angle 7.36542 / 5.26 ( 5619) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8890 (mm) REVERT: A 148 ASN cc_start: 0.8837 (t0) cc_final: 0.8353 (t0) REVERT: A 281 GLN cc_start: 0.8752 (pt0) cc_final: 0.8434 (pp30) REVERT: B 127 ASP cc_start: 0.6983 (p0) cc_final: 0.6639 (p0) REVERT: B 255 LYS cc_start: 0.9118 (pttm) cc_final: 0.8675 (pttm) REVERT: B 256 TYR cc_start: 0.8100 (m-80) cc_final: 0.7576 (m-80) REVERT: B 306 MET cc_start: 0.9050 (tmm) cc_final: 0.8753 (ttm) REVERT: B 369 MET cc_start: 0.2813 (ptt) cc_final: 0.2472 (pmm) REVERT: B 424 MET cc_start: 0.7378 (mmm) cc_final: 0.7132 (mmm) REVERT: C 124 MET cc_start: -0.3759 (ttt) cc_final: -0.4207 (tpp) REVERT: C 293 MET cc_start: 0.7822 (tmm) cc_final: 0.7262 (ppp) REVERT: C 547 MET cc_start: 0.7140 (mmt) cc_final: 0.6731 (mpp) REVERT: C 775 MET cc_start: 0.3303 (mmt) cc_final: 0.2637 (mmt) REVERT: C 780 MET cc_start: 0.7984 (mmm) cc_final: 0.7717 (mmm) REVERT: C 862 MET cc_start: 0.6293 (mmp) cc_final: 0.5643 (tpp) REVERT: C 990 ARG cc_start: 0.5336 (pmt-80) cc_final: 0.4292 (mmt-90) REVERT: D 121 GLU cc_start: 0.8965 (tt0) cc_final: 0.8511 (pt0) REVERT: D 309 MET cc_start: 0.8267 (mmm) cc_final: 0.7939 (tpt) REVERT: K 156 MET cc_start: 0.7649 (mmm) cc_final: 0.7430 (mmm) REVERT: P 244 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7039 (mp) REVERT: P 305 MET cc_start: 0.8393 (tmm) cc_final: 0.7700 (tmm) REVERT: P 395 THR cc_start: 0.8527 (m) cc_final: 0.8287 (t) REVERT: I 63 ARG cc_start: 0.8946 (ptp-170) cc_final: 0.8600 (ptp-170) REVERT: J 161 MET cc_start: 0.6963 (mmm) cc_final: 0.5680 (mmm) REVERT: J 171 TYR cc_start: 0.8280 (m-80) cc_final: 0.8064 (m-80) REVERT: J 221 MET cc_start: 0.8806 (ptm) cc_final: 0.8557 (ptm) REVERT: J 316 MET cc_start: 0.6756 (tpp) cc_final: 0.6396 (tpp) REVERT: J 375 ASN cc_start: 0.8184 (p0) cc_final: 0.7879 (p0) REVERT: Z 386 MET cc_start: 0.6826 (mmt) cc_final: 0.6594 (mmt) REVERT: Z 625 LEU cc_start: 0.8474 (mt) cc_final: 0.8252 (mt) REVERT: Z 706 MET cc_start: 0.7624 (mmm) cc_final: 0.7389 (mmm) REVERT: Z 716 GLN cc_start: 0.7335 (tt0) cc_final: 0.7127 (pp30) REVERT: Z 773 MET cc_start: 0.8269 (mpp) cc_final: 0.7432 (mpp) REVERT: Z 787 MET cc_start: 0.7815 (mmm) cc_final: 0.7584 (mmm) REVERT: N 40 LEU cc_start: 0.9446 (mt) cc_final: 0.9104 (pp) REVERT: N 73 TRP cc_start: 0.9132 (m100) cc_final: 0.8674 (m100) REVERT: N 141 GLN cc_start: 0.9003 (mt0) cc_final: 0.8745 (tt0) REVERT: N 180 HIS cc_start: 0.8269 (m-70) cc_final: 0.7610 (m-70) outliers start: 52 outliers final: 42 residues processed: 344 average time/residue: 0.2080 time to fit residues: 121.9440 Evaluate side-chains 336 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain P residue 173 ASP Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain P residue 400 MET Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 306 PHE Chi-restraints excluded: chain Z residue 380 LEU Chi-restraints excluded: chain Z residue 581 ASP Chi-restraints excluded: chain Z residue 595 LEU Chi-restraints excluded: chain Z residue 664 LEU Chi-restraints excluded: chain L residue 114 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: [432, 197, 388, 455, 215, 20, 132, 261, 248, 207, 401] chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 ASN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 499 HIS Z 712 ASN ** N 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.090771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.069440 restraints weight = 275653.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.070268 restraints weight = 152843.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.070180 restraints weight = 101356.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.070257 restraints weight = 111367.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.070450 restraints weight = 94512.965| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37049 Z= 0.202 Angle : 0.633 10.636 50099 Z= 0.330 Chirality : 0.042 0.163 5749 Planarity : 0.004 0.064 6452 Dihedral : 7.977 81.690 5219 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.32 % Allowed : 14.16 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.63 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.13), residues: 4585 helix: 1.22 (0.10), residues: 2643 sheet: -0.61 (0.26), residues: 371 loop : 0.57 (0.17), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 798 TYR 0.026 0.001 TYR A 145 PHE 0.024 0.002 PHE N 120 TRP 0.018 0.001 TRP L 100 HIS 0.007 0.001 HIS J 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (37049) covalent geometry : angle 0.63299 / 0.33 (50099) hydrogen bonds : bond 0.05244 / 3.49 ( 1940) hydrogen bonds : angle 5.16489 / 3.69 ( 5619) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 299 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9108 (pmm) cc_final: 0.8717 (pmm) REVERT: B 127 ASP cc_start: 0.7016 (p0) cc_final: 0.6633 (p0) REVERT: B 167 MET cc_start: 0.2122 (OUTLIER) cc_final: 0.1686 (ttt) REVERT: B 255 LYS cc_start: 0.9091 (pttm) cc_final: 0.8724 (pttm) REVERT: B 256 TYR cc_start: 0.8169 (m-80) cc_final: 0.7659 (m-80) REVERT: B 339 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9175 (tp) REVERT: B 369 MET cc_start: 0.2955 (ptt) cc_final: 0.2624 (pmm) REVERT: C 124 MET cc_start: -0.3774 (ttt) cc_final: -0.4446 (tpp) REVERT: C 293 MET cc_start: 0.7758 (tmm) cc_final: 0.7300 (ppp) REVERT: C 415 MET cc_start: 0.7254 (tpp) cc_final: 0.6766 (mmm) REVERT: C 775 MET cc_start: 0.3613 (mmt) cc_final: 0.2944 (mmt) REVERT: C 862 MET cc_start: 0.6975 (mmp) cc_final: 0.6683 (mmp) REVERT: C 990 ARG cc_start: 0.5403 (pmt-80) cc_final: 0.4355 (mmt-90) REVERT: D 231 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.7105 (mm) REVERT: D 309 MET cc_start: 0.7916 (mmm) cc_final: 0.7195 (tpt) REVERT: P 58 MET cc_start: 0.8278 (mmp) cc_final: 0.7829 (tpt) REVERT: P 305 MET cc_start: 0.8320 (tmm) cc_final: 0.7648 (tmm) REVERT: P 395 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8156 (t) REVERT: I 65 LEU cc_start: 0.9439 (mt) cc_final: 0.9181 (mt) REVERT: J 161 MET cc_start: 0.6935 (mmm) cc_final: 0.5752 (mmm) REVERT: J 303 MET cc_start: 0.9280 (pmm) cc_final: 0.8871 (pmm) REVERT: J 316 MET cc_start: 0.7149 (tpp) cc_final: 0.6927 (tpp) REVERT: Z 386 MET cc_start: 0.6689 (mmt) cc_final: 0.6320 (mmt) REVERT: Z 625 LEU cc_start: 0.8402 (mt) cc_final: 0.8162 (mt) REVERT: Z 773 MET cc_start: 0.8132 (mpp) cc_final: 0.7323 (mpp) REVERT: N 73 TRP cc_start: 0.9255 (m100) cc_final: 0.8757 (m100) REVERT: N 76 PHE cc_start: 0.9459 (t80) cc_final: 0.9104 (m-80) REVERT: N 106 GLN cc_start: 0.9231 (mp10) cc_final: 0.9021 (pm20) REVERT: N 180 HIS cc_start: 0.8215 (m-70) cc_final: 0.7789 (m-70) outliers start: 93 outliers final: 52 residues processed: 377 average time/residue: 0.2052 time to fit residues: 130.9329 Evaluate side-chains 336 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 280 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 181 ASP Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 323 ILE Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 173 ASP Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 306 PHE Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain Z residue 581 ASP Chi-restraints excluded: chain Z residue 595 LEU Chi-restraints excluded: chain Z residue 609 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 700 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: [435, 290, 296, 349, 416, 108, 100, 183, 121, 409, 451] chunk 435 optimal weight: 20.0000 chunk 290 optimal weight: 0.9990 chunk 296 optimal weight: 4.9990 chunk 349 optimal weight: 9.9990 chunk 416 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 409 optimal weight: 0.9990 chunk 451 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 ASN ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 GLN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.089959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.064992 restraints weight = 263332.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.065477 restraints weight = 134979.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.065810 restraints weight = 93072.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.066473 restraints weight = 78008.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.066592 restraints weight = 70217.320| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37049 Z= 0.196 Angle : 0.615 11.448 50099 Z= 0.316 Chirality : 0.042 0.188 5749 Planarity : 0.004 0.067 6452 Dihedral : 7.835 82.695 5191 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.07 % Allowed : 14.19 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.63 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.13), residues: 4585 helix: 1.26 (0.10), residues: 2630 sheet: -0.62 (0.27), residues: 363 loop : 0.54 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 187 TYR 0.026 0.001 TYR A 145 PHE 0.033 0.002 PHE C 389 TRP 0.011 0.001 TRP L 75 HIS 0.008 0.001 HIS J 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (37049) covalent geometry : angle 0.61458 / 0.32 (50099) hydrogen bonds : bond 0.04343 / 2.87 ( 1940) hydrogen bonds : angle 4.89119 / 3.48 ( 5619) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 306 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8120 (mp0) REVERT: A 299 ARG cc_start: 0.6229 (OUTLIER) cc_final: 0.5953 (mmt180) REVERT: B 127 ASP cc_start: 0.7335 (p0) cc_final: 0.6969 (p0) REVERT: B 167 MET cc_start: 0.1389 (OUTLIER) cc_final: 0.1152 (ttt) REVERT: B 255 LYS cc_start: 0.8847 (pttm) cc_final: 0.8432 (pttm) REVERT: B 256 TYR cc_start: 0.7690 (m-80) cc_final: 0.7232 (m-80) REVERT: B 339 ILE cc_start: 0.9475 (OUTLIER) cc_final: 0.9243 (tp) REVERT: B 424 MET cc_start: 0.7004 (mmm) cc_final: 0.6673 (mmm) REVERT: C 124 MET cc_start: -0.1082 (ttt) cc_final: -0.1878 (tpp) REVERT: C 775 MET cc_start: 0.3391 (mmt) cc_final: 0.2732 (mmt) REVERT: C 862 MET cc_start: 0.6696 (mmp) cc_final: 0.6305 (mmp) REVERT: C 990 ARG cc_start: 0.5639 (pmt-80) cc_final: 0.4730 (mmt180) REVERT: D 17 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7999 (tp30) REVERT: D 231 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.7001 (mm) REVERT: K 208 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8976 (pm20) REVERT: P 58 MET cc_start: 0.8301 (mmp) cc_final: 0.7856 (tpt) REVERT: P 305 MET cc_start: 0.8277 (tmm) cc_final: 0.7561 (tmm) REVERT: P 395 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8157 (t) REVERT: I 63 ARG cc_start: 0.9032 (ptp-170) cc_final: 0.8801 (ptp-170) REVERT: I 64 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8886 (mm) REVERT: J 131 LEU cc_start: 0.9182 (mt) cc_final: 0.8958 (mp) REVERT: J 161 MET cc_start: 0.7134 (mmm) cc_final: 0.5683 (mmm) REVERT: J 303 MET cc_start: 0.9134 (pmm) cc_final: 0.8856 (pmm) REVERT: J 313 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6789 (mtmt) REVERT: Z 386 MET cc_start: 0.6558 (mmt) cc_final: 0.6264 (mmt) REVERT: Z 773 MET cc_start: 0.7813 (mpp) cc_final: 0.7093 (mpp) REVERT: Z 787 MET cc_start: 0.7924 (mmm) cc_final: 0.7093 (mmm) REVERT: N 59 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8277 (pmm) REVERT: N 73 TRP cc_start: 0.9387 (m-10) cc_final: 0.9030 (m100) REVERT: N 76 PHE cc_start: 0.9578 (t80) cc_final: 0.9324 (m-80) REVERT: N 125 PHE cc_start: 0.9679 (t80) cc_final: 0.9421 (t80) REVERT: N 180 HIS cc_start: 0.8308 (m-70) cc_final: 0.7861 (m-70) outliers start: 123 outliers final: 69 residues processed: 403 average time/residue: 0.2155 time to fit residues: 146.4538 Evaluate side-chains 360 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 281 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 181 ASP Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 323 ILE Chi-restraints excluded: chain K residue 384 ASP Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain P residue 173 ASP Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain P residue 199 LEU Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 134 SER Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 306 PHE Chi-restraints excluded: chain J residue 313 LYS Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain Z residue 455 MET Chi-restraints excluded: chain Z residue 581 ASP Chi-restraints excluded: chain Z residue 591 LEU Chi-restraints excluded: chain Z residue 595 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 664 LEU Chi-restraints excluded: chain Z residue 700 CYS Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain N residue 59 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: [456, 398, 6, 328, 234, 354, 81, 339, 76, 80, 110] chunk 456 optimal weight: 6.9990 chunk 398 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 chunk 328 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 339 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 68 HIS ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.090718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.069304 restraints weight = 275375.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.069882 restraints weight = 166804.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.069765 restraints weight = 107060.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.069911 restraints weight = 108973.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.070058 restraints weight = 96318.176| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37049 Z= 0.159 Angle : 0.599 13.113 50099 Z= 0.303 Chirality : 0.041 0.294 5749 Planarity : 0.004 0.064 6452 Dihedral : 7.745 86.086 5190 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.67 % Allowed : 14.74 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.13), residues: 4585 helix: 1.35 (0.10), residues: 2638 sheet: -0.70 (0.26), residues: 371 loop : 0.63 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 786 TYR 0.026 0.001 TYR A 145 PHE 0.037 0.002 PHE C 389 TRP 0.011 0.001 TRP N 42 HIS 0.007 0.001 HIS J 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (37049) covalent geometry : angle 0.59938 / 0.30 (50099) hydrogen bonds : bond 0.03945 / 2.60 ( 1940) hydrogen bonds : angle 4.72981 / 3.36 ( 5619) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 296 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8554 (mp0) REVERT: B 127 ASP cc_start: 0.7497 (p0) cc_final: 0.6937 (p0) REVERT: B 167 MET cc_start: 0.2746 (OUTLIER) cc_final: 0.2368 (ttt) REVERT: B 255 LYS cc_start: 0.9192 (pttm) cc_final: 0.8704 (pttm) REVERT: B 256 TYR cc_start: 0.8314 (m-80) cc_final: 0.7657 (m-80) REVERT: B 339 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9237 (tp) REVERT: B 369 MET cc_start: 0.4840 (pmm) cc_final: 0.4343 (pmm) REVERT: B 424 MET cc_start: 0.7172 (mmm) cc_final: 0.6891 (mmm) REVERT: C 124 MET cc_start: -0.3735 (ttt) cc_final: -0.4496 (tpp) REVERT: C 293 MET cc_start: 0.7658 (tmm) cc_final: 0.7360 (ppp) REVERT: C 775 MET cc_start: 0.3502 (mmt) cc_final: 0.2768 (mmt) REVERT: C 862 MET cc_start: 0.6870 (mmp) cc_final: 0.6514 (mmp) REVERT: C 990 ARG cc_start: 0.5583 (pmt-80) cc_final: 0.4619 (mmt180) REVERT: D 231 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7062 (mm) REVERT: D 309 MET cc_start: 0.7630 (mmm) cc_final: 0.7032 (tpt) REVERT: K 208 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8777 (pm20) REVERT: P 58 MET cc_start: 0.8242 (mmp) cc_final: 0.7847 (tpt) REVERT: P 305 MET cc_start: 0.8362 (tmm) cc_final: 0.7763 (tmm) REVERT: P 395 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8126 (t) REVERT: J 131 LEU cc_start: 0.9192 (mt) cc_final: 0.8922 (mp) REVERT: J 161 MET cc_start: 0.6769 (mmm) cc_final: 0.5484 (mmm) REVERT: J 171 TYR cc_start: 0.8159 (m-80) cc_final: 0.7805 (m-80) REVERT: J 221 MET cc_start: 0.8845 (ptm) cc_final: 0.8580 (ptm) REVERT: J 313 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7396 (tptp) REVERT: J 316 MET cc_start: 0.6890 (tpp) cc_final: 0.6626 (tpp) REVERT: J 375 ASN cc_start: 0.7931 (p0) cc_final: 0.7707 (p0) REVERT: Z 773 MET cc_start: 0.8238 (mpp) cc_final: 0.7412 (mpp) REVERT: N 73 TRP cc_start: 0.9317 (m-10) cc_final: 0.8863 (m100) REVERT: N 76 PHE cc_start: 0.9545 (OUTLIER) cc_final: 0.9226 (m-80) REVERT: N 106 GLN cc_start: 0.9229 (mp10) cc_final: 0.9018 (pm20) REVERT: N 124 GLN cc_start: 0.9261 (mt0) cc_final: 0.9036 (mp10) REVERT: N 125 PHE cc_start: 0.9682 (t80) cc_final: 0.9403 (t80) REVERT: N 180 HIS cc_start: 0.8368 (m-70) cc_final: 0.7927 (m-70) outliers start: 107 outliers final: 68 residues processed: 382 average time/residue: 0.2017 time to fit residues: 131.7030 Evaluate side-chains 351 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 276 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 181 ASP Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 323 ILE Chi-restraints excluded: chain K residue 384 ASP Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain P residue 173 ASP Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 306 PHE Chi-restraints excluded: chain J residue 313 LYS Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain Z residue 455 MET Chi-restraints excluded: chain Z residue 581 ASP Chi-restraints excluded: chain Z residue 591 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 664 LEU Chi-restraints excluded: chain Z residue 700 CYS Chi-restraints excluded: chain Z residue 920 VAL Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 173 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: [131, 243, 341, 445, 402, 221, 27, 250, 154, 279, 179] chunk 131 optimal weight: 10.0000 chunk 243 optimal weight: 0.5980 chunk 341 optimal weight: 8.9990 chunk 445 optimal weight: 9.9990 chunk 402 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 250 optimal weight: 8.9990 chunk 154 optimal weight: 0.0670 chunk 279 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 HIS ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN K 169 ASN P 412 HIS J 264 ASN Z 111 GLN ** N 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.091400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.069466 restraints weight = 273947.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.070540 restraints weight = 172025.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.070833 restraints weight = 116721.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.071114 restraints weight = 93386.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.071093 restraints weight = 80068.399| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37049 Z= 0.123 Angle : 0.581 14.755 50099 Z= 0.289 Chirality : 0.041 0.311 5749 Planarity : 0.004 0.062 6452 Dihedral : 7.556 88.205 5185 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.47 % Allowed : 15.66 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.13), residues: 4585 helix: 1.51 (0.10), residues: 2636 sheet: -0.70 (0.26), residues: 373 loop : 0.67 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 711 TYR 0.022 0.001 TYR A 145 PHE 0.038 0.002 PHE C 389 TRP 0.010 0.001 TRP L 75 HIS 0.006 0.001 HIS J 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (37049) covalent geometry : angle 0.58119 / 0.29 (50099) hydrogen bonds : bond 0.03668 / 2.41 ( 1940) hydrogen bonds : angle 4.55810 / 3.24 ( 5619) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 307 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 ASP cc_start: 0.7460 (p0) cc_final: 0.7029 (p0) REVERT: B 167 MET cc_start: 0.2200 (OUTLIER) cc_final: 0.1925 (ttt) REVERT: B 255 LYS cc_start: 0.9096 (pttm) cc_final: 0.8612 (pttm) REVERT: B 256 TYR cc_start: 0.8146 (m-80) cc_final: 0.7506 (m-80) REVERT: B 369 MET cc_start: 0.4626 (pmm) cc_final: 0.4179 (pmm) REVERT: C 124 MET cc_start: -0.3452 (ttt) cc_final: -0.4251 (tpp) REVERT: C 293 MET cc_start: 0.7532 (tmm) cc_final: 0.7244 (ppp) REVERT: C 775 MET cc_start: 0.3416 (mmt) cc_final: 0.3110 (mmt) REVERT: C 834 LEU cc_start: 0.9001 (mm) cc_final: 0.8484 (tt) REVERT: C 862 MET cc_start: 0.7059 (mmp) cc_final: 0.6721 (mmp) REVERT: C 990 ARG cc_start: 0.5600 (pmt-80) cc_final: 0.4650 (mmt180) REVERT: D 139 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8541 (mm) REVERT: D 231 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6863 (mm) REVERT: D 309 MET cc_start: 0.7510 (mmm) cc_final: 0.6873 (tpt) REVERT: K 109 MET cc_start: 0.8664 (mmm) cc_final: 0.8396 (mmm) REVERT: K 208 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8747 (pm20) REVERT: P 58 MET cc_start: 0.8301 (mmp) cc_final: 0.7901 (tpt) REVERT: P 305 MET cc_start: 0.8347 (tmm) cc_final: 0.8116 (tmm) REVERT: I 24 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7638 (mm-30) REVERT: I 127 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5932 (tm-30) REVERT: J 161 MET cc_start: 0.6963 (mmm) cc_final: 0.5678 (mmm) REVERT: J 221 MET cc_start: 0.8742 (ptm) cc_final: 0.8465 (ptm) REVERT: J 290 ARG cc_start: 0.8771 (mpt-90) cc_final: 0.8444 (mpt-90) REVERT: Z 773 MET cc_start: 0.7915 (mpp) cc_final: 0.7158 (mpp) REVERT: N 10 CYS cc_start: 0.8913 (m) cc_final: 0.8657 (m) REVERT: N 40 LEU cc_start: 0.9220 (mm) cc_final: 0.9006 (pp) REVERT: N 42 TRP cc_start: 0.8698 (m100) cc_final: 0.8258 (m100) REVERT: N 59 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8224 (pmm) REVERT: N 73 TRP cc_start: 0.9267 (m-10) cc_final: 0.8781 (m100) REVERT: N 76 PHE cc_start: 0.9549 (OUTLIER) cc_final: 0.9236 (m-80) REVERT: N 106 GLN cc_start: 0.9266 (mp10) cc_final: 0.9024 (pm20) REVERT: N 124 GLN cc_start: 0.9266 (mt0) cc_final: 0.9030 (mp10) REVERT: N 125 PHE cc_start: 0.9672 (t80) cc_final: 0.9350 (t80) REVERT: N 180 HIS cc_start: 0.8320 (m-70) cc_final: 0.7995 (m-70) outliers start: 99 outliers final: 61 residues processed: 386 average time/residue: 0.2060 time to fit residues: 136.2572 Evaluate side-chains 350 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 282 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 384 ASP Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain P residue 126 THR Chi-restraints excluded: chain P residue 173 ASP Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 306 PHE Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain Z residue 455 MET Chi-restraints excluded: chain Z residue 581 ASP Chi-restraints excluded: chain Z residue 595 LEU Chi-restraints excluded: chain Z residue 664 LEU Chi-restraints excluded: chain Z residue 920 VAL Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 59 MET Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 92 TYR Chi-restraints excluded: chain N residue 173 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: [286, 455, 71, 91, 339, 380, 218, 375, 10, 388, 171] chunk 286 optimal weight: 6.9990 chunk 455 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 339 optimal weight: 30.0000 chunk 380 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 375 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 388 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 GLN ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 ASN K 393 ASN P 53 HIS Z 280 GLN ** Z 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN ** N 180 HIS ** 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 = 0.4278 r_free = 0.4278 target = 0.089566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.064264 restraints weight = 264599.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.065340 restraints weight = 137913.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.065697 restraints weight = 95611.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.065818 restraints weight = 78909.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.065818 restraints weight = 73200.986| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37049 Z= 0.195 Angle : 0.623 14.163 50099 Z= 0.314 Chirality : 0.042 0.263 5749 Planarity : 0.004 0.065 6452 Dihedral : 7.637 86.540 5181 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.82 % Allowed : 15.91 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.13), residues: 4585 helix: 1.40 (0.10), residues: 2627 sheet: -0.88 (0.25), residues: 378 loop : 0.63 (0.17), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 711 TYR 0.024 0.001 TYR A 145 PHE 0.040 0.002 PHE K 400 TRP 0.011 0.001 TRP N 42 HIS 0.013 0.001 HIS P 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (37049) covalent geometry : angle 0.62290 / 0.31 (50099) hydrogen bonds : bond 0.03762 / 2.48 ( 1940) hydrogen bonds : angle 4.69568 / 3.33 ( 5619) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 289 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 ASP cc_start: 0.7565 (p0) cc_final: 0.6991 (p0) REVERT: B 167 MET cc_start: 0.2101 (OUTLIER) cc_final: 0.1808 (ttt) REVERT: B 256 TYR cc_start: 0.7854 (m-80) cc_final: 0.7577 (m-80) REVERT: B 306 MET cc_start: 0.8950 (ttm) cc_final: 0.8489 (tmm) REVERT: B 369 MET cc_start: 0.4156 (pmm) cc_final: 0.3782 (pmm) REVERT: B 424 MET cc_start: 0.6737 (mmm) cc_final: 0.6254 (mmm) REVERT: C 124 MET cc_start: -0.0577 (ttt) cc_final: -0.1339 (tpp) REVERT: C 293 MET cc_start: 0.8042 (tmm) cc_final: 0.7776 (ppp) REVERT: C 775 MET cc_start: 0.3142 (mmt) cc_final: 0.2825 (mmt) REVERT: C 834 LEU cc_start: 0.8505 (mm) cc_final: 0.7872 (tt) REVERT: C 862 MET cc_start: 0.6964 (mmp) cc_final: 0.6585 (mmp) REVERT: C 990 ARG cc_start: 0.5698 (pmt-80) cc_final: 0.4850 (mmt180) REVERT: D 231 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7091 (mm) REVERT: D 309 MET cc_start: 0.7496 (mmm) cc_final: 0.7221 (tpt) REVERT: K 208 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8938 (pm20) REVERT: P 58 MET cc_start: 0.8297 (mmp) cc_final: 0.7880 (tpt) REVERT: P 84 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: P 305 MET cc_start: 0.8470 (tmm) cc_final: 0.8093 (tmm) REVERT: P 395 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8118 (t) REVERT: I 24 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7890 (mm-30) REVERT: I 127 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5960 (tm-30) REVERT: J 161 MET cc_start: 0.6891 (mmm) cc_final: 0.5618 (mmm) REVERT: J 221 MET cc_start: 0.8938 (ptm) cc_final: 0.8723 (ptm) REVERT: J 316 MET cc_start: 0.6952 (tpp) cc_final: 0.6698 (tpp) REVERT: Z 386 MET cc_start: 0.6508 (mmt) cc_final: 0.6256 (mmt) REVERT: Z 706 MET cc_start: 0.7804 (mmm) cc_final: 0.7573 (mmm) REVERT: Z 773 MET cc_start: 0.7729 (mpp) cc_final: 0.6961 (mpp) REVERT: N 10 CYS cc_start: 0.9043 (m) cc_final: 0.8784 (m) REVERT: N 73 TRP cc_start: 0.9372 (m-10) cc_final: 0.8908 (m100) REVERT: N 76 PHE cc_start: 0.9610 (t80) cc_final: 0.9353 (m-80) REVERT: N 78 ILE cc_start: 0.9592 (mp) cc_final: 0.9100 (tt) REVERT: N 125 PHE cc_start: 0.9711 (t80) cc_final: 0.9473 (t80) REVERT: N 180 HIS cc_start: 0.8452 (m-70) cc_final: 0.8095 (m-70) outliers start: 113 outliers final: 78 residues processed: 377 average time/residue: 0.2015 time to fit residues: 129.9079 Evaluate side-chains 351 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 267 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 323 ILE Chi-restraints excluded: chain K residue 384 ASP Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain P residue 84 GLU Chi-restraints excluded: chain P residue 126 THR Chi-restraints excluded: chain P residue 173 ASP Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 330 VAL Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 306 PHE Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain Z residue 295 THR Chi-restraints excluded: chain Z residue 455 MET Chi-restraints excluded: chain Z residue 523 LEU Chi-restraints excluded: chain Z residue 547 LEU Chi-restraints excluded: chain Z residue 581 ASP Chi-restraints excluded: chain Z residue 591 LEU Chi-restraints excluded: chain Z residue 595 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 664 LEU Chi-restraints excluded: chain Z residue 700 CYS Chi-restraints excluded: chain Z residue 920 VAL Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 92 TYR Chi-restraints excluded: chain N residue 173 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: [4, 349, 168, 196, 394, 338, 31, 262, 62, 440, 26] chunk 4 optimal weight: 10.0000 chunk 349 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 394 optimal weight: 0.8980 chunk 338 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 440 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 161 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN K 393 ASN N 3 ASN ** N 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.090883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.070182 restraints weight = 277222.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.070950 restraints weight = 183416.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.070497 restraints weight = 115417.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.070751 restraints weight = 127392.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.070955 restraints weight = 101775.866| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37049 Z= 0.134 Angle : 0.601 13.372 50099 Z= 0.297 Chirality : 0.042 0.282 5749 Planarity : 0.004 0.063 6452 Dihedral : 7.538 86.904 5181 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.50 % Allowed : 16.68 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.13), residues: 4585 helix: 1.51 (0.10), residues: 2632 sheet: -0.86 (0.26), residues: 369 loop : 0.67 (0.17), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 56 TYR 0.019 0.001 TYR Z 406 PHE 0.039 0.002 PHE C 389 TRP 0.011 0.001 TRP N 42 HIS 0.006 0.001 HIS J 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (37049) covalent geometry : angle 0.60139 / 0.30 (50099) hydrogen bonds : bond 0.03562 / 2.34 ( 1940) hydrogen bonds : angle 4.56991 / 3.23 ( 5619) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 293 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 ASP cc_start: 0.7424 (p0) cc_final: 0.6918 (p0) REVERT: B 167 MET cc_start: 0.2424 (OUTLIER) cc_final: 0.2184 (ttt) REVERT: B 255 LYS cc_start: 0.9170 (pttm) cc_final: 0.8677 (pttm) REVERT: B 256 TYR cc_start: 0.8162 (m-80) cc_final: 0.7478 (m-80) REVERT: B 306 MET cc_start: 0.8939 (ttm) cc_final: 0.8451 (tmm) REVERT: B 369 MET cc_start: 0.4518 (pmm) cc_final: 0.4066 (pmm) REVERT: B 411 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8510 (p) REVERT: B 424 MET cc_start: 0.7101 (mmm) cc_final: 0.6825 (mmm) REVERT: C 124 MET cc_start: -0.3669 (ttt) cc_final: -0.4422 (tpp) REVERT: C 775 MET cc_start: 0.3542 (mmt) cc_final: 0.3194 (mmt) REVERT: C 815 MET cc_start: 0.9144 (mmm) cc_final: 0.8873 (mmt) REVERT: C 862 MET cc_start: 0.7148 (mmp) cc_final: 0.6899 (mmp) REVERT: C 990 ARG cc_start: 0.5475 (pmt-80) cc_final: 0.4454 (mmt180) REVERT: D 231 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6955 (mm) REVERT: D 309 MET cc_start: 0.7357 (mmm) cc_final: 0.7122 (tpt) REVERT: K 109 MET cc_start: 0.8682 (mmm) cc_final: 0.8444 (mmm) REVERT: K 208 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8962 (pm20) REVERT: K 249 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8586 (p) REVERT: P 58 MET cc_start: 0.8305 (mmp) cc_final: 0.7897 (tpt) REVERT: P 305 MET cc_start: 0.8347 (tmm) cc_final: 0.8112 (tmm) REVERT: P 324 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7963 (pp) REVERT: I 24 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7706 (mm-30) REVERT: I 63 ARG cc_start: 0.8913 (ptp-170) cc_final: 0.8667 (ptp-170) REVERT: I 127 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5978 (tm-30) REVERT: J 161 MET cc_start: 0.6679 (mmm) cc_final: 0.5546 (mmm) REVERT: J 171 TYR cc_start: 0.8337 (m-80) cc_final: 0.8013 (m-80) REVERT: J 221 MET cc_start: 0.8789 (ptm) cc_final: 0.8585 (ptm) REVERT: J 290 ARG cc_start: 0.8840 (mpt-90) cc_final: 0.8456 (mpt-90) REVERT: J 316 MET cc_start: 0.7114 (tpp) cc_final: 0.6901 (tpp) REVERT: Z 773 MET cc_start: 0.7942 (mpp) cc_final: 0.7141 (mpp) REVERT: N 10 CYS cc_start: 0.9090 (m) cc_final: 0.8847 (m) REVERT: N 11 MET cc_start: 0.8488 (mtm) cc_final: 0.8245 (mtm) REVERT: N 73 TRP cc_start: 0.9176 (m-10) cc_final: 0.8608 (m100) REVERT: N 76 PHE cc_start: 0.9536 (t80) cc_final: 0.9237 (m-80) REVERT: N 78 ILE cc_start: 0.9628 (mp) cc_final: 0.9115 (tt) REVERT: N 125 PHE cc_start: 0.9666 (t80) cc_final: 0.9422 (t80) REVERT: N 180 HIS cc_start: 0.8312 (m-70) cc_final: 0.8019 (m-70) outliers start: 100 outliers final: 69 residues processed: 374 average time/residue: 0.2011 time to fit residues: 128.5006 Evaluate side-chains 360 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 284 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 384 ASP Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain P residue 126 THR Chi-restraints excluded: chain P residue 173 ASP Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 306 PHE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain Z residue 455 MET Chi-restraints excluded: chain Z residue 547 LEU Chi-restraints excluded: chain Z residue 581 ASP Chi-restraints excluded: chain Z residue 595 LEU Chi-restraints excluded: chain Z residue 664 LEU Chi-restraints excluded: chain Z residue 700 CYS Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 92 TYR Chi-restraints excluded: chain N residue 173 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: [105, 322, 388, 40, 70, 270, 364, 13, 210, 155, 38] chunk 105 optimal weight: 20.0000 chunk 322 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 270 optimal weight: 0.8980 chunk 364 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 210 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 905 ASN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 ASN K 393 ASN ** N 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.091396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.070596 restraints weight = 274083.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.071596 restraints weight = 148288.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.070968 restraints weight = 99814.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.071164 restraints weight = 136961.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.071512 restraints weight = 102148.081| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37049 Z= 0.115 Angle : 0.607 16.041 50099 Z= 0.295 Chirality : 0.042 0.279 5749 Planarity : 0.004 0.061 6452 Dihedral : 7.380 85.070 5176 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.10 % Allowed : 17.21 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.13), residues: 4585 helix: 1.57 (0.10), residues: 2631 sheet: -0.68 (0.26), residues: 360 loop : 0.71 (0.17), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 56 TYR 0.021 0.001 TYR A 145 PHE 0.039 0.002 PHE C 389 TRP 0.012 0.001 TRP N 42 HIS 0.005 0.001 HIS J 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (37049) covalent geometry : angle 0.60684 / 0.29 (50099) hydrogen bonds : bond 0.03445 / 2.27 ( 1940) hydrogen bonds : angle 4.45973 / 3.16 ( 5619) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 304 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 ASP cc_start: 0.7455 (p0) cc_final: 0.6827 (p0) REVERT: B 255 LYS cc_start: 0.9204 (pttm) cc_final: 0.8713 (pttm) REVERT: B 256 TYR cc_start: 0.8358 (m-80) cc_final: 0.7683 (m-80) REVERT: B 306 MET cc_start: 0.8997 (ttm) cc_final: 0.8510 (tmm) REVERT: B 369 MET cc_start: 0.5018 (pmm) cc_final: 0.4739 (pmm) REVERT: B 411 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8392 (p) REVERT: B 424 MET cc_start: 0.7170 (mmm) cc_final: 0.6902 (mmm) REVERT: C 124 MET cc_start: -0.3499 (ttt) cc_final: -0.4291 (tpp) REVERT: C 415 MET cc_start: 0.6945 (tpp) cc_final: 0.5997 (mmm) REVERT: C 775 MET cc_start: 0.3082 (mmt) cc_final: 0.2753 (mmt) REVERT: C 815 MET cc_start: 0.9208 (mmm) cc_final: 0.8959 (mmt) REVERT: C 834 LEU cc_start: 0.9051 (mm) cc_final: 0.8526 (tt) REVERT: C 862 MET cc_start: 0.7115 (mmp) cc_final: 0.6834 (mmp) REVERT: C 990 ARG cc_start: 0.5659 (pmt-80) cc_final: 0.4748 (mmt180) REVERT: D 231 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6872 (mm) REVERT: D 309 MET cc_start: 0.7309 (mmm) cc_final: 0.7093 (tpt) REVERT: K 109 MET cc_start: 0.8660 (mmm) cc_final: 0.8400 (mmm) REVERT: K 156 MET cc_start: 0.8013 (mmm) cc_final: 0.7795 (mmm) REVERT: K 161 ARG cc_start: 0.5944 (tmt170) cc_final: 0.5532 (tmt170) REVERT: K 208 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8953 (pm20) REVERT: K 249 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8519 (p) REVERT: P 324 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7943 (pp) REVERT: I 24 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7787 (mm-30) REVERT: I 121 MET cc_start: 0.8988 (tpp) cc_final: 0.8456 (tpp) REVERT: I 127 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5950 (tm-30) REVERT: J 161 MET cc_start: 0.6564 (mmm) cc_final: 0.5459 (mmm) REVERT: J 171 TYR cc_start: 0.8249 (m-80) cc_final: 0.7988 (m-80) REVERT: J 270 PHE cc_start: 0.8259 (t80) cc_final: 0.8039 (t80) REVERT: J 290 ARG cc_start: 0.8912 (mpt-90) cc_final: 0.8477 (mpt-90) REVERT: Z 339 MET cc_start: 0.8353 (mmm) cc_final: 0.7706 (mmm) REVERT: Z 773 MET cc_start: 0.8038 (mpp) cc_final: 0.7226 (mpp) REVERT: Z 787 MET cc_start: 0.7768 (mmm) cc_final: 0.7128 (mmm) REVERT: N 10 CYS cc_start: 0.9077 (m) cc_final: 0.8743 (m) REVERT: N 11 MET cc_start: 0.8380 (mtm) cc_final: 0.7286 (mtm) REVERT: N 73 TRP cc_start: 0.9325 (m-10) cc_final: 0.8821 (m100) REVERT: N 76 PHE cc_start: 0.9583 (OUTLIER) cc_final: 0.9280 (m-80) REVERT: N 125 PHE cc_start: 0.9680 (t80) cc_final: 0.9449 (t80) REVERT: N 180 HIS cc_start: 0.8407 (m-70) cc_final: 0.8087 (m-70) outliers start: 84 outliers final: 63 residues processed: 368 average time/residue: 0.2082 time to fit residues: 129.9285 Evaluate side-chains 361 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 291 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 323 ILE Chi-restraints excluded: chain K residue 384 ASP Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain P residue 126 THR Chi-restraints excluded: chain P residue 173 ASP Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 303 MET Chi-restraints excluded: chain J residue 306 PHE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain Z residue 547 LEU Chi-restraints excluded: chain Z residue 581 ASP Chi-restraints excluded: chain Z residue 595 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 92 TYR Chi-restraints excluded: chain N residue 173 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: [445, 243, 369, 439, 346, 374, 164, 329, 217, 443, 43] chunk 445 optimal weight: 7.9990 chunk 243 optimal weight: 0.6980 chunk 369 optimal weight: 1.9990 chunk 439 optimal weight: 0.2980 chunk 346 optimal weight: 5.9990 chunk 374 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 329 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 443 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN K 169 ASN K 393 ASN P 71 ASN P 253 GLN J 244 HIS ** Z 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.089798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.064517 restraints weight = 262513.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.065516 restraints weight = 137877.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.066059 restraints weight = 95911.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.066334 restraints weight = 78550.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.066304 restraints weight = 71491.999| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37049 Z= 0.184 Angle : 0.645 14.705 50099 Z= 0.321 Chirality : 0.043 0.304 5749 Planarity : 0.004 0.081 6452 Dihedral : 7.497 87.931 5173 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.50 % Allowed : 17.11 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.13), residues: 4585 helix: 1.42 (0.10), residues: 2632 sheet: -0.79 (0.26), residues: 360 loop : 0.66 (0.17), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 37 TYR 0.028 0.001 TYR A 145 PHE 0.042 0.002 PHE C 389 TRP 0.082 0.002 TRP N 42 HIS 0.006 0.001 HIS D 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (37049) covalent geometry : angle 0.64549 / 0.32 (50099) hydrogen bonds : bond 0.03606 / 2.38 ( 1940) hydrogen bonds : angle 4.62250 / 3.26 ( 5619) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 286 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 ASP cc_start: 0.7540 (p0) cc_final: 0.6881 (p0) REVERT: B 306 MET cc_start: 0.8860 (ttm) cc_final: 0.8398 (tmm) REVERT: B 411 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8591 (p) REVERT: B 424 MET cc_start: 0.7200 (mmm) cc_final: 0.6855 (mmm) REVERT: C 124 MET cc_start: -0.0713 (ttt) cc_final: -0.1461 (tpp) REVERT: C 293 MET cc_start: 0.7543 (ppp) cc_final: 0.7035 (ppp) REVERT: C 415 MET cc_start: 0.7598 (tpp) cc_final: 0.7279 (mmm) REVERT: C 775 MET cc_start: 0.3082 (mmt) cc_final: 0.2797 (mmt) REVERT: C 815 MET cc_start: 0.9312 (mmm) cc_final: 0.9049 (mmt) REVERT: C 862 MET cc_start: 0.7012 (mmp) cc_final: 0.6684 (mmp) REVERT: C 990 ARG cc_start: 0.5817 (pmt-80) cc_final: 0.4982 (mmt180) REVERT: D 231 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7103 (mm) REVERT: K 109 MET cc_start: 0.8817 (mmm) cc_final: 0.8528 (mmm) REVERT: K 156 MET cc_start: 0.8033 (mmm) cc_final: 0.6765 (mmm) REVERT: K 249 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8706 (p) REVERT: P 58 MET cc_start: 0.8002 (mmp) cc_final: 0.7546 (tpt) REVERT: P 324 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7912 (pp) REVERT: I 24 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7985 (mm-30) REVERT: I 121 MET cc_start: 0.9058 (tpp) cc_final: 0.8570 (tpp) REVERT: I 127 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.5986 (tm-30) REVERT: J 161 MET cc_start: 0.6792 (mmm) cc_final: 0.5605 (mmm) REVERT: J 171 TYR cc_start: 0.8350 (m-80) cc_final: 0.8118 (m-80) REVERT: J 253 MET cc_start: 0.8873 (ptm) cc_final: 0.8638 (ptm) REVERT: J 270 PHE cc_start: 0.8282 (t80) cc_final: 0.8004 (t80) REVERT: J 316 MET cc_start: 0.6978 (tpp) cc_final: 0.6534 (tpp) REVERT: Z 386 MET cc_start: 0.6965 (mtt) cc_final: 0.6713 (mtt) REVERT: Z 773 MET cc_start: 0.7729 (mpp) cc_final: 0.6975 (mpp) REVERT: N 11 MET cc_start: 0.8458 (mtm) cc_final: 0.8043 (mtt) REVERT: N 42 TRP cc_start: 0.9464 (m100) cc_final: 0.9096 (m100) REVERT: N 73 TRP cc_start: 0.9366 (m-10) cc_final: 0.8924 (m100) REVERT: N 76 PHE cc_start: 0.9612 (OUTLIER) cc_final: 0.9400 (m-80) REVERT: N 106 GLN cc_start: 0.9282 (pm20) cc_final: 0.8972 (pm20) REVERT: N 180 HIS cc_start: 0.8468 (m-70) cc_final: 0.8120 (m-70) outliers start: 100 outliers final: 79 residues processed: 364 average time/residue: 0.2004 time to fit residues: 126.2185 Evaluate side-chains 361 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 276 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 323 ILE Chi-restraints excluded: chain K residue 384 ASP Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 126 THR Chi-restraints excluded: chain P residue 173 ASP Chi-restraints excluded: chain P residue 258 GLU Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 306 PHE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain Z residue 295 THR Chi-restraints excluded: chain Z residue 455 MET Chi-restraints excluded: chain Z residue 523 LEU Chi-restraints excluded: chain Z residue 547 LEU Chi-restraints excluded: chain Z residue 581 ASP Chi-restraints excluded: chain Z residue 595 LEU Chi-restraints excluded: chain Z residue 664 LEU Chi-restraints excluded: chain Z residue 700 CYS Chi-restraints excluded: chain Z residue 920 VAL Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 173 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: [228, 192, 389, 43, 110, 58, 433, 376, 281, 290, 184] chunk 228 optimal weight: 0.5980 chunk 192 optimal weight: 2.9990 chunk 389 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 433 optimal weight: 20.0000 chunk 376 optimal weight: 5.9990 chunk 281 optimal weight: 4.9990 chunk 290 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 ASN P 71 ASN J 244 HIS ** Z 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.090847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.070007 restraints weight = 276637.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.070647 restraints weight = 161979.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.070268 restraints weight = 110355.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.070499 restraints weight = 122521.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.070708 restraints weight = 97492.034| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37049 Z= 0.130 Angle : 0.652 15.027 50099 Z= 0.319 Chirality : 0.043 0.341 5749 Planarity : 0.004 0.077 6452 Dihedral : 7.417 86.884 5171 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.90 % Allowed : 17.93 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.13), residues: 4585 helix: 1.47 (0.10), residues: 2630 sheet: -0.75 (0.26), residues: 359 loop : 0.68 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 132 TYR 0.032 0.001 TYR A 145 PHE 0.046 0.002 PHE C 389 TRP 0.063 0.002 TRP N 42 HIS 0.005 0.001 HIS J 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (37049) covalent geometry : angle 0.65196 / 0.32 (50099) hydrogen bonds : bond 0.03513 / 2.32 ( 1940) hydrogen bonds : angle 4.53323 / 3.21 ( 5619) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9170 Ramachandran restraints generated. 4585 Oldfield, 0 Emsley, 4585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 286 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 ASP cc_start: 0.7361 (p0) cc_final: 0.6700 (p0) REVERT: B 256 TYR cc_start: 0.8158 (m-80) cc_final: 0.7498 (m-80) REVERT: B 306 MET cc_start: 0.8974 (ttm) cc_final: 0.8483 (tmm) REVERT: B 411 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8276 (p) REVERT: B 424 MET cc_start: 0.7195 (mmm) cc_final: 0.6914 (mmm) REVERT: C 124 MET cc_start: -0.3561 (ttt) cc_final: -0.4326 (tpp) REVERT: C 293 MET cc_start: 0.6656 (ppp) cc_final: 0.6027 (ppp) REVERT: C 415 MET cc_start: 0.6994 (tpp) cc_final: 0.6164 (mmm) REVERT: C 775 MET cc_start: 0.3456 (mmt) cc_final: 0.3099 (mmt) REVERT: C 815 MET cc_start: 0.9258 (mmm) cc_final: 0.8917 (mmt) REVERT: C 862 MET cc_start: 0.7139 (mmp) cc_final: 0.6849 (mmp) REVERT: C 990 ARG cc_start: 0.5711 (pmt-80) cc_final: 0.4796 (mmt180) REVERT: D 231 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.7026 (mm) REVERT: K 109 MET cc_start: 0.8624 (mmm) cc_final: 0.8392 (mmm) REVERT: K 249 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8623 (p) REVERT: P 58 MET cc_start: 0.8007 (mmp) cc_final: 0.7565 (tpt) REVERT: P 324 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7951 (pp) REVERT: I 24 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7746 (mm-30) REVERT: I 63 ARG cc_start: 0.8837 (ptp-170) cc_final: 0.8549 (ptp90) REVERT: I 121 MET cc_start: 0.8964 (tpp) cc_final: 0.8551 (tpp) REVERT: I 127 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5985 (tm-30) REVERT: J 161 MET cc_start: 0.6565 (mmm) cc_final: 0.5470 (mmm) REVERT: J 171 TYR cc_start: 0.8289 (m-80) cc_final: 0.8069 (m-80) REVERT: J 270 PHE cc_start: 0.8287 (t80) cc_final: 0.8047 (t80) REVERT: J 290 ARG cc_start: 0.8893 (mpt-90) cc_final: 0.8499 (mpt-90) REVERT: J 316 MET cc_start: 0.6662 (tpp) cc_final: 0.6263 (tpp) REVERT: Z 386 MET cc_start: 0.7137 (mtt) cc_final: 0.6902 (mtt) REVERT: Z 773 MET cc_start: 0.7953 (mpp) cc_final: 0.7137 (mpp) REVERT: N 11 MET cc_start: 0.8686 (mtm) cc_final: 0.8384 (mtt) REVERT: N 42 TRP cc_start: 0.9498 (m100) cc_final: 0.9202 (m100) REVERT: N 59 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8356 (pmm) REVERT: N 73 TRP cc_start: 0.9325 (m-10) cc_final: 0.8814 (m100) REVERT: N 76 PHE cc_start: 0.9581 (OUTLIER) cc_final: 0.9327 (m-80) REVERT: N 106 GLN cc_start: 0.9312 (pm20) cc_final: 0.9019 (pm20) REVERT: N 180 HIS cc_start: 0.8392 (m-70) cc_final: 0.8069 (m-70) outliers start: 76 outliers final: 66 residues processed: 344 average time/residue: 0.2011 time to fit residues: 119.3450 Evaluate side-chains 351 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 278 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 384 ASP Chi-restraints excluded: chain P residue 126 THR Chi-restraints excluded: chain P residue 173 ASP Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 244 HIS Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 303 MET Chi-restraints excluded: chain J residue 306 PHE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain Z residue 295 THR Chi-restraints excluded: chain Z residue 547 LEU Chi-restraints excluded: chain Z residue 581 ASP Chi-restraints excluded: chain Z residue 595 LEU Chi-restraints excluded: chain Z residue 700 CYS Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 59 MET Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 92 TYR Chi-restraints excluded: chain N residue 173 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: [78, 46, 267, 161, 172, 25, 147, 26, 90, 80, 116] chunk 78 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 267 optimal weight: 0.0060 chunk 161 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 25 optimal weight: 0.0030 chunk 147 optimal weight: 8.9990 chunk 26 optimal weight: 0.0980 chunk 90 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 overall best weight: 0.5608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN K 169 ASN K 393 ASN J 244 HIS ** Z 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 180 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.091523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.070696 restraints weight = 274301.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.071283 restraints weight = 163874.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.070959 restraints weight = 110642.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.071339 restraints weight = 101386.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.071329 restraints weight = 88409.398| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37049 Z= 0.115 Angle : 0.645 15.186 50099 Z= 0.312 Chirality : 0.043 0.426 5749 Planarity : 0.004 0.077 6452 Dihedral : 7.291 86.129 5171 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.85 % Allowed : 18.16 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.13), residues: 4585 helix: 1.55 (0.10), residues: 2628 sheet: -0.70 (0.27), residues: 351 loop : 0.73 (0.17), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 63 TYR 0.027 0.001 TYR A 145 PHE 0.045 0.001 PHE C 389 TRP 0.045 0.001 TRP N 42 HIS 0.010 0.001 HIS J 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (37049) covalent geometry : angle 0.64503 / 0.31 (50099) hydrogen bonds : bond 0.03423 / 2.26 ( 1940) hydrogen bonds : angle 4.43911 / 3.14 ( 5619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8616.81 seconds wall clock time: 148 minutes 44.24 seconds (8924.24 seconds total)