Starting phenix.real_space_refine on Thu Aug 6 20:49:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fnf_29311/08_2026/8fnf_29311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fnf_29311/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fnf_29311/08_2026/8fnf_29311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fnf_29311/08_2026/8fnf_29311.map" model { file = "/net/cci-nas-00/data/ceres_data/8fnf_29311/08_2026/8fnf_29311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fnf_29311/08_2026/8fnf_29311.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fnf_29311/08_2026/8fnf_29311.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fnf_29311/08_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-2.2rc3-6140/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: {'RNAv2': 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: {'RNAv2': 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: 2.81, per 1000 atoms: 0.16 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: 1.18 Conformation dependent library (CDL) restraints added in 642.3 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: 1.46 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: 2.46 Time building geometry restraints manager: 1.60 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: 23381 2.39 - 4.77: 432 4.77 - 7.16: 50 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 - 33.32: 9971 33.32 - 66.64: 511 66.64 - 99.96: 52 99.96 - 133.28: 0 133.28 - 166.60: 2 Dihedral angle restraints: 10536 sinusoidal: 4500 harmonic: 6036 Sorted by residual: dihedral pdb=" C4' A m 114 " pdb=" C3' A m 114 " pdb=" C2' A m 114 " pdb=" C1' A m 114 " ideal model delta sinusoidal sigma weight residual 36.34 -37.43 73.78 1 3.10e+00 1.04e-01 7.20e+02 dihedral pdb=" C4' A m 115 " pdb=" C3' A m 115 " pdb=" C2' A m 115 " pdb=" C1' A m 115 " ideal model delta sinusoidal sigma weight residual 36.35 -37.37 73.72 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' A g -9 " pdb=" C3' A g -9 " pdb=" C2' A g -9 " pdb=" C1' A g -9 " ideal model delta sinusoidal sigma weight residual 36.35 -37.29 73.63 1 3.10e+00 1.04e-01 7.17e+02 ... (remaining 10533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2434 0.068 - 0.136: 213 0.136 - 0.204: 14 0.204 - 0.272: 59 0.272 - 0.340: 12 Chirality restraints: 2732 Sorted by residual: chirality pdb=" P A g -7 " pdb=" OP1 A g -7 " pdb=" OP2 A g -7 " pdb=" O5' A g -7 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C2' A g -7 " pdb=" C3' A g -7 " pdb=" O2' A g -7 " pdb=" C1' A g -7 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" P G m 110 " pdb=" OP1 G m 110 " pdb=" OP2 G m 110 " pdb=" O5' G m 110 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.780 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- 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= 0.183 Angle : 0.718 11.934 23869 Z= 0.390 Chirality : 0.057 0.340 2732 Planarity : 0.005 0.110 2959 Dihedral : 18.751 166.603 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 0.00364 / 0.18 (17499) covalent geometry : angle 0.71845 / 0.39 (23869) hydrogen bonds : bond 0.14981 / 7.79 ( 897) hydrogen bonds : angle 5.21883 / 3.15 ( 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 : 0.502 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: 0.1339 time to fit residues: 53.3277 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 : 0.515 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.185879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.148755 restraints weight = 20105.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.149173 restraints weight = 20296.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.151173 restraints weight = 17336.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151376 restraints weight = 14546.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.151472 restraints weight = 13889.972| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17499 Z= 0.164 Angle : 0.864 17.494 23869 Z= 0.383 Chirality : 0.075 0.924 2732 Planarity : 0.004 0.065 2959 Dihedral : 13.391 173.588 2683 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.09 % Allowed : 18.43 % Favored : 79.48 % 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: 1.15 (0.19), residues: 2047 helix: 1.71 (0.15), residues: 1241 sheet: -0.34 (0.48), residues: 98 loop : -0.74 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG14 123 TYR 0.011 0.001 TYR10 200 PHE 0.017 0.001 PHE 8 83 TRP 0.010 0.001 TRP14 175 HIS 0.006 0.001 HIS 6 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (17499) covalent geometry : angle 0.86444 / 0.38 (23869) hydrogen bonds : bond 0.04432 / 2.30 ( 897) hydrogen bonds : angle 3.94662 / 2.45 ( 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 270 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 37 MET cc_start: 0.7265 (mmm) cc_final: 0.6879 (mmm) REVERT: 5 99 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7133 (mtp) REVERT: 5 134 LEU cc_start: 0.7437 (pp) cc_final: 0.7164 (pp) REVERT: 5 156 GLN cc_start: 0.6722 (mm-40) cc_final: 0.6264 (tt0) REVERT: 5 267 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7798 (mm-30) REVERT: 6 213 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.7887 (mm) REVERT: 8 212 MET cc_start: 0.8534 (mmm) cc_final: 0.7912 (tpt) REVERT: 10 308 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8193 (ptp) REVERT: 10 341 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8746 (mp) REVERT: 10 400 MET cc_start: 0.7379 (mmt) cc_final: 0.7154 (mmt) REVERT: 10 460 LYS cc_start: 0.7815 (tppp) cc_final: 0.7309 (tmtt) REVERT: 14 171 LEU cc_start: 0.7726 (mp) cc_final: 0.7516 (mt) REVERT: 14 181 MET cc_start: 0.8696 (tmm) cc_final: 0.8114 (ttt) REVERT: 14 254 LEU cc_start: 0.8481 (mt) cc_final: 0.8178 (mm) outliers start: 37 outliers final: 16 residues processed: 261 average time/residue: 0.1260 time to fit residues: 48.9974 Evaluate side-chains 231 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 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 8 residue 531 LEU 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 351 HIS Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 14 residue 63 THR 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: 0.9990 chunk 103 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 9 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 119 GLN 5 127 ASN 5 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.183096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145922 restraints weight = 20088.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146981 restraints weight = 19832.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.148529 restraints weight = 18229.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149277 restraints weight = 14927.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149439 restraints weight = 13523.942| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17499 Z= 0.133 Angle : 0.644 11.417 23869 Z= 0.304 Chirality : 0.053 0.741 2732 Planarity : 0.004 0.054 2959 Dihedral : 13.672 163.827 2676 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.60 % Allowed : 19.62 % Favored : 77.78 % 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: 1.39 (0.19), residues: 2047 helix: 1.87 (0.15), residues: 1252 sheet: -0.21 (0.49), residues: 98 loop : -0.65 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG10 507 TYR 0.010 0.001 TYR10 215 PHE 0.015 0.001 PHE 8 83 TRP 0.012 0.001 TRP14 175 HIS 0.004 0.001 HIS 5 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (17499) covalent geometry : angle 0.64418 / 0.30 (23869) hydrogen bonds : bond 0.03831 / 2.00 ( 897) hydrogen bonds : angle 3.65607 / 2.29 ( 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 274 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 99 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7101 (mtp) REVERT: 5 134 LEU cc_start: 0.7717 (pp) cc_final: 0.7446 (pp) REVERT: 5 158 PHE cc_start: 0.7477 (m-80) cc_final: 0.7211 (m-80) REVERT: 5 270 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8495 (ttmt) REVERT: 6 213 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.7736 (mm) REVERT: 8 212 MET cc_start: 0.8504 (mmm) cc_final: 0.8084 (tpt) REVERT: 8 244 ASN cc_start: 0.7472 (m-40) cc_final: 0.7264 (m-40) REVERT: 8 273 SER cc_start: 0.8326 (t) cc_final: 0.8113 (t) REVERT: 8 329 ARG cc_start: 0.7443 (mtm110) cc_final: 0.7157 (ttp80) REVERT: 8 335 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6878 (t0) REVERT: 10 308 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8176 (ptp) REVERT: 10 400 MET cc_start: 0.7484 (mmt) cc_final: 0.7187 (mmt) REVERT: 10 460 LYS cc_start: 0.7923 (tppp) cc_final: 0.7505 (tmtt) REVERT: 14 181 MET cc_start: 0.8535 (tmm) cc_final: 0.8090 (ttt) REVERT: 14 254 LEU cc_start: 0.8554 (mt) cc_final: 0.8280 (mm) outliers start: 46 outliers final: 19 residues processed: 267 average time/residue: 0.1232 time to fit residues: 48.5509 Evaluate side-chains 237 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 5 residue 270 LYS 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 48 THR Chi-restraints excluded: chain 8 residue 112 ILE Chi-restraints excluded: chain 8 residue 179 ILE 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 494 LEU Chi-restraints excluded: chain 8 residue 516 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 463 VAL Chi-restraints excluded: chain 14 residue 63 THR Chi-restraints excluded: chain 14 residue 124 LEU Chi-restraints excluded: chain 14 residue 209 THR 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: 2.9990 chunk 127 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 144 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 127 ASN 6 424 GLN ** 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 = 0.4028 r_free = 0.4028 target = 0.181705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145067 restraints weight = 20075.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144996 restraints weight = 19253.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146760 restraints weight = 16604.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147463 restraints weight = 13859.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.147642 restraints weight = 12637.721| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17499 Z= 0.120 Angle : 0.602 10.217 23869 Z= 0.282 Chirality : 0.049 0.442 2732 Planarity : 0.004 0.047 2959 Dihedral : 13.320 176.973 2676 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.71 % Allowed : 19.73 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.19), residues: 2047 helix: 2.05 (0.15), residues: 1246 sheet: -0.14 (0.49), residues: 98 loop : -0.58 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 113 TYR 0.009 0.001 TYR10 215 PHE 0.021 0.001 PHE10 339 TRP 0.010 0.001 TRP14 175 HIS 0.003 0.001 HIS 5 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (17499) covalent geometry : angle 0.60196 / 0.28 (23869) hydrogen bonds : bond 0.03417 / 1.79 ( 897) hydrogen bonds : angle 3.51625 / 2.19 ( 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 277 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: 5 37 MET cc_start: 0.7423 (mmm) cc_final: 0.6847 (mmm) REVERT: 5 99 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7164 (mtp) REVERT: 5 134 LEU cc_start: 0.7552 (pp) cc_final: 0.7292 (pp) REVERT: 5 197 LYS cc_start: 0.8009 (tppt) cc_final: 0.7783 (tttt) REVERT: 6 98 SER cc_start: 0.8860 (t) cc_final: 0.8643 (p) REVERT: 6 213 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7794 (mm) REVERT: 8 212 MET cc_start: 0.8323 (mmm) cc_final: 0.8067 (tpt) REVERT: 8 323 MET cc_start: 0.8117 (mmm) cc_final: 0.7857 (mmt) REVERT: 8 335 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.6420 (t0) REVERT: 10 276 MET cc_start: 0.6800 (mmm) cc_final: 0.6177 (tmm) REVERT: 10 308 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8077 (ptp) REVERT: 10 400 MET cc_start: 0.7398 (mmt) cc_final: 0.7170 (mmt) REVERT: 10 412 ASP cc_start: 0.7965 (t0) cc_final: 0.7670 (t0) REVERT: 14 181 MET cc_start: 0.8533 (tmm) cc_final: 0.8182 (ttt) REVERT: 14 217 MET cc_start: 0.8140 (mtm) cc_final: 0.7880 (mtm) outliers start: 48 outliers final: 26 residues processed: 266 average time/residue: 0.1491 time to fit residues: 58.6147 Evaluate side-chains 241 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 405 ASP Chi-restraints excluded: chain 6 residue 464 LEU 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 152 THR Chi-restraints excluded: chain 8 residue 175 LEU Chi-restraints excluded: chain 8 residue 215 ILE 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 516 VAL Chi-restraints excluded: chain 8 residue 531 LEU Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 272 GLU 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: 0.9980 chunk 191 optimal weight: 0.0870 chunk 113 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 127 ASN 8 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.177520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.141321 restraints weight = 19983.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141752 restraints weight = 19468.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143817 restraints weight = 16325.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144057 restraints weight = 13642.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144297 restraints weight = 12536.270| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3091 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= 0.132 Angle : 0.592 10.269 23869 Z= 0.281 Chirality : 0.048 0.419 2732 Planarity : 0.004 0.046 2959 Dihedral : 13.395 173.618 2676 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.05 % Allowed : 20.07 % Favored : 76.88 % 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: 1.67 (0.19), residues: 2047 helix: 2.11 (0.15), residues: 1246 sheet: -0.16 (0.50), residues: 98 loop : -0.54 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG10 507 TYR 0.010 0.001 TYR10 215 PHE 0.021 0.001 PHE10 339 TRP 0.009 0.001 TRP14 175 HIS 0.004 0.001 HIS 5 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (17499) covalent geometry : angle 0.59224 / 0.28 (23869) hydrogen bonds : bond 0.03712 / 1.94 ( 897) hydrogen bonds : angle 3.52016 / 2.17 ( 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 288 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 234 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: 5 99 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7179 (mtp) REVERT: 5 134 LEU cc_start: 0.7955 (pp) cc_final: 0.7613 (pp) REVERT: 6 136 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8635 (tt) REVERT: 6 213 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8390 (mm) REVERT: 8 212 MET cc_start: 0.8523 (mmm) cc_final: 0.8097 (tpt) REVERT: 8 317 ASP cc_start: 0.7333 (p0) cc_final: 0.6743 (t0) REVERT: 8 335 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6586 (t0) REVERT: 10 276 MET cc_start: 0.6945 (mmm) cc_final: 0.6307 (tmm) REVERT: 10 308 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8137 (ptp) REVERT: 10 341 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8173 (mp) REVERT: 10 400 MET cc_start: 0.7719 (mmt) cc_final: 0.7413 (mmt) REVERT: 10 412 ASP cc_start: 0.7977 (t0) cc_final: 0.7623 (t0) REVERT: 14 85 GLN cc_start: 0.6716 (tp-100) cc_final: 0.5893 (tt0) REVERT: 14 181 MET cc_start: 0.8491 (tmm) cc_final: 0.8165 (ttt) REVERT: 14 283 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7239 (mt-10) REVERT: 14 330 LYS cc_start: 0.7611 (ptpt) cc_final: 0.7220 (ptpp) outliers start: 54 outliers final: 35 residues processed: 274 average time/residue: 0.1303 time to fit residues: 53.7737 Evaluate side-chains 255 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 5 residue 217 MET Chi-restraints excluded: chain 5 residue 304 GLN 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 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 8 residue 516 VAL 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 341 LEU 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 111 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.174293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137673 restraints weight = 20007.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.138085 restraints weight = 18756.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139681 restraints weight = 16397.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.140297 restraints weight = 14216.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140756 restraints weight = 12974.221| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17499 Z= 0.144 Angle : 0.608 10.548 23869 Z= 0.289 Chirality : 0.048 0.436 2732 Planarity : 0.004 0.043 2959 Dihedral : 13.242 168.661 2676 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.11 % Allowed : 20.75 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.19), residues: 2047 helix: 2.15 (0.15), residues: 1241 sheet: -0.09 (0.50), residues: 98 loop : -0.66 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG14 232 TYR 0.011 0.001 TYR10 215 PHE 0.016 0.001 PHE10 407 TRP 0.008 0.001 TRP14 175 HIS 0.009 0.001 HIS10 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (17499) covalent geometry : angle 0.60810 / 0.29 (23869) hydrogen bonds : bond 0.03998 / 2.09 ( 897) hydrogen bonds : angle 3.52545 / 2.17 ( 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 277 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 222 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: 5 99 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7150 (mtp) REVERT: 5 134 LEU cc_start: 0.7832 (pp) cc_final: 0.7462 (pp) REVERT: 5 149 VAL cc_start: 0.8149 (t) cc_final: 0.7892 (t) REVERT: 6 136 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8552 (tt) REVERT: 6 213 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8417 (mm) REVERT: 8 197 SER cc_start: 0.8542 (m) cc_final: 0.8245 (t) REVERT: 8 207 ASN cc_start: 0.7129 (t0) cc_final: 0.6833 (t0) REVERT: 8 212 MET cc_start: 0.8431 (mmm) cc_final: 0.8046 (tpt) REVERT: 8 317 ASP cc_start: 0.7547 (p0) cc_final: 0.6921 (t0) REVERT: 8 323 MET cc_start: 0.8227 (mmm) cc_final: 0.7960 (mmt) REVERT: 8 335 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6444 (t0) REVERT: 10 276 MET cc_start: 0.6974 (mmm) cc_final: 0.6372 (tmm) REVERT: 10 308 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8121 (ptp) REVERT: 10 400 MET cc_start: 0.7797 (mmt) cc_final: 0.7521 (mmt) REVERT: 10 412 ASP cc_start: 0.8220 (t0) cc_final: 0.7792 (t0) REVERT: 10 518 ASN cc_start: 0.7743 (p0) cc_final: 0.7389 (m110) REVERT: 14 85 GLN cc_start: 0.6859 (tp-100) cc_final: 0.6187 (tt0) REVERT: 14 86 PHE cc_start: 0.7797 (m-80) cc_final: 0.7323 (m-10) REVERT: 14 181 MET cc_start: 0.8593 (tmm) cc_final: 0.8294 (ttt) REVERT: 14 283 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7374 (mt-10) REVERT: 14 330 LYS cc_start: 0.7734 (ptpt) cc_final: 0.7280 (ptpp) outliers start: 55 outliers final: 41 residues processed: 264 average time/residue: 0.1288 time to fit residues: 50.5323 Evaluate side-chains 259 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 304 GLN 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 251 SER Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 434 SER 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 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 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 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 8 residue 516 VAL 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 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 242 VAL Chi-restraints excluded: chain 14 residue 293 PHE 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: 0.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 195 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 127 ASN 8 256 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.173792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137584 restraints weight = 19924.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.138556 restraints weight = 19171.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140311 restraints weight = 16804.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.140796 restraints weight = 13877.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.140932 restraints weight = 13653.610| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.003 0.041 17499 Z= 0.133 Angle : 0.593 10.923 23869 Z= 0.281 Chirality : 0.047 0.448 2732 Planarity : 0.004 0.046 2959 Dihedral : 13.248 166.383 2676 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.34 % Allowed : 20.69 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.19), residues: 2047 helix: 2.21 (0.15), residues: 1229 sheet: -0.01 (0.50), residues: 98 loop : -0.59 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG10 507 TYR 0.011 0.001 TYR10 215 PHE 0.013 0.001 PHE10 407 TRP 0.010 0.001 TRP14 175 HIS 0.007 0.001 HIS10 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (17499) covalent geometry : angle 0.59287 / 0.28 (23869) hydrogen bonds : bond 0.03717 / 1.95 ( 897) hydrogen bonds : angle 3.47672 / 2.15 ( 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 286 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 37 MET cc_start: 0.7407 (mmm) cc_final: 0.6652 (mmm) REVERT: 5 99 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.6994 (mtp) REVERT: 5 149 VAL cc_start: 0.8242 (t) cc_final: 0.8012 (t) REVERT: 6 136 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8578 (tt) REVERT: 8 197 SER cc_start: 0.8566 (m) cc_final: 0.8286 (t) REVERT: 8 207 ASN cc_start: 0.7128 (t0) cc_final: 0.6854 (t0) REVERT: 8 212 MET cc_start: 0.8492 (mmm) cc_final: 0.8122 (tpt) REVERT: 8 317 ASP cc_start: 0.7496 (p0) cc_final: 0.6941 (t0) REVERT: 8 335 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.6342 (t0) REVERT: 8 428 ASP cc_start: 0.7074 (t0) cc_final: 0.6718 (t0) REVERT: 10 188 ARG cc_start: 0.8531 (tpp80) cc_final: 0.7932 (mmp80) REVERT: 10 276 MET cc_start: 0.6956 (mmm) cc_final: 0.6393 (tmm) REVERT: 10 308 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8105 (ptp) REVERT: 10 400 MET cc_start: 0.7906 (mmt) cc_final: 0.7628 (mmt) REVERT: 10 412 ASP cc_start: 0.8233 (t0) cc_final: 0.7823 (t0) REVERT: 10 483 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.7037 (ttt) REVERT: 10 518 ASN cc_start: 0.7876 (p0) cc_final: 0.7518 (m110) REVERT: 10 534 GLU cc_start: 0.6901 (tp30) cc_final: 0.6629 (tp30) REVERT: 14 85 GLN cc_start: 0.6916 (tp-100) cc_final: 0.6505 (tt0) REVERT: 14 181 MET cc_start: 0.8535 (tmm) cc_final: 0.8281 (ttt) REVERT: 14 283 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7430 (mt-10) REVERT: 14 330 LYS cc_start: 0.7742 (ptpt) cc_final: 0.7330 (ptpp) outliers start: 59 outliers final: 40 residues processed: 269 average time/residue: 0.1273 time to fit residues: 51.0252 Evaluate side-chains 262 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 304 GLN Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 195 THR Chi-restraints excluded: chain 6 residue 251 SER Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 434 SER 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 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 343 MET 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 8 residue 516 VAL 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 111 LEU Chi-restraints excluded: chain 14 residue 201 HIS Chi-restraints excluded: chain 14 residue 293 PHE 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: 3.9990 chunk 110 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 98 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 5 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 321 ASN 6 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.168368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132156 restraints weight = 20161.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132843 restraints weight = 19584.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.134282 restraints weight = 16487.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135130 restraints weight = 14208.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.135175 restraints weight = 13183.400| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17499 Z= 0.194 Angle : 0.661 10.911 23869 Z= 0.319 Chirality : 0.050 0.457 2732 Planarity : 0.005 0.045 2959 Dihedral : 13.214 165.013 2676 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.22 % Allowed : 21.25 % Favored : 75.52 % 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: 1.45 (0.19), residues: 2047 helix: 2.01 (0.15), residues: 1225 sheet: 0.02 (0.51), residues: 95 loop : -0.73 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG10 507 TYR 0.013 0.001 TYR10 215 PHE 0.037 0.002 PHE10 532 TRP 0.008 0.001 TRP14 233 HIS 0.008 0.001 HIS10 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.19 (17499) covalent geometry : angle 0.66140 / 0.32 (23869) hydrogen bonds : bond 0.04986 / 2.61 ( 897) hydrogen bonds : angle 3.72387 / 2.27 ( 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 285 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: 5 99 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7004 (mtp) REVERT: 5 149 VAL cc_start: 0.8347 (t) cc_final: 0.8139 (t) REVERT: 5 268 MET cc_start: 0.8516 (mmm) cc_final: 0.8238 (mtt) REVERT: 6 136 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8484 (tt) REVERT: 8 197 SER cc_start: 0.8722 (m) cc_final: 0.8383 (t) REVERT: 8 207 ASN cc_start: 0.7177 (t0) cc_final: 0.6893 (t0) REVERT: 8 210 TYR cc_start: 0.7595 (m-80) cc_final: 0.7289 (m-80) REVERT: 8 212 MET cc_start: 0.8430 (mmm) cc_final: 0.7914 (tpt) REVERT: 8 317 ASP cc_start: 0.7616 (p0) cc_final: 0.7092 (t0) REVERT: 8 335 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.6413 (t0) REVERT: 8 428 ASP cc_start: 0.7320 (t0) cc_final: 0.6988 (t0) REVERT: 10 188 ARG cc_start: 0.8649 (tpp80) cc_final: 0.7987 (mmp80) REVERT: 10 308 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8141 (ptp) REVERT: 10 351 HIS cc_start: 0.7833 (OUTLIER) cc_final: 0.6685 (t-90) REVERT: 10 400 MET cc_start: 0.7848 (mmt) cc_final: 0.7643 (mmt) REVERT: 10 412 ASP cc_start: 0.8389 (t0) cc_final: 0.7911 (t0) REVERT: 10 483 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.7141 (ttt) REVERT: 10 518 ASN cc_start: 0.7970 (p0) cc_final: 0.7686 (m-40) REVERT: 14 85 GLN cc_start: 0.6971 (tp-100) cc_final: 0.6655 (tt0) REVERT: 14 104 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7799 (mp) REVERT: 14 181 MET cc_start: 0.8642 (tmm) cc_final: 0.8285 (ttt) REVERT: 14 283 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7541 (mt-10) REVERT: 14 330 LYS cc_start: 0.7811 (ptpt) cc_final: 0.7369 (ptpp) outliers start: 57 outliers final: 42 residues processed: 270 average time/residue: 0.1459 time to fit residues: 58.9240 Evaluate side-chains 263 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 217 MET Chi-restraints excluded: chain 5 residue 304 GLN 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 251 SER Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 434 SER Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 508 ILE 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 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 343 MET 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 516 VAL 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 351 HIS Chi-restraints excluded: chain 10 residue 440 GLU Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 10 residue 479 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 104 LEU Chi-restraints excluded: chain 14 residue 201 HIS Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 293 PHE Chi-restraints excluded: chain 14 residue 316 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: 3.9990 chunk 176 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 158 optimal weight: 0.3980 chunk 96 optimal weight: 0.0470 chunk 185 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 5 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 476 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.172244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.136642 restraints weight = 19965.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.136737 restraints weight = 19519.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.138722 restraints weight = 17487.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139159 restraints weight = 13984.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139323 restraints weight = 12734.761| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17499 Z= 0.115 Angle : 0.590 11.243 23869 Z= 0.281 Chirality : 0.047 0.461 2732 Planarity : 0.004 0.046 2959 Dihedral : 13.197 167.213 2676 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.43 % Allowed : 22.78 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.19), residues: 2047 helix: 2.18 (0.15), residues: 1222 sheet: 0.08 (0.51), residues: 97 loop : -0.69 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG14 232 TYR 0.010 0.001 TYR10 215 PHE 0.017 0.001 PHE 6 494 TRP 0.009 0.001 TRP14 175 HIS 0.007 0.001 HIS10 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (17499) covalent geometry : angle 0.58987 / 0.28 (23869) hydrogen bonds : bond 0.03559 / 1.87 ( 897) hydrogen bonds : angle 3.48056 / 2.15 ( 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 261 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: 5 37 MET cc_start: 0.7336 (mmm) cc_final: 0.6654 (mmm) REVERT: 5 99 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7028 (mtp) REVERT: 6 98 SER cc_start: 0.8705 (t) cc_final: 0.8406 (p) REVERT: 6 136 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8607 (tt) REVERT: 8 110 ASP cc_start: 0.7592 (t70) cc_final: 0.7309 (t0) REVERT: 8 207 ASN cc_start: 0.6993 (t0) cc_final: 0.6724 (t0) REVERT: 8 210 TYR cc_start: 0.7572 (m-80) cc_final: 0.7313 (m-80) REVERT: 8 212 MET cc_start: 0.8438 (mmm) cc_final: 0.8017 (tpt) REVERT: 8 220 MET cc_start: 0.8164 (tpt) cc_final: 0.7919 (tpp) REVERT: 8 317 ASP cc_start: 0.7474 (p0) cc_final: 0.7029 (t0) REVERT: 8 335 ASP cc_start: 0.6712 (OUTLIER) cc_final: 0.6336 (t0) REVERT: 8 428 ASP cc_start: 0.7145 (t0) cc_final: 0.6806 (t0) REVERT: 10 188 ARG cc_start: 0.8647 (tpp80) cc_final: 0.7991 (mmp80) REVERT: 10 308 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8083 (ptp) REVERT: 10 351 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.6707 (t-90) REVERT: 10 400 MET cc_start: 0.7919 (mmt) cc_final: 0.7684 (mmt) REVERT: 10 412 ASP cc_start: 0.8223 (t0) cc_final: 0.7723 (t0) REVERT: 14 181 MET cc_start: 0.8556 (tmm) cc_final: 0.8243 (ttt) REVERT: 14 283 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7456 (mt-10) REVERT: 14 330 LYS cc_start: 0.7709 (ptpt) cc_final: 0.7295 (ptpp) outliers start: 43 outliers final: 35 residues processed: 249 average time/residue: 0.1280 time to fit residues: 47.6937 Evaluate side-chains 248 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 304 GLN 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 405 ASP Chi-restraints excluded: chain 6 residue 434 SER 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 6 residue 508 ILE 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 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 343 MET 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 516 VAL Chi-restraints excluded: chain 8 residue 531 LEU Chi-restraints excluded: chain 10 residue 114 VAL 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 479 VAL Chi-restraints excluded: chain 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 201 HIS Chi-restraints excluded: chain 14 residue 293 PHE 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: 0.6980 chunk 172 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 115 optimal weight: 0.3980 chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 5 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.172840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136778 restraints weight = 19812.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.137277 restraints weight = 19286.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.138678 restraints weight = 16564.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139333 restraints weight = 14584.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139320 restraints weight = 13624.736| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17499 Z= 0.113 Angle : 0.596 11.255 23869 Z= 0.282 Chirality : 0.047 0.452 2732 Planarity : 0.004 0.047 2959 Dihedral : 13.160 167.957 2676 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.26 % Allowed : 22.84 % Favored : 74.90 % 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: 1.64 (0.19), residues: 2047 helix: 2.16 (0.15), residues: 1232 sheet: 0.21 (0.51), residues: 102 loop : -0.72 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 7 113 TYR 0.017 0.001 TYR 7 144 PHE 0.014 0.001 PHE 6 494 TRP 0.011 0.001 TRP14 175 HIS 0.007 0.001 HIS10 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (17499) covalent geometry : angle 0.59599 / 0.28 (23869) hydrogen bonds : bond 0.03423 / 1.80 ( 897) hydrogen bonds : angle 3.41896 / 2.12 ( 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 259 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: 5 37 MET cc_start: 0.7335 (mmm) cc_final: 0.6634 (mmm) REVERT: 5 99 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7025 (mtp) REVERT: 6 98 SER cc_start: 0.8716 (t) cc_final: 0.8458 (p) REVERT: 6 136 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8618 (tt) REVERT: 6 462 LYS cc_start: 0.7907 (mttp) cc_final: 0.7690 (mmmt) REVERT: 7 113 ARG cc_start: 0.7525 (ttp-110) cc_final: 0.7120 (mtm110) REVERT: 8 110 ASP cc_start: 0.7583 (t70) cc_final: 0.7306 (t0) REVERT: 8 207 ASN cc_start: 0.7011 (t0) cc_final: 0.6745 (t0) REVERT: 8 210 TYR cc_start: 0.7578 (m-80) cc_final: 0.7288 (m-80) REVERT: 8 212 MET cc_start: 0.8424 (mmm) cc_final: 0.8015 (tpt) REVERT: 8 317 ASP cc_start: 0.7408 (p0) cc_final: 0.6949 (t0) REVERT: 8 335 ASP cc_start: 0.6677 (OUTLIER) cc_final: 0.6302 (t0) REVERT: 8 428 ASP cc_start: 0.7135 (t0) cc_final: 0.6784 (t0) REVERT: 10 188 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8035 (mmp80) REVERT: 10 272 GLU cc_start: 0.8029 (tp30) cc_final: 0.7783 (mm-30) REVERT: 10 308 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8077 (ptp) REVERT: 10 351 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.6657 (t-90) REVERT: 10 400 MET cc_start: 0.7915 (mmt) cc_final: 0.7680 (mmt) REVERT: 10 412 ASP cc_start: 0.8268 (t0) cc_final: 0.7772 (t0) REVERT: 10 485 GLN cc_start: 0.6828 (mm-40) cc_final: 0.5908 (tt0) REVERT: 10 532 PHE cc_start: 0.7395 (m-80) cc_final: 0.6951 (m-80) REVERT: 14 181 MET cc_start: 0.8522 (tmm) cc_final: 0.8259 (ttt) REVERT: 14 330 LYS cc_start: 0.7705 (ptpt) cc_final: 0.7320 (ptpp) outliers start: 40 outliers final: 32 residues processed: 248 average time/residue: 0.1350 time to fit residues: 50.4536 Evaluate side-chains 245 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 304 GLN 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 434 SER Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 472 LEU 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 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 343 MET 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 516 VAL Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 245 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 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 63 THR Chi-restraints excluded: chain 14 residue 201 HIS Chi-restraints excluded: chain 14 residue 293 PHE 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: 2.9990 chunk 98 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 51 optimal weight: 0.2980 chunk 148 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 5 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.173702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.138046 restraints weight = 19927.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.138442 restraints weight = 19418.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140229 restraints weight = 16664.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.140803 restraints weight = 13839.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.140805 restraints weight = 12932.004| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4790 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= 0.108 Angle : 0.589 11.066 23869 Z= 0.277 Chirality : 0.046 0.434 2732 Planarity : 0.004 0.047 2959 Dihedral : 13.095 169.145 2674 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.26 % Allowed : 22.95 % Favored : 74.79 % 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: 1.73 (0.19), residues: 2047 helix: 2.20 (0.15), residues: 1237 sheet: 0.28 (0.52), residues: 102 loop : -0.63 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG14 232 TYR 0.009 0.001 TYR10 215 PHE 0.013 0.001 PHE 6 494 TRP 0.011 0.001 TRP14 175 HIS 0.007 0.001 HIS10 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (17499) covalent geometry : angle 0.58922 / 0.28 (23869) hydrogen bonds : bond 0.03224 / 1.69 ( 897) hydrogen bonds : angle 3.37888 / 2.11 ( 2658) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2465.66 seconds wall clock time: 43 minutes 18.14 seconds (2598.14 seconds total)