Starting phenix.real_space_refine on Sat Jul 4 00:52:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fnf_29311/07_2026/8fnf_29311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fnf_29311/07_2026/8fnf_29311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fnf_29311/07_2026/8fnf_29311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fnf_29311/07_2026/8fnf_29311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fnf_29311/07_2026/8fnf_29311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fnf_29311/07_2026/8fnf_29311.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fnf_29311/07_2026/8fnf_29311.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fnf_29311/07_2026/8fnf_29311.cif" } resolution = 3.5 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= 0.003 sd= 0.130 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 36 5.49 5 S 116 5.16 5 C 10684 2.51 5 N 2981 2.21 5 O 3263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17080 Number of models: 1 Model: "" Number of chains: 8 Chain: "m" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 432 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 14, 'rna3p': 5} Chain: "g" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 7, 'rna3p': 8} Chain: "5" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2327 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain: "6" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3582 Classifications: {'peptide': 452} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 440} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "7" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 547 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "8" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4076 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 25, 'TRANS': 490} Chain: "10" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3290 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 14, 'TRANS': 401} Chain breaks: 3 Chain: "14" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2496 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 24, 'TRANS': 289} Time building chain proxies: 3.49, per 1000 atoms: 0.20 Number of scatterers: 17080 At special positions: 0 Unit cell: (108.9, 124.3, 146.3, 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 116 16.00 P 36 15.00 O 3263 8.00 N 2981 7.00 C 10684 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: 1.59 Conformation dependent library (CDL) restraints added in 807.7 milliseconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3918 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 8 sheets defined 67.1% alpha, 5.7% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain '5' and resid 27 through 31 removed outlier: 4.155A pdb=" N ILE 5 31 " --> pdb=" O PRO 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 34 through 51 Processing helix chain '5' and resid 66 through 74 removed outlier: 3.559A pdb=" N ALA 5 69 " --> pdb=" O SER 5 66 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL 5 72 " --> pdb=" O ALA 5 69 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ALA 5 73 " --> pdb=" O LEU 5 70 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP 5 74 " --> pdb=" O ARG 5 71 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 93 No H-bonds generated for 'chain '5' and resid 91 through 93' Processing helix chain '5' and resid 94 through 108 Processing helix chain '5' and resid 116 through 121 removed outlier: 3.702A pdb=" N THR 5 121 " --> pdb=" O TYR 5 117 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 159 removed outlier: 3.574A pdb=" N HIS 5 151 " --> pdb=" O ASN 5 147 " (cutoff:3.500A) Processing helix chain '5' and resid 180 through 183 Processing helix chain '5' and resid 198 through 212 Processing helix chain '5' and resid 247 through 256 Processing helix chain '5' and resid 265 through 271 removed outlier: 3.604A pdb=" N ASP 5 269 " --> pdb=" O TRP 5 265 " (cutoff:3.500A) Processing helix chain '6' and resid 62 through 78 Processing helix chain '6' and resid 83 through 95 removed outlier: 3.580A pdb=" N ALA 6 87 " --> pdb=" O ASN 6 83 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN 6 88 " --> pdb=" O PRO 6 84 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 119 removed outlier: 3.583A pdb=" N PHE 6 119 " --> pdb=" O THR 6 115 " (cutoff:3.500A) Processing helix chain '6' and resid 125 through 138 Processing helix chain '6' and resid 146 through 157 removed outlier: 4.524A pdb=" N THR 6 156 " --> pdb=" O THR 6 152 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU 6 157 " --> pdb=" O ALA 6 153 " (cutoff:3.500A) Processing helix chain '6' and resid 159 through 176 Processing helix chain '6' and resid 181 through 195 removed outlier: 3.823A pdb=" N THR 6 186 " --> pdb=" O ALA 6 182 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR 6 195 " --> pdb=" O ALA 6 191 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 216 removed outlier: 4.026A pdb=" N VAL 6 216 " --> pdb=" O THR 6 212 " (cutoff:3.500A) Processing helix chain '6' and resid 220 through 234 removed outlier: 3.538A pdb=" N LEU 6 234 " --> pdb=" O ALA 6 230 " (cutoff:3.500A) Processing helix chain '6' and resid 238 through 253 removed outlier: 3.501A pdb=" N PHE 6 242 " --> pdb=" O ASP 6 238 " (cutoff:3.500A) Processing helix chain '6' and resid 254 through 256 No H-bonds generated for 'chain '6' and resid 254 through 256' Processing helix chain '6' and resid 257 through 272 Proline residue: 6 263 - end of helix removed outlier: 3.852A pdb=" N GLY 6 272 " --> pdb=" O PHE 6 268 " (cutoff:3.500A) Processing helix chain '6' and resid 275 through 288 removed outlier: 3.663A pdb=" N SER 6 279 " --> pdb=" O ASP 6 275 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS 6 280 " --> pdb=" O PRO 6 276 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG 6 281 " --> pdb=" O LYS 6 277 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU 6 288 " --> pdb=" O THR 6 284 " (cutoff:3.500A) Processing helix chain '6' and resid 289 through 293 Processing helix chain '6' and resid 294 through 309 removed outlier: 3.705A pdb=" N GLY 6 309 " --> pdb=" O PHE 6 305 " (cutoff:3.500A) Processing helix chain '6' and resid 312 through 326 removed outlier: 3.919A pdb=" N VAL 6 318 " --> pdb=" O GLN 6 314 " (cutoff:3.500A) Processing helix chain '6' and resid 327 through 330 removed outlier: 3.502A pdb=" N PHE 6 330 " --> pdb=" O ILE 6 327 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 327 through 330' Processing helix chain '6' and resid 331 through 346 Processing helix chain '6' and resid 349 through 362 removed outlier: 3.760A pdb=" N ASN 6 355 " --> pdb=" O GLU 6 351 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA 6 362 " --> pdb=" O GLU 6 358 " (cutoff:3.500A) Processing helix chain '6' and resid 363 through 367 Processing helix chain '6' and resid 368 through 382 Processing helix chain '6' and resid 386 through 400 Processing helix chain '6' and resid 401 through 404 removed outlier: 3.729A pdb=" N PHE 6 404 " --> pdb=" O ALA 6 401 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 401 through 404' Processing helix chain '6' and resid 405 through 419 removed outlier: 3.744A pdb=" N LEU 6 409 " --> pdb=" O ASP 6 405 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL 6 410 " --> pdb=" O ALA 6 406 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR 6 419 " --> pdb=" O ALA 6 415 " (cutoff:3.500A) Processing helix chain '6' and resid 423 through 434 removed outlier: 3.593A pdb=" N ALA 6 429 " --> pdb=" O ASP 6 425 " (cutoff:3.500A) Processing helix chain '6' and resid 435 through 441 removed outlier: 3.734A pdb=" N CYS 6 438 " --> pdb=" O VAL 6 435 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ARG 6 439 " --> pdb=" O TYR 6 436 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU 6 441 " --> pdb=" O CYS 6 438 " (cutoff:3.500A) Processing helix chain '6' and resid 442 through 456 Processing helix chain '6' and resid 460 through 474 Proline residue: 6 466 - end of helix Processing helix chain '6' and resid 474 through 480 Processing helix chain '6' and resid 481 through 483 No H-bonds generated for 'chain '6' and resid 481 through 483' Processing helix chain '6' and resid 484 through 495 Processing helix chain '6' and resid 500 through 509 Processing helix chain '7' and resid 81 through 98 Processing helix chain '7' and resid 103 through 118 removed outlier: 4.061A pdb=" N LEU 7 118 " --> pdb=" O ASP 7 114 " (cutoff:3.500A) Processing helix chain '7' and resid 119 through 124 Processing helix chain '7' and resid 127 through 145 removed outlier: 3.874A pdb=" N LYS 7 143 " --> pdb=" O ALA 7 139 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR 7 144 " --> pdb=" O TYR 7 140 " (cutoff:3.500A) Processing helix chain '8' and resid 21 through 33 Processing helix chain '8' and resid 39 through 53 Processing helix chain '8' and resid 61 through 74 removed outlier: 3.696A pdb=" N GLY 8 67 " --> pdb=" O ASP 8 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG 8 74 " --> pdb=" O ASP 8 70 " (cutoff:3.500A) Processing helix chain '8' and resid 81 through 96 removed outlier: 3.752A pdb=" N VAL 8 95 " --> pdb=" O THR 8 91 " (cutoff:3.500A) Processing helix chain '8' and resid 108 through 112 removed outlier: 3.656A pdb=" N ILE 8 112 " --> pdb=" O GLU 8 109 " (cutoff:3.500A) Processing helix chain '8' and resid 113 through 127 removed outlier: 3.799A pdb=" N LEU 8 121 " --> pdb=" O LEU 8 117 " (cutoff:3.500A) Processing helix chain '8' and resid 131 through 143 removed outlier: 3.597A pdb=" N PHE 8 143 " --> pdb=" O LEU 8 139 " (cutoff:3.500A) Processing helix chain '8' and resid 150 through 164 Processing helix chain '8' and resid 168 through 181 removed outlier: 3.516A pdb=" N VAL 8 172 " --> pdb=" O ASN 8 168 " (cutoff:3.500A) Processing helix chain '8' and resid 187 through 201 removed outlier: 3.585A pdb=" N CYS 8 201 " --> pdb=" O SER 8 197 " (cutoff:3.500A) Processing helix chain '8' and resid 205 through 218 Processing helix chain '8' and resid 224 through 239 Processing helix chain '8' and resid 242 through 253 Processing helix chain '8' and resid 254 through 256 No H-bonds generated for 'chain '8' and resid 254 through 256' Processing helix chain '8' and resid 261 through 276 Processing helix chain '8' and resid 279 through 294 removed outlier: 3.871A pdb=" N ILE 8 283 " --> pdb=" O GLN 8 279 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU 8 292 " --> pdb=" O ASP 8 288 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL 8 293 " --> pdb=" O ALA 8 289 " (cutoff:3.500A) Processing helix chain '8' and resid 295 through 297 No H-bonds generated for 'chain '8' and resid 295 through 297' Processing helix chain '8' and resid 298 through 312 Processing helix chain '8' and resid 316 through 328 Processing helix chain '8' and resid 329 through 334 removed outlier: 3.768A pdb=" N ALA 8 332 " --> pdb=" O ARG 8 329 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET 8 334 " --> pdb=" O ALA 8 331 " (cutoff:3.500A) Processing helix chain '8' and resid 335 through 347 removed outlier: 4.519A pdb=" N ALA 8 340 " --> pdb=" O PRO 8 336 " (cutoff:3.500A) Proline residue: 8 341 - end of helix Processing helix chain '8' and resid 353 through 367 Processing helix chain '8' and resid 372 through 383 Processing helix chain '8' and resid 386 through 390 Processing helix chain '8' and resid 393 through 406 Processing helix chain '8' and resid 407 through 409 No H-bonds generated for 'chain '8' and resid 407 through 409' Processing helix chain '8' and resid 410 through 424 Processing helix chain '8' and resid 428 through 442 removed outlier: 3.871A pdb=" N TYR 8 442 " --> pdb=" O THR 8 438 " (cutoff:3.500A) Processing helix chain '8' and resid 450 through 461 removed outlier: 3.544A pdb=" N LEU 8 454 " --> pdb=" O LEU 8 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE 8 459 " --> pdb=" O MET 8 455 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR 8 460 " --> pdb=" O GLY 8 456 " (cutoff:3.500A) Processing helix chain '8' and resid 464 through 479 Proline residue: 8 477 - end of helix Processing helix chain '8' and resid 483 through 498 Processing helix chain '8' and resid 501 through 517 removed outlier: 4.071A pdb=" N TYR 8 505 " --> pdb=" O ASP 8 501 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG 8 511 " --> pdb=" O ALA 8 507 " (cutoff:3.500A) Processing helix chain '8' and resid 524 through 533 removed outlier: 3.522A pdb=" N ARG 8 533 " --> pdb=" O VAL 8 529 " (cutoff:3.500A) Processing helix chain '10' and resid 117 through 141 removed outlier: 4.108A pdb=" N ALA10 121 " --> pdb=" O THR10 117 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS10 141 " --> pdb=" O ALA10 137 " (cutoff:3.500A) Processing helix chain '10' and resid 155 through 183 Processing helix chain '10' and resid 191 through 207 removed outlier: 3.867A pdb=" N LYS10 205 " --> pdb=" O THR10 201 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU10 206 " --> pdb=" O THR10 202 " (cutoff:3.500A) Processing helix chain '10' and resid 211 through 233 removed outlier: 3.701A pdb=" N MET10 221 " --> pdb=" O ALA10 217 " (cutoff:3.500A) Processing helix chain '10' and resid 236 through 249 removed outlier: 3.637A pdb=" N VAL10 240 " --> pdb=" O SER10 236 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU10 241 " --> pdb=" O ALA10 237 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR10 249 " --> pdb=" O THR10 245 " (cutoff:3.500A) Processing helix chain '10' and resid 254 through 265 Processing helix chain '10' and resid 275 through 289 removed outlier: 3.854A pdb=" N THR10 289 " --> pdb=" O ARG10 285 " (cutoff:3.500A) Processing helix chain '10' and resid 294 through 306 removed outlier: 3.688A pdb=" N LEU10 298 " --> pdb=" O ALA10 294 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP10 299 " --> pdb=" O LYS10 295 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE10 300 " --> pdb=" O GLU10 296 " (cutoff:3.500A) Processing helix chain '10' and resid 308 through 315 Processing helix chain '10' and resid 316 through 318 No H-bonds generated for 'chain '10' and resid 316 through 318' Processing helix chain '10' and resid 320 through 334 removed outlier: 3.805A pdb=" N LEU10 325 " --> pdb=" O LEU10 321 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU10 328 " --> pdb=" O LEU10 324 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS10 334 " --> pdb=" O CYS10 330 " (cutoff:3.500A) Processing helix chain '10' and resid 338 through 340 No H-bonds generated for 'chain '10' and resid 338 through 340' Processing helix chain '10' and resid 341 through 351 removed outlier: 3.728A pdb=" N ALA10 345 " --> pdb=" O LEU10 341 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA10 348 " --> pdb=" O LEU10 344 " (cutoff:3.500A) Processing helix chain '10' and resid 356 through 370 removed outlier: 3.845A pdb=" N ALA10 361 " --> pdb=" O PRO10 357 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR10 362 " --> pdb=" O HIS10 358 " (cutoff:3.500A) Processing helix chain '10' and resid 374 through 387 removed outlier: 3.615A pdb=" N ARG10 380 " --> pdb=" O GLU10 376 " (cutoff:3.500A) Processing helix chain '10' and resid 392 through 408 removed outlier: 3.519A pdb=" N ALA10 396 " --> pdb=" O THR10 392 " (cutoff:3.500A) Processing helix chain '10' and resid 416 through 418 No H-bonds generated for 'chain '10' and resid 416 through 418' Processing helix chain '10' and resid 419 through 437 removed outlier: 3.605A pdb=" N THR10 423 " --> pdb=" O ASN10 419 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE10 434 " --> pdb=" O MET10 430 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG10 437 " --> pdb=" O GLN10 433 " (cutoff:3.500A) Processing helix chain '10' and resid 445 through 460 removed outlier: 3.876A pdb=" N ILE10 449 " --> pdb=" O ALA10 445 " (cutoff:3.500A) Processing helix chain '10' and resid 464 through 486 removed outlier: 3.527A pdb=" N ASP10 477 " --> pdb=" O SER10 473 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET10 478 " --> pdb=" O GLN10 474 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS10 486 " --> pdb=" O VAL10 482 " (cutoff:3.500A) Processing helix chain '10' and resid 502 through 517 Processing helix chain '10' and resid 521 through 535 removed outlier: 3.602A pdb=" N SER10 525 " --> pdb=" O ALA10 521 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN10 526 " --> pdb=" O PRO10 522 " (cutoff:3.500A) Processing helix chain '14' and resid 49 through 53 removed outlier: 3.525A pdb=" N ASP14 52 " --> pdb=" O ASP14 49 " (cutoff:3.500A) Processing helix chain '14' and resid 66 through 70 removed outlier: 3.973A pdb=" N PHE14 70 " --> pdb=" O VAL14 67 " (cutoff:3.500A) Processing helix chain '14' and resid 76 through 87 removed outlier: 3.637A pdb=" N VAL14 80 " --> pdb=" O SER14 76 " (cutoff:3.500A) Processing helix chain '14' and resid 97 through 111 Processing helix chain '14' and resid 120 through 124 Processing helix chain '14' and resid 143 through 146 Processing helix chain '14' and resid 149 through 155 removed outlier: 3.668A pdb=" N ILE14 154 " --> pdb=" O MET14 150 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR14 155 " --> pdb=" O HIS14 151 " (cutoff:3.500A) Processing helix chain '14' and resid 156 through 167 removed outlier: 3.765A pdb=" N ALA14 162 " --> pdb=" O THR14 158 " (cutoff:3.500A) Processing helix chain '14' and resid 194 through 198 Processing helix chain '14' and resid 249 through 256 Processing helix chain '14' and resid 257 through 260 Processing helix chain '14' and resid 262 through 272 Processing sheet with id=AA1, first strand: chain '5' and resid 57 through 61 removed outlier: 6.569A pdb=" N ALA 5 13 " --> pdb=" O HIS 5 59 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N MET 5 61 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL 5 15 " --> pdb=" O MET 5 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '5' and resid 76 through 79 Processing sheet with id=AA3, first strand: chain '5' and resid 131 through 132 Processing sheet with id=AA4, first strand: chain '5' and resid 185 through 188 removed outlier: 6.296A pdb=" N LEU 5 193 " --> pdb=" O VAL 5 220 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU 5 222 " --> pdb=" O LEU 5 193 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR 5 195 " --> pdb=" O LEU 5 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 228 through 230 removed outlier: 3.702A pdb=" N VAL 5 242 " --> pdb=" O ILE 5 261 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '14' and resid 88 through 90 removed outlier: 6.418A pdb=" N VAL14 304 " --> pdb=" O MET14 181 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET14 181 " --> pdb=" O VAL14 304 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N CYS14 306 " --> pdb=" O VAL14 179 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL14 179 " --> pdb=" O CYS14 306 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE14 308 " --> pdb=" O ASP14 177 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASP14 177 " --> pdb=" O PHE14 308 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N HIS14 310 " --> pdb=" O TRP14 175 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA14 126 " --> pdb=" O GLN14 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '14' and resid 88 through 90 removed outlier: 6.418A pdb=" N VAL14 304 " --> pdb=" O MET14 181 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET14 181 " --> pdb=" O VAL14 304 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N CYS14 306 " --> pdb=" O VAL14 179 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL14 179 " --> pdb=" O CYS14 306 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE14 308 " --> pdb=" O ASP14 177 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASP14 177 " --> pdb=" O PHE14 308 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N HIS14 310 " --> pdb=" O TRP14 175 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL14 172 " --> pdb=" O VAL14 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '14' and resid 275 through 276 912 hydrogen bonds defined for protein. 2658 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 2.05 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: 5570 1.34 - 1.46: 3920 1.46 - 1.58: 7744 1.58 - 1.71: 70 1.71 - 1.83: 195 Bond restraints: 17499 Sorted by residual: bond pdb=" SD MET10 528 " pdb=" CE MET10 528 " ideal model delta sigma weight residual 1.791 1.741 0.050 2.50e-02 1.60e+03 3.99e+00 bond pdb=" CA ARG 8 511 " pdb=" C ARG 8 511 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.30e-02 5.92e+03 3.84e+00 bond pdb=" CA ASP14 66 " pdb=" C ASP14 66 " ideal model delta sigma weight residual 1.528 1.502 0.027 1.39e-02 5.18e+03 3.70e+00 bond pdb=" CA SER 5 116 " pdb=" C SER 5 116 " ideal model delta sigma weight residual 1.526 1.505 0.020 1.23e-02 6.61e+03 2.78e+00 bond pdb=" CB PRO 8 240 " pdb=" CG PRO 8 240 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.63e+00 ... (remaining 17494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 23523 2.39 - 4.77: 308 4.77 - 7.16: 32 7.16 - 9.55: 4 9.55 - 11.93: 2 Bond angle restraints: 23869 Sorted by residual: angle pdb=" C LYS 8 517 " pdb=" CA LYS 8 517 " pdb=" CB LYS 8 517 " ideal model delta sigma weight residual 116.54 110.54 6.00 1.15e+00 7.56e-01 2.72e+01 angle pdb=" N VAL 5 192 " pdb=" CA VAL 5 192 " pdb=" C VAL 5 192 " ideal model delta sigma weight residual 108.36 114.13 -5.77 1.43e+00 4.89e-01 1.63e+01 angle pdb=" CB MET10 528 " pdb=" CG MET10 528 " pdb=" SD MET10 528 " ideal model delta sigma weight residual 112.70 100.77 11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C THR 8 520 " pdb=" N PRO 8 521 " pdb=" CA PRO 8 521 " ideal model delta sigma weight residual 119.05 114.84 4.21 1.11e+00 8.12e-01 1.44e+01 angle pdb=" N VAL 8 529 " pdb=" CA VAL 8 529 " pdb=" C VAL 8 529 " ideal model delta sigma weight residual 110.42 106.89 3.53 9.40e-01 1.13e+00 1.41e+01 ... (remaining 23864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.96: 10081 33.96 - 67.91: 418 67.91 - 101.87: 33 101.87 - 135.82: 1 135.82 - 169.78: 3 Dihedral angle restraints: 10536 sinusoidal: 4500 harmonic: 6036 Sorted by residual: dihedral pdb=" O4' U g -2 " pdb=" C1' U g -2 " pdb=" N1 U g -2 " pdb=" C2 U g -2 " ideal model delta sinusoidal sigma weight residual 232.00 62.22 169.78 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O4' U g -10 " pdb=" C1' U g -10 " pdb=" N1 U g -10 " pdb=" C2 U g -10 " ideal model delta sinusoidal sigma weight residual -160.00 -44.64 -115.36 1 1.50e+01 4.44e-03 6.09e+01 dihedral pdb=" O4' A m 117 " pdb=" C1' A m 117 " pdb=" N9 A m 117 " pdb=" C4 A m 117 " ideal model delta sinusoidal sigma weight residual 254.00 162.84 91.16 1 1.70e+01 3.46e-03 3.39e+01 ... (remaining 10533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2110 0.044 - 0.088: 513 0.088 - 0.133: 100 0.133 - 0.177: 7 0.177 - 0.221: 2 Chirality restraints: 2732 Sorted by residual: chirality pdb=" C3' U g -2 " pdb=" C4' U g -2 " pdb=" O3' U g -2 " pdb=" C2' U g -2 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C3' U g -3 " pdb=" C4' U g -3 " pdb=" O3' U g -3 " pdb=" C2' U g -3 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASP10 335 " pdb=" N ASP10 335 " pdb=" C ASP10 335 " pdb=" CB ASP10 335 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 2729 not shown) Planarity restraints: 2959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY 8 239 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO 8 240 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO 8 240 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO 8 240 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN 5 123 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C ASN 5 123 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN 5 123 " -0.017 2.00e-02 2.50e+03 pdb=" N CYS 5 124 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER 8 81 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO 8 82 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO 8 82 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO 8 82 " 0.028 5.00e-02 4.00e+02 ... (remaining 2956 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2236 2.75 - 3.29: 16512 3.29 - 3.82: 27533 3.82 - 4.36: 31096 4.36 - 4.90: 54795 Nonbonded interactions: 132172 Sorted by model distance: nonbonded pdb=" O ILE14 154 " pdb=" OH TYR14 311 " model vdw 2.212 3.040 nonbonded pdb=" N GLU 8 37 " pdb=" OE1 GLU 8 37 " model vdw 2.233 3.120 nonbonded pdb=" N GLN14 143 " pdb=" OE1 GLN14 143 " model vdw 2.236 3.120 nonbonded pdb=" O ALA 5 73 " pdb=" OG SER 5 128 " model vdw 2.241 3.040 nonbonded pdb=" NE1 TRP 6 451 " pdb=" OE1 GLU 6 490 " model vdw 2.250 3.120 ... (remaining 132167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.520 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.004 0.081 17499 Z= 0.180 Angle : 0.658 11.934 23869 Z= 0.375 Chirality : 0.039 0.221 2732 Planarity : 0.005 0.110 2959 Dihedral : 17.630 169.779 6618 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.02 % Allowed : 18.65 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.62 (0.19), residues: 2047 helix: 1.33 (0.15), residues: 1208 sheet: -0.27 (0.49), residues: 90 loop : -0.99 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG10 291 TYR 0.015 0.001 TYR14 88 PHE 0.022 0.002 PHE 8 83 TRP 0.014 0.001 TRP14 175 HIS 0.007 0.001 HIS 6 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (17499) covalent geometry : angle 0.65804 / 0.37 (23869) hydrogen bonds : bond 0.14981 / 9.00 ( 897) hydrogen bonds : angle 5.21883 / 3.48 ( 2658) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 88 LEU cc_start: 0.8255 (mt) cc_final: 0.7593 (tt) REVERT: 5 123 ASN cc_start: 0.6988 (t0) cc_final: 0.6492 (m110) REVERT: 5 156 GLN cc_start: 0.6771 (mm-40) cc_final: 0.5933 (tt0) REVERT: 5 292 MET cc_start: 0.7283 (tpp) cc_final: 0.7055 (mmt) REVERT: 6 505 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7380 (mp10) REVERT: 8 329 ARG cc_start: 0.7476 (mtm110) cc_final: 0.7235 (ttp80) REVERT: 10 308 MET cc_start: 0.8504 (ptm) cc_final: 0.8242 (ptp) REVERT: 10 460 LYS cc_start: 0.7935 (tppp) cc_final: 0.7315 (tmtt) outliers start: 18 outliers final: 6 residues processed: 270 average time/residue: 0.1258 time to fit residues: 49.8768 Evaluate side-chains 232 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 226 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 8 residue 516 VAL Chi-restraints excluded: chain 10 residue 481 ILE Chi-restraints excluded: chain 14 residue 177 ASP Chi-restraints excluded: chain 14 residue 286 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 127 ASN 5 174 GLN 5 236 HIS 6 340 ASN 6 381 HIS 8 98 ASN 8 214 GLN 8 532 GLN 10 122 HIS 10 251 ASN 10 273 ASN 14 193 GLN 14 310 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.189043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.149544 restraints weight = 20071.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.149844 restraints weight = 19025.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.151513 restraints weight = 16356.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.152250 restraints weight = 14223.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.152260 restraints weight = 12869.853| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17499 Z= 0.128 Angle : 0.537 8.151 23869 Z= 0.277 Chirality : 0.038 0.162 2732 Planarity : 0.004 0.063 2959 Dihedral : 11.345 161.928 2683 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.15 % Allowed : 18.32 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.19), residues: 2047 helix: 1.71 (0.15), residues: 1241 sheet: -0.33 (0.48), residues: 98 loop : -0.73 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG14 123 TYR 0.010 0.001 TYR10 215 PHE 0.022 0.001 PHE 8 83 TRP 0.011 0.001 TRP14 175 HIS 0.007 0.001 HIS 6 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (17499) covalent geometry : angle 0.53692 / 0.28 (23869) hydrogen bonds : bond 0.04200 / 2.49 ( 897) hydrogen bonds : angle 3.90387 / 2.66 ( 2658) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 37 MET cc_start: 0.7484 (mmm) cc_final: 0.6957 (mmm) REVERT: 5 99 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7084 (mtp) REVERT: 5 134 LEU cc_start: 0.7222 (pp) cc_final: 0.6893 (pp) REVERT: 5 156 GLN cc_start: 0.6780 (mm-40) cc_final: 0.6163 (tt0) REVERT: 5 267 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8053 (mm-30) REVERT: 6 213 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7703 (mm) REVERT: 10 308 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8140 (ptp) REVERT: 10 341 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8732 (mp) REVERT: 10 400 MET cc_start: 0.7198 (mmt) cc_final: 0.6984 (mmt) REVERT: 10 460 LYS cc_start: 0.7691 (tppp) cc_final: 0.7080 (tmtt) REVERT: 14 171 LEU cc_start: 0.7861 (mp) cc_final: 0.7628 (mt) REVERT: 14 181 MET cc_start: 0.8650 (tmm) cc_final: 0.8083 (ttt) REVERT: 14 254 LEU cc_start: 0.8423 (mt) cc_final: 0.8080 (mm) outliers start: 38 outliers final: 16 residues processed: 263 average time/residue: 0.1347 time to fit residues: 52.8751 Evaluate side-chains 233 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 251 SER Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 7 residue 123 ILE Chi-restraints excluded: chain 8 residue 48 THR Chi-restraints excluded: chain 8 residue 112 ILE Chi-restraints excluded: chain 8 residue 152 THR Chi-restraints excluded: chain 8 residue 372 THR Chi-restraints excluded: chain 8 residue 516 VAL Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 245 THR Chi-restraints excluded: chain 10 residue 308 MET Chi-restraints excluded: chain 10 residue 341 LEU Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 14 residue 63 THR Chi-restraints excluded: chain 14 residue 124 LEU Chi-restraints excluded: chain 14 residue 328 THR Chi-restraints excluded: chain 14 residue 332 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 157 optimal weight: 0.0070 chunk 103 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 9 optimal weight: 0.0010 chunk 154 optimal weight: 0.8980 chunk 205 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 119 GLN 5 127 ASN 5 174 GLN 6 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.187744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.149789 restraints weight = 20045.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.150859 restraints weight = 19052.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.152934 restraints weight = 16289.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.153086 restraints weight = 13428.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.153143 restraints weight = 12484.892| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17499 Z= 0.098 Angle : 0.478 8.819 23869 Z= 0.244 Chirality : 0.036 0.174 2732 Planarity : 0.004 0.051 2959 Dihedral : 11.120 163.354 2676 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.87 % Allowed : 20.24 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.19), residues: 2047 helix: 1.98 (0.15), residues: 1257 sheet: -0.22 (0.49), residues: 98 loop : -0.54 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG10 291 TYR 0.009 0.001 TYR10 200 PHE 0.019 0.001 PHE 8 83 TRP 0.011 0.001 TRP14 175 HIS 0.004 0.000 HIS 5 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (17499) covalent geometry : angle 0.47772 / 0.24 (23869) hydrogen bonds : bond 0.03332 / 1.98 ( 897) hydrogen bonds : angle 3.59937 / 2.47 ( 2658) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: 5 37 MET cc_start: 0.7394 (mmm) cc_final: 0.6909 (mmm) REVERT: 5 99 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7167 (mtp) REVERT: 5 134 LEU cc_start: 0.7504 (pp) cc_final: 0.7195 (pp) REVERT: 5 156 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6331 (tt0) REVERT: 5 267 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8061 (mm-30) REVERT: 7 113 ARG cc_start: 0.5802 (ttp-110) cc_final: 0.5565 (mtm110) REVERT: 8 329 ARG cc_start: 0.7472 (mtm110) cc_final: 0.7082 (ttp80) REVERT: 10 308 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8066 (ptp) REVERT: 10 460 LYS cc_start: 0.7750 (tppp) cc_final: 0.7200 (tmtt) REVERT: 14 181 MET cc_start: 0.8616 (tmm) cc_final: 0.8155 (ttt) REVERT: 14 254 LEU cc_start: 0.8478 (mt) cc_final: 0.8159 (mm) REVERT: 14 336 MET cc_start: 0.6336 (ttt) cc_final: 0.6022 (ttt) outliers start: 33 outliers final: 11 residues processed: 256 average time/residue: 0.1419 time to fit residues: 54.0276 Evaluate side-chains 229 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 216 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 251 SER Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 8 residue 112 ILE Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 494 LEU Chi-restraints excluded: chain 10 residue 308 MET Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 14 residue 328 THR Chi-restraints excluded: chain 14 residue 332 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 64 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 4 optimal weight: 0.0270 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 173 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 127 ASN 6 340 ASN ** 8 129 GLN ** 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 = 0.4059 r_free = 0.4059 target = 0.184746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146401 restraints weight = 20005.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146906 restraints weight = 18766.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148449 restraints weight = 16907.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.149204 restraints weight = 13983.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149462 restraints weight = 12499.531| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17499 Z= 0.104 Angle : 0.476 7.610 23869 Z= 0.244 Chirality : 0.037 0.258 2732 Planarity : 0.004 0.047 2959 Dihedral : 10.995 163.035 2675 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.49 % Allowed : 19.22 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.19), residues: 2047 helix: 2.14 (0.15), residues: 1246 sheet: -0.02 (0.50), residues: 98 loop : -0.46 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 8 495 TYR 0.014 0.001 TYR10 253 PHE 0.020 0.001 PHE10 339 TRP 0.010 0.001 TRP14 175 HIS 0.004 0.001 HIS 5 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (17499) covalent geometry : angle 0.47632 / 0.24 (23869) hydrogen bonds : bond 0.03283 / 1.95 ( 897) hydrogen bonds : angle 3.47393 / 2.38 ( 2658) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 99 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7091 (mtp) REVERT: 5 134 LEU cc_start: 0.7478 (pp) cc_final: 0.7187 (pp) REVERT: 5 156 GLN cc_start: 0.6851 (mm-40) cc_final: 0.6487 (tt0) REVERT: 6 213 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7701 (mm) REVERT: 7 113 ARG cc_start: 0.5867 (ttp-110) cc_final: 0.5553 (mtm110) REVERT: 8 212 MET cc_start: 0.8284 (mmm) cc_final: 0.7800 (tpt) REVERT: 8 275 MET cc_start: 0.8162 (mmt) cc_final: 0.7928 (mmt) REVERT: 8 323 MET cc_start: 0.8067 (mmm) cc_final: 0.7848 (mmt) REVERT: 8 329 ARG cc_start: 0.7550 (mtm110) cc_final: 0.7166 (ttp80) REVERT: 8 335 ASP cc_start: 0.6878 (OUTLIER) cc_final: 0.6566 (t0) REVERT: 10 308 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7995 (ptp) REVERT: 10 460 LYS cc_start: 0.7777 (tppp) cc_final: 0.7163 (tmtt) REVERT: 14 181 MET cc_start: 0.8456 (tmm) cc_final: 0.8073 (ttt) REVERT: 14 217 MET cc_start: 0.8163 (mtm) cc_final: 0.7815 (mtm) REVERT: 14 336 MET cc_start: 0.6625 (ttt) cc_final: 0.6267 (ttt) outliers start: 44 outliers final: 24 residues processed: 261 average time/residue: 0.1363 time to fit residues: 52.5575 Evaluate side-chains 240 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 251 SER Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 8 residue 112 ILE Chi-restraints excluded: chain 8 residue 175 LEU Chi-restraints excluded: chain 8 residue 215 ILE Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 271 CYS Chi-restraints excluded: chain 8 residue 335 ASP Chi-restraints excluded: chain 8 residue 372 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 8 residue 515 PHE Chi-restraints excluded: chain 8 residue 531 LEU Chi-restraints excluded: chain 10 residue 178 LYS Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 247 VAL Chi-restraints excluded: chain 10 residue 308 MET Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 63 THR Chi-restraints excluded: chain 14 residue 124 LEU Chi-restraints excluded: chain 14 residue 328 THR Chi-restraints excluded: chain 14 residue 332 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 190 optimal weight: 3.9990 chunk 191 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 196 optimal weight: 0.0370 chunk 74 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 0.0060 overall best weight: 1.2878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 127 ASN 6 424 GLN 8 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.175335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138109 restraints weight = 19950.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138497 restraints weight = 19436.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.140235 restraints weight = 16930.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140665 restraints weight = 14302.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140926 restraints weight = 13042.181| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17499 Z= 0.145 Angle : 0.536 11.867 23869 Z= 0.276 Chirality : 0.039 0.182 2732 Planarity : 0.004 0.045 2959 Dihedral : 11.050 163.653 2675 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.39 % Allowed : 19.39 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.19), residues: 2047 helix: 2.05 (0.15), residues: 1250 sheet: -0.07 (0.47), residues: 108 loop : -0.62 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG10 291 TYR 0.012 0.001 TYR10 253 PHE 0.022 0.002 PHE 8 83 TRP 0.011 0.001 TRP14 175 HIS 0.005 0.001 HIS 5 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (17499) covalent geometry : angle 0.53604 / 0.28 (23869) hydrogen bonds : bond 0.04319 / 2.57 ( 897) hydrogen bonds : angle 3.59987 / 2.42 ( 2658) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 245 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: 5 99 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7241 (mtp) REVERT: 5 134 LEU cc_start: 0.7738 (pp) cc_final: 0.7336 (pp) REVERT: 5 149 VAL cc_start: 0.7908 (t) cc_final: 0.7645 (t) REVERT: 6 136 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8471 (tt) REVERT: 6 213 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8162 (mm) REVERT: 8 70 ASP cc_start: 0.7563 (m-30) cc_final: 0.7339 (m-30) REVERT: 8 207 ASN cc_start: 0.7160 (t0) cc_final: 0.6855 (t0) REVERT: 8 212 MET cc_start: 0.8536 (mmm) cc_final: 0.8071 (tpt) REVERT: 8 275 MET cc_start: 0.8310 (mmt) cc_final: 0.8075 (mmt) REVERT: 8 317 ASP cc_start: 0.7672 (p0) cc_final: 0.6848 (t0) REVERT: 8 319 MET cc_start: 0.8552 (tpp) cc_final: 0.8246 (mmt) REVERT: 8 335 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6533 (t0) REVERT: 10 276 MET cc_start: 0.7211 (mmm) cc_final: 0.6310 (tmm) REVERT: 10 308 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8114 (ptp) REVERT: 10 341 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8245 (mp) REVERT: 10 412 ASP cc_start: 0.8207 (t0) cc_final: 0.7870 (t0) REVERT: 14 85 GLN cc_start: 0.6756 (tp-100) cc_final: 0.5821 (tt0) REVERT: 14 181 MET cc_start: 0.8616 (tmm) cc_final: 0.8304 (ttt) REVERT: 14 283 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7402 (mt-10) REVERT: 14 330 LYS cc_start: 0.7644 (ptpt) cc_final: 0.7230 (ptpp) outliers start: 60 outliers final: 34 residues processed: 291 average time/residue: 0.1386 time to fit residues: 60.4231 Evaluate side-chains 259 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 251 SER Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 472 LEU Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 8 residue 48 THR Chi-restraints excluded: chain 8 residue 112 ILE Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 8 residue 152 THR Chi-restraints excluded: chain 8 residue 175 LEU Chi-restraints excluded: chain 8 residue 215 ILE Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 271 CYS Chi-restraints excluded: chain 8 residue 335 ASP Chi-restraints excluded: chain 8 residue 372 THR Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 8 residue 494 LEU Chi-restraints excluded: chain 8 residue 497 LEU Chi-restraints excluded: chain 8 residue 515 PHE Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 245 THR Chi-restraints excluded: chain 10 residue 247 VAL Chi-restraints excluded: chain 10 residue 308 MET Chi-restraints excluded: chain 10 residue 341 LEU Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 63 THR Chi-restraints excluded: chain 14 residue 111 LEU Chi-restraints excluded: chain 14 residue 154 ILE Chi-restraints excluded: chain 14 residue 302 ASP Chi-restraints excluded: chain 14 residue 324 LEU Chi-restraints excluded: chain 14 residue 328 THR Chi-restraints excluded: chain 14 residue 332 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 127 ASN 8 256 HIS 10 485 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.177334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140205 restraints weight = 19932.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140756 restraints weight = 20004.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.142352 restraints weight = 18521.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.143001 restraints weight = 15749.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.143028 restraints weight = 13452.735| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17499 Z= 0.102 Angle : 0.483 9.202 23869 Z= 0.247 Chirality : 0.037 0.181 2732 Planarity : 0.004 0.045 2959 Dihedral : 10.961 162.498 2675 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.37 % Allowed : 20.86 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.19), residues: 2047 helix: 2.24 (0.15), residues: 1241 sheet: -0.04 (0.50), residues: 100 loop : -0.56 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG14 232 TYR 0.011 0.001 TYR10 200 PHE 0.018 0.001 PHE 8 83 TRP 0.009 0.001 TRP14 175 HIS 0.009 0.001 HIS10 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (17499) covalent geometry : angle 0.48298 / 0.25 (23869) hydrogen bonds : bond 0.03339 / 1.99 ( 897) hydrogen bonds : angle 3.41080 / 2.30 ( 2658) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: 5 99 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7145 (mtp) REVERT: 5 102 MET cc_start: 0.8497 (tpt) cc_final: 0.8227 (tpp) REVERT: 5 134 LEU cc_start: 0.7913 (pp) cc_final: 0.7650 (pp) REVERT: 5 149 VAL cc_start: 0.7843 (t) cc_final: 0.7623 (t) REVERT: 6 136 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8663 (tt) REVERT: 6 213 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8250 (mm) REVERT: 8 70 ASP cc_start: 0.7466 (m-30) cc_final: 0.7247 (m-30) REVERT: 8 207 ASN cc_start: 0.7078 (t0) cc_final: 0.6779 (t0) REVERT: 8 212 MET cc_start: 0.8553 (mmm) cc_final: 0.8045 (tpt) REVERT: 8 275 MET cc_start: 0.8165 (mmt) cc_final: 0.7934 (mmt) REVERT: 8 317 ASP cc_start: 0.7290 (p0) cc_final: 0.6768 (t0) REVERT: 8 335 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6669 (t0) REVERT: 10 276 MET cc_start: 0.6940 (mmm) cc_final: 0.6175 (tmm) REVERT: 10 308 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8090 (ptp) REVERT: 10 412 ASP cc_start: 0.7929 (t0) cc_final: 0.7606 (t0) REVERT: 10 483 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6938 (ttt) REVERT: 10 518 ASN cc_start: 0.7555 (p0) cc_final: 0.7067 (m110) REVERT: 14 85 GLN cc_start: 0.6672 (tp-100) cc_final: 0.6048 (tt0) REVERT: 14 181 MET cc_start: 0.8481 (tmm) cc_final: 0.8164 (ttt) REVERT: 14 283 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7163 (mt-10) REVERT: 14 330 LYS cc_start: 0.7554 (ptpt) cc_final: 0.7179 (ptpp) outliers start: 42 outliers final: 25 residues processed: 259 average time/residue: 0.1477 time to fit residues: 56.5425 Evaluate side-chains 243 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 175 LEU Chi-restraints excluded: chain 8 residue 189 LEU Chi-restraints excluded: chain 8 residue 215 ILE Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 271 CYS Chi-restraints excluded: chain 8 residue 335 ASP Chi-restraints excluded: chain 8 residue 372 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 8 residue 494 LEU Chi-restraints excluded: chain 8 residue 497 LEU Chi-restraints excluded: chain 8 residue 515 PHE Chi-restraints excluded: chain 8 residue 531 LEU Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 308 MET Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 63 THR Chi-restraints excluded: chain 14 residue 324 LEU Chi-restraints excluded: chain 14 residue 328 THR Chi-restraints excluded: chain 14 residue 332 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 127 ASN 6 321 ASN 8 256 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.171266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134799 restraints weight = 19937.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135820 restraints weight = 20249.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.137355 restraints weight = 17441.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137992 restraints weight = 13480.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138164 restraints weight = 13032.437| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17499 Z= 0.162 Angle : 0.542 9.747 23869 Z= 0.279 Chirality : 0.039 0.186 2732 Planarity : 0.004 0.045 2959 Dihedral : 11.053 163.939 2675 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.88 % Allowed : 20.75 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.19), residues: 2047 helix: 2.04 (0.15), residues: 1241 sheet: -0.05 (0.49), residues: 100 loop : -0.68 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 7 113 TYR 0.012 0.001 TYR10 215 PHE 0.021 0.002 PHE 8 83 TRP 0.010 0.001 TRP14 175 HIS 0.007 0.001 HIS10 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (17499) covalent geometry : angle 0.54234 / 0.28 (23869) hydrogen bonds : bond 0.04482 / 2.67 ( 897) hydrogen bonds : angle 3.59115 / 2.40 ( 2658) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: 5 99 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7228 (mtp) REVERT: 5 149 VAL cc_start: 0.7970 (t) cc_final: 0.7769 (t) REVERT: 6 102 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7169 (pt0) REVERT: 6 136 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8534 (tt) REVERT: 6 213 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8411 (mm) REVERT: 8 70 ASP cc_start: 0.7580 (m-30) cc_final: 0.7329 (m-30) REVERT: 8 197 SER cc_start: 0.8608 (m) cc_final: 0.8302 (t) REVERT: 8 207 ASN cc_start: 0.7151 (t0) cc_final: 0.6848 (t0) REVERT: 8 210 TYR cc_start: 0.7419 (m-80) cc_final: 0.7117 (m-80) REVERT: 8 212 MET cc_start: 0.8483 (mmm) cc_final: 0.8063 (tpt) REVERT: 8 317 ASP cc_start: 0.7570 (p0) cc_final: 0.6941 (t0) REVERT: 8 335 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6537 (t0) REVERT: 8 428 ASP cc_start: 0.7093 (t0) cc_final: 0.6712 (t0) REVERT: 10 276 MET cc_start: 0.7102 (mmm) cc_final: 0.6336 (tmm) REVERT: 10 308 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8132 (ptp) REVERT: 10 412 ASP cc_start: 0.8325 (t0) cc_final: 0.7927 (t0) REVERT: 10 518 ASN cc_start: 0.7792 (p0) cc_final: 0.7309 (m110) REVERT: 14 85 GLN cc_start: 0.6841 (tp-100) cc_final: 0.6318 (tt0) REVERT: 14 181 MET cc_start: 0.8588 (tmm) cc_final: 0.8291 (ttt) REVERT: 14 185 ARG cc_start: 0.8190 (mtt-85) cc_final: 0.7985 (mtt-85) REVERT: 14 283 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7399 (mt-10) REVERT: 14 330 LYS cc_start: 0.7740 (ptpt) cc_final: 0.7262 (ptpp) outliers start: 51 outliers final: 34 residues processed: 255 average time/residue: 0.1448 time to fit residues: 55.3210 Evaluate side-chains 251 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 6 residue 102 GLN Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 472 LEU Chi-restraints excluded: chain 6 residue 508 ILE Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 48 THR Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 8 residue 152 THR Chi-restraints excluded: chain 8 residue 175 LEU Chi-restraints excluded: chain 8 residue 179 ILE Chi-restraints excluded: chain 8 residue 189 LEU Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 271 CYS Chi-restraints excluded: chain 8 residue 335 ASP Chi-restraints excluded: chain 8 residue 372 THR Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 8 residue 485 MET Chi-restraints excluded: chain 8 residue 494 LEU Chi-restraints excluded: chain 8 residue 515 PHE Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 245 THR Chi-restraints excluded: chain 10 residue 247 VAL Chi-restraints excluded: chain 10 residue 308 MET Chi-restraints excluded: chain 10 residue 440 GLU Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 63 THR Chi-restraints excluded: chain 14 residue 324 LEU Chi-restraints excluded: chain 14 residue 328 THR Chi-restraints excluded: chain 14 residue 332 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 50 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.171925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135677 restraints weight = 20039.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.136024 restraints weight = 20393.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.137669 restraints weight = 18034.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.138316 restraints weight = 14257.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138426 restraints weight = 14028.142| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17499 Z= 0.132 Angle : 0.520 10.628 23869 Z= 0.266 Chirality : 0.038 0.203 2732 Planarity : 0.004 0.045 2959 Dihedral : 11.038 162.485 2675 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.49 % Allowed : 21.59 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.19), residues: 2047 helix: 2.16 (0.15), residues: 1225 sheet: 0.09 (0.50), residues: 99 loop : -0.68 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG 8 178 TYR 0.011 0.001 TYR10 200 PHE 0.018 0.001 PHE 8 83 TRP 0.009 0.001 TRP14 175 HIS 0.008 0.001 HIS10 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (17499) covalent geometry : angle 0.51993 / 0.27 (23869) hydrogen bonds : bond 0.03894 / 2.32 ( 897) hydrogen bonds : angle 3.52498 / 2.36 ( 2658) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: 5 37 MET cc_start: 0.7425 (mmm) cc_final: 0.6664 (mmm) REVERT: 5 99 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7001 (mtp) REVERT: 6 136 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8599 (tt) REVERT: 6 213 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8373 (mm) REVERT: 8 70 ASP cc_start: 0.7561 (m-30) cc_final: 0.7317 (m-30) REVERT: 8 197 SER cc_start: 0.8629 (m) cc_final: 0.8326 (t) REVERT: 8 207 ASN cc_start: 0.7104 (t0) cc_final: 0.6846 (t0) REVERT: 8 210 TYR cc_start: 0.7532 (m-80) cc_final: 0.7285 (m-80) REVERT: 8 212 MET cc_start: 0.8510 (mmm) cc_final: 0.8292 (tpp) REVERT: 8 317 ASP cc_start: 0.7467 (p0) cc_final: 0.6958 (t0) REVERT: 8 335 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6494 (t0) REVERT: 8 428 ASP cc_start: 0.7137 (t0) cc_final: 0.6768 (t0) REVERT: 10 276 MET cc_start: 0.6943 (mmm) cc_final: 0.6311 (tmm) REVERT: 10 308 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8113 (ptp) REVERT: 10 351 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.6672 (t-90) REVERT: 10 412 ASP cc_start: 0.8261 (t0) cc_final: 0.7854 (t0) REVERT: 10 483 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7103 (ttt) REVERT: 10 518 ASN cc_start: 0.7904 (p0) cc_final: 0.7546 (m110) REVERT: 14 85 GLN cc_start: 0.6887 (tp-100) cc_final: 0.6579 (tt0) REVERT: 14 181 MET cc_start: 0.8561 (tmm) cc_final: 0.8293 (ttt) REVERT: 14 283 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7364 (mt-10) REVERT: 14 330 LYS cc_start: 0.7764 (ptpt) cc_final: 0.7331 (ptpp) outliers start: 44 outliers final: 28 residues processed: 253 average time/residue: 0.1448 time to fit residues: 54.4294 Evaluate side-chains 249 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 5 residue 127 ASN Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 195 THR Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 500 CYS Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 48 THR Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 152 THR Chi-restraints excluded: chain 8 residue 175 LEU Chi-restraints excluded: chain 8 residue 189 LEU Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 271 CYS Chi-restraints excluded: chain 8 residue 335 ASP Chi-restraints excluded: chain 8 residue 372 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 8 residue 485 MET Chi-restraints excluded: chain 8 residue 494 LEU Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 308 MET Chi-restraints excluded: chain 10 residue 351 HIS Chi-restraints excluded: chain 10 residue 440 GLU Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 63 THR Chi-restraints excluded: chain 14 residue 324 LEU Chi-restraints excluded: chain 14 residue 328 THR Chi-restraints excluded: chain 14 residue 332 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 121 optimal weight: 1.9990 chunk 176 optimal weight: 0.0000 chunk 181 optimal weight: 0.0570 chunk 73 optimal weight: 0.9990 chunk 155 optimal weight: 0.0970 chunk 158 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.174727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138740 restraints weight = 19955.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.138786 restraints weight = 19407.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140056 restraints weight = 17374.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.140492 restraints weight = 15362.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.140637 restraints weight = 13818.888| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17499 Z= 0.099 Angle : 0.504 11.691 23869 Z= 0.256 Chirality : 0.036 0.187 2732 Planarity : 0.004 0.046 2959 Dihedral : 10.947 161.986 2675 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.15 % Allowed : 22.05 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.19), residues: 2047 helix: 2.28 (0.15), residues: 1229 sheet: 0.15 (0.47), residues: 114 loop : -0.69 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG10 507 TYR 0.010 0.001 TYR10 200 PHE 0.024 0.001 PHE10 532 TRP 0.010 0.001 TRP14 175 HIS 0.007 0.001 HIS10 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (17499) covalent geometry : angle 0.50388 / 0.26 (23869) hydrogen bonds : bond 0.03195 / 1.90 ( 897) hydrogen bonds : angle 3.38229 / 2.28 ( 2658) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: 5 37 MET cc_start: 0.7345 (mmm) cc_final: 0.6532 (mmm) REVERT: 5 99 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.6948 (mtp) REVERT: 6 136 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8540 (tt) REVERT: 8 70 ASP cc_start: 0.7603 (m-30) cc_final: 0.7321 (m-30) REVERT: 8 207 ASN cc_start: 0.7004 (t0) cc_final: 0.6681 (t0) REVERT: 8 210 TYR cc_start: 0.7478 (m-80) cc_final: 0.7235 (m-80) REVERT: 8 317 ASP cc_start: 0.7626 (p0) cc_final: 0.6963 (t0) REVERT: 8 335 ASP cc_start: 0.6638 (OUTLIER) cc_final: 0.6233 (t0) REVERT: 10 188 ARG cc_start: 0.8585 (tpp80) cc_final: 0.7928 (mmp80) REVERT: 10 276 MET cc_start: 0.6796 (mmm) cc_final: 0.6205 (tmm) REVERT: 10 351 HIS cc_start: 0.7786 (OUTLIER) cc_final: 0.6548 (t-90) REVERT: 10 412 ASP cc_start: 0.8370 (t0) cc_final: 0.7932 (t0) REVERT: 10 483 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7036 (ttt) REVERT: 10 518 ASN cc_start: 0.7885 (p0) cc_final: 0.7542 (m110) REVERT: 14 85 GLN cc_start: 0.6776 (tp-100) cc_final: 0.6466 (tt0) REVERT: 14 181 MET cc_start: 0.8495 (tmm) cc_final: 0.8267 (ttt) REVERT: 14 330 LYS cc_start: 0.7774 (ptpt) cc_final: 0.7302 (ptpp) outliers start: 38 outliers final: 27 residues processed: 246 average time/residue: 0.1483 time to fit residues: 53.9353 Evaluate side-chains 242 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 5 residue 127 ASN Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 472 LEU Chi-restraints excluded: chain 6 residue 500 CYS Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 152 THR Chi-restraints excluded: chain 8 residue 175 LEU Chi-restraints excluded: chain 8 residue 189 LEU Chi-restraints excluded: chain 8 residue 215 ILE Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 271 CYS Chi-restraints excluded: chain 8 residue 335 ASP Chi-restraints excluded: chain 8 residue 372 THR Chi-restraints excluded: chain 8 residue 485 MET Chi-restraints excluded: chain 8 residue 494 LEU Chi-restraints excluded: chain 8 residue 531 LEU Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 351 HIS Chi-restraints excluded: chain 10 residue 440 GLU Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 154 ILE Chi-restraints excluded: chain 14 residue 324 LEU Chi-restraints excluded: chain 14 residue 328 THR Chi-restraints excluded: chain 14 residue 332 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 103 optimal weight: 0.0030 chunk 172 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 0.0970 chunk 122 optimal weight: 0.6980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.175325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139772 restraints weight = 19700.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140188 restraints weight = 18223.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141423 restraints weight = 16892.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.141834 restraints weight = 14274.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142116 restraints weight = 13461.017| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17499 Z= 0.096 Angle : 0.505 12.910 23869 Z= 0.253 Chirality : 0.036 0.191 2732 Planarity : 0.004 0.047 2959 Dihedral : 10.884 162.115 2675 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.81 % Allowed : 22.39 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 2047 helix: 2.33 (0.15), residues: 1229 sheet: 0.21 (0.47), residues: 114 loop : -0.66 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG14 232 TYR 0.010 0.001 TYR 6 507 PHE 0.016 0.001 PHE10 339 TRP 0.011 0.001 TRP14 175 HIS 0.007 0.001 HIS10 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (17499) covalent geometry : angle 0.50491 / 0.25 (23869) hydrogen bonds : bond 0.03091 / 1.84 ( 897) hydrogen bonds : angle 3.32997 / 2.24 ( 2658) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: 5 99 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7011 (mtp) REVERT: 6 136 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8593 (tt) REVERT: 8 70 ASP cc_start: 0.7556 (m-30) cc_final: 0.7278 (m-30) REVERT: 8 182 TYR cc_start: 0.6538 (m-10) cc_final: 0.6335 (m-10) REVERT: 8 207 ASN cc_start: 0.6930 (t0) cc_final: 0.6624 (t0) REVERT: 8 317 ASP cc_start: 0.7473 (p0) cc_final: 0.6950 (t0) REVERT: 8 335 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6288 (t0) REVERT: 10 276 MET cc_start: 0.6796 (mmm) cc_final: 0.6159 (tmm) REVERT: 10 351 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.6629 (t-90) REVERT: 10 412 ASP cc_start: 0.8286 (t0) cc_final: 0.7879 (t0) REVERT: 10 483 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.7048 (ttt) REVERT: 10 518 ASN cc_start: 0.7822 (p0) cc_final: 0.7581 (m110) REVERT: 14 85 GLN cc_start: 0.6770 (tp-100) cc_final: 0.6543 (tt0) REVERT: 14 181 MET cc_start: 0.8449 (tmm) cc_final: 0.8243 (ttt) REVERT: 14 330 LYS cc_start: 0.7706 (ptpt) cc_final: 0.7272 (ptpp) outliers start: 32 outliers final: 27 residues processed: 245 average time/residue: 0.1469 time to fit residues: 53.8303 Evaluate side-chains 248 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 251 SER Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 472 LEU Chi-restraints excluded: chain 6 residue 500 CYS Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 152 THR Chi-restraints excluded: chain 8 residue 189 LEU Chi-restraints excluded: chain 8 residue 215 ILE Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 271 CYS Chi-restraints excluded: chain 8 residue 335 ASP Chi-restraints excluded: chain 8 residue 372 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 8 residue 485 MET Chi-restraints excluded: chain 8 residue 494 LEU Chi-restraints excluded: chain 8 residue 531 LEU Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 351 HIS Chi-restraints excluded: chain 10 residue 440 GLU Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 154 ILE Chi-restraints excluded: chain 14 residue 324 LEU Chi-restraints excluded: chain 14 residue 328 THR Chi-restraints excluded: chain 14 residue 332 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 127 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 148 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 5 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.174589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.138705 restraints weight = 19831.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.138886 restraints weight = 19027.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.140515 restraints weight = 17361.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141013 restraints weight = 14232.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141088 restraints weight = 13211.152| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17499 Z= 0.104 Angle : 0.511 11.452 23869 Z= 0.257 Chirality : 0.037 0.192 2732 Planarity : 0.004 0.046 2959 Dihedral : 10.820 162.325 2675 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.04 % Allowed : 22.56 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 2047 helix: 2.30 (0.15), residues: 1235 sheet: 0.27 (0.47), residues: 114 loop : -0.63 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG14 232 TYR 0.017 0.001 TYR 7 144 PHE 0.015 0.001 PHE10 339 TRP 0.011 0.001 TRP14 175 HIS 0.007 0.001 HIS10 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (17499) covalent geometry : angle 0.51095 / 0.26 (23869) hydrogen bonds : bond 0.03242 / 1.93 ( 897) hydrogen bonds : angle 3.33842 / 2.25 ( 2658) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2676.10 seconds wall clock time: 47 minutes 9.59 seconds (2829.59 seconds total)