Starting phenix.real_space_refine on Sun Jun 15 11:36:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fnf_29311/06_2025/8fnf_29311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fnf_29311/06_2025/8fnf_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_29311/06_2025/8fnf_29311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fnf_29311/06_2025/8fnf_29311.map" model { file = "/net/cci-nas-00/data/ceres_data/8fnf_29311/06_2025/8fnf_29311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fnf_29311/06_2025/8fnf_29311.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17080 Number of models: 1 Model: "" Number of chains: 8 Chain: "m" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 432 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 14, 'rna3p': 5} Chain: "g" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 7, 'rna3p': 8} Chain: "5" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2327 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain: "6" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3582 Classifications: {'peptide': 452} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 440} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "7" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 547 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "8" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4076 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 25, 'TRANS': 490} Chain: "10" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3290 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 14, 'TRANS': 401} Chain breaks: 3 Chain: "14" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2496 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 24, 'TRANS': 289} Time building chain proxies: 9.79, per 1000 atoms: 0.57 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: 4.38 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 5.21 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: 5.15 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5570 1.34 - 1.46: 3920 1.46 - 1.58: 7744 1.58 - 1.71: 70 1.71 - 1.83: 195 Bond restraints: 17499 Sorted by residual: bond pdb=" SD MET10 528 " pdb=" CE MET10 528 " ideal model delta sigma weight residual 1.791 1.741 0.050 2.50e-02 1.60e+03 3.99e+00 bond pdb=" CA ARG 8 511 " pdb=" C ARG 8 511 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.30e-02 5.92e+03 3.84e+00 bond pdb=" CA ASP14 66 " pdb=" C ASP14 66 " ideal model delta sigma weight residual 1.528 1.502 0.027 1.39e-02 5.18e+03 3.70e+00 bond pdb=" CA SER 5 116 " pdb=" C SER 5 116 " ideal model delta sigma weight residual 1.526 1.505 0.020 1.23e-02 6.61e+03 2.78e+00 bond pdb=" CB PRO 8 240 " pdb=" CG PRO 8 240 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.63e+00 ... (remaining 17494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 23523 2.39 - 4.77: 308 4.77 - 7.16: 32 7.16 - 9.55: 4 9.55 - 11.93: 2 Bond angle restraints: 23869 Sorted by residual: angle pdb=" C LYS 8 517 " pdb=" CA LYS 8 517 " pdb=" CB LYS 8 517 " ideal model delta sigma weight residual 116.54 110.54 6.00 1.15e+00 7.56e-01 2.72e+01 angle pdb=" N VAL 5 192 " pdb=" CA VAL 5 192 " pdb=" C VAL 5 192 " ideal model delta sigma weight residual 108.36 114.13 -5.77 1.43e+00 4.89e-01 1.63e+01 angle pdb=" CB MET10 528 " pdb=" CG MET10 528 " pdb=" SD MET10 528 " ideal model delta sigma weight residual 112.70 100.77 11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C THR 8 520 " pdb=" N PRO 8 521 " pdb=" CA PRO 8 521 " ideal model delta sigma weight residual 119.05 114.84 4.21 1.11e+00 8.12e-01 1.44e+01 angle pdb=" N VAL 8 529 " pdb=" CA VAL 8 529 " pdb=" C VAL 8 529 " ideal model delta sigma weight residual 110.42 106.89 3.53 9.40e-01 1.13e+00 1.41e+01 ... (remaining 23864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.96: 10119 33.96 - 67.91: 456 67.91 - 101.87: 33 101.87 - 135.82: 1 135.82 - 169.78: 3 Dihedral angle restraints: 10612 sinusoidal: 4576 harmonic: 6036 Sorted by residual: dihedral pdb=" O4' U g -2 " pdb=" C1' U g -2 " pdb=" N1 U g -2 " pdb=" C2 U g -2 " ideal model delta sinusoidal sigma weight residual 232.00 62.22 169.78 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O4' U g -10 " pdb=" C1' U g -10 " pdb=" N1 U g -10 " pdb=" C2 U g -10 " ideal model delta sinusoidal sigma weight residual -160.00 -44.64 -115.36 1 1.50e+01 4.44e-03 6.09e+01 dihedral pdb=" O4' A m 117 " pdb=" C1' A m 117 " pdb=" N9 A m 117 " pdb=" C4 A m 117 " ideal model delta sinusoidal sigma weight residual 254.00 162.84 91.16 1 1.70e+01 3.46e-03 3.39e+01 ... (remaining 10609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2110 0.044 - 0.088: 513 0.088 - 0.133: 100 0.133 - 0.177: 7 0.177 - 0.221: 2 Chirality restraints: 2732 Sorted by residual: chirality pdb=" C3' U g -2 " pdb=" C4' U g -2 " pdb=" O3' U g -2 " pdb=" C2' U g -2 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C3' U g -3 " pdb=" C4' U g -3 " pdb=" O3' U g -3 " pdb=" C2' U g -3 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASP10 335 " pdb=" N ASP10 335 " pdb=" C ASP10 335 " pdb=" CB ASP10 335 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 2729 not shown) Planarity restraints: 2959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY 8 239 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO 8 240 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO 8 240 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO 8 240 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN 5 123 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C ASN 5 123 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN 5 123 " -0.017 2.00e-02 2.50e+03 pdb=" N CYS 5 124 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER 8 81 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO 8 82 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO 8 82 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO 8 82 " 0.028 5.00e-02 4.00e+02 ... (remaining 2956 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2236 2.75 - 3.29: 16512 3.29 - 3.82: 27533 3.82 - 4.36: 31096 4.36 - 4.90: 54795 Nonbonded interactions: 132172 Sorted by model distance: nonbonded pdb=" O ILE14 154 " pdb=" OH TYR14 311 " model vdw 2.212 3.040 nonbonded pdb=" N GLU 8 37 " pdb=" OE1 GLU 8 37 " model vdw 2.233 3.120 nonbonded pdb=" N GLN14 143 " pdb=" OE1 GLN14 143 " model vdw 2.236 3.120 nonbonded pdb=" O ALA 5 73 " pdb=" OG SER 5 128 " model vdw 2.241 3.040 nonbonded pdb=" NE1 TRP 6 451 " pdb=" OE1 GLU 6 490 " model vdw 2.250 3.120 ... (remaining 132167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.300 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 17499 Z= 0.180 Angle : 0.658 11.934 23869 Z= 0.375 Chirality : 0.039 0.221 2732 Planarity : 0.005 0.110 2959 Dihedral : 18.021 169.779 6694 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.014 0.001 TRP14 175 HIS 0.007 0.001 HIS 6 367 PHE 0.022 0.002 PHE 8 83 TYR 0.015 0.001 TYR14 88 ARG 0.006 0.001 ARG10 291 Details of bonding type rmsd hydrogen bonds : bond 0.14981 ( 897) hydrogen bonds : angle 5.21883 ( 2658) covalent geometry : bond 0.00357 (17499) covalent geometry : angle 0.65804 (23869) *********************** 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 : 1.714 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: 0.3215 time to fit residues: 125.7002 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 : 1.728 ------------------------------------------------------------------------------- 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 174 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 87 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 127 ASN 5 174 GLN 5 236 HIS 6 340 ASN 6 381 HIS 8 98 ASN 8 214 GLN ** 8 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 122 HIS 10 251 ASN 10 273 ASN 14 193 GLN 14 310 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.183615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145696 restraints weight = 19993.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145793 restraints weight = 18929.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.147907 restraints weight = 17530.161| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1336 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= 0.140 Angle : 0.551 8.679 23869 Z= 0.284 Chirality : 0.039 0.154 2732 Planarity : 0.004 0.064 2959 Dihedral : 12.698 161.907 2759 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.43 % Allowed : 18.37 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.19), residues: 2047 helix: 1.65 (0.15), residues: 1243 sheet: -0.32 (0.48), residues: 98 loop : -0.74 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 175 HIS 0.007 0.001 HIS 6 381 PHE 0.023 0.002 PHE 8 83 TYR 0.012 0.001 TYR 5 208 ARG 0.006 0.001 ARG14 123 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 897) hydrogen bonds : angle 3.88063 ( 2658) covalent geometry : bond 0.00326 (17499) covalent geometry : angle 0.55099 (23869) *********************** 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 276 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 37 MET cc_start: 0.7438 (mmm) cc_final: 0.6943 (mmm) REVERT: 5 99 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7066 (mtp) REVERT: 5 134 LEU cc_start: 0.7333 (pp) cc_final: 0.6958 (pp) REVERT: 5 156 GLN cc_start: 0.6764 (mm-40) cc_final: 0.6261 (tt0) REVERT: 6 213 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7638 (mm) REVERT: 10 308 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8191 (ptp) REVERT: 10 400 MET cc_start: 0.7294 (mmt) cc_final: 0.7036 (mmt) REVERT: 10 460 LYS cc_start: 0.7820 (tppp) cc_final: 0.7325 (tmtt) REVERT: 14 171 LEU cc_start: 0.7939 (mp) cc_final: 0.7717 (mt) REVERT: 14 181 MET cc_start: 0.8621 (tmm) cc_final: 0.8109 (ttt) REVERT: 14 254 LEU cc_start: 0.8461 (mt) cc_final: 0.8151 (mm) outliers start: 43 outliers final: 17 residues processed: 263 average time/residue: 0.3230 time to fit residues: 125.6225 Evaluate side-chains 230 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 5 residue 249 SER 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 152 THR Chi-restraints excluded: chain 8 residue 372 THR Chi-restraints excluded: chain 8 residue 516 VAL Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 245 THR Chi-restraints excluded: chain 10 residue 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 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 47 optimal weight: 0.5980 chunk 151 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 119 GLN 5 127 ASN 5 174 GLN 8 532 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.181287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143512 restraints weight = 19907.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.144364 restraints weight = 18507.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.146427 restraints weight = 16525.614| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17499 Z= 0.117 Angle : 0.495 9.068 23869 Z= 0.254 Chirality : 0.037 0.178 2732 Planarity : 0.004 0.052 2959 Dihedral : 12.480 164.431 2752 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.71 % Allowed : 19.79 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.19), residues: 2047 helix: 1.88 (0.15), residues: 1257 sheet: -0.22 (0.49), residues: 98 loop : -0.58 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP14 175 HIS 0.003 0.001 HIS 5 151 PHE 0.021 0.001 PHE 8 83 TYR 0.011 0.001 TYR10 200 ARG 0.004 0.000 ARG10 291 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 897) hydrogen bonds : angle 3.63189 ( 2658) covalent geometry : bond 0.00261 (17499) covalent geometry : angle 0.49537 (23869) *********************** 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: 48 poor density : 226 time to evaluate : 1.767 Fit side-chains revert: symmetry clash REVERT: 5 99 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7151 (mtp) REVERT: 5 134 LEU cc_start: 0.7593 (pp) cc_final: 0.7229 (pp) REVERT: 5 156 GLN cc_start: 0.6890 (mm-40) cc_final: 0.6570 (tt0) REVERT: 5 158 PHE cc_start: 0.7824 (m-80) cc_final: 0.7586 (m-80) REVERT: 5 270 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8313 (ttmt) REVERT: 6 136 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8479 (tt) REVERT: 6 213 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7511 (mm) REVERT: 6 505 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: 7 113 ARG cc_start: 0.5927 (ttp-110) cc_final: 0.5618 (mtm110) REVERT: 8 212 MET cc_start: 0.8352 (mmm) cc_final: 0.8134 (mmt) REVERT: 8 319 MET cc_start: 0.8297 (tpp) cc_final: 0.8031 (mmt) REVERT: 8 335 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6636 (t0) REVERT: 8 409 MET cc_start: 0.8484 (mtt) cc_final: 0.8105 (mtp) REVERT: 10 308 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8132 (ptp) REVERT: 10 341 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8062 (mp) REVERT: 10 400 MET cc_start: 0.7449 (mmt) cc_final: 0.7135 (mmt) REVERT: 10 412 ASP cc_start: 0.8020 (t0) cc_final: 0.7734 (t0) REVERT: 10 460 LYS cc_start: 0.7874 (tppp) cc_final: 0.7173 (tmtt) REVERT: 14 181 MET cc_start: 0.8559 (tmm) cc_final: 0.8163 (ttt) REVERT: 14 217 MET cc_start: 0.8228 (mtm) cc_final: 0.7906 (mtm) outliers start: 48 outliers final: 20 residues processed: 263 average time/residue: 0.3175 time to fit residues: 123.1505 Evaluate side-chains 239 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 270 LYS 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 505 GLN Chi-restraints excluded: chain 7 residue 125 SER Chi-restraints excluded: chain 8 residue 48 THR Chi-restraints excluded: chain 8 residue 112 ILE Chi-restraints excluded: chain 8 residue 175 LEU Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 271 CYS Chi-restraints excluded: chain 8 residue 335 ASP Chi-restraints excluded: chain 8 residue 372 THR Chi-restraints excluded: chain 8 residue 494 LEU Chi-restraints excluded: chain 8 residue 515 PHE Chi-restraints excluded: chain 8 residue 516 VAL Chi-restraints excluded: chain 10 residue 308 MET Chi-restraints excluded: chain 10 residue 341 LEU Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 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 164 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 127 ASN 6 424 GLN 8 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.176426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139433 restraints weight = 19737.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.140219 restraints weight = 18908.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.141542 restraints weight = 17235.542| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2689 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= 0.135 Angle : 0.511 7.782 23869 Z= 0.264 Chirality : 0.038 0.174 2732 Planarity : 0.004 0.048 2959 Dihedral : 12.438 162.290 2752 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.28 % Allowed : 20.63 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.19), residues: 2047 helix: 2.02 (0.15), residues: 1242 sheet: -0.20 (0.48), residues: 98 loop : -0.63 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 175 HIS 0.003 0.001 HIS 5 214 PHE 0.022 0.001 PHE 8 83 TYR 0.015 0.001 TYR 8 330 ARG 0.013 0.000 ARG 8 329 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 897) hydrogen bonds : angle 3.60293 ( 2658) covalent geometry : bond 0.00319 (17499) covalent geometry : angle 0.51148 (23869) *********************** 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 294 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 236 time to evaluate : 1.903 Fit side-chains REVERT: 5 99 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7131 (mtp) REVERT: 5 134 LEU cc_start: 0.7726 (pp) cc_final: 0.7351 (pp) REVERT: 5 270 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8319 (mttt) REVERT: 6 213 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.7938 (mm) REVERT: 6 505 GLN cc_start: 0.7276 (mp10) cc_final: 0.7030 (mp10) REVERT: 7 113 ARG cc_start: 0.6659 (ttp-110) cc_final: 0.6379 (mtm110) REVERT: 8 212 MET cc_start: 0.8449 (mmm) cc_final: 0.8012 (tpt) REVERT: 8 317 ASP cc_start: 0.7653 (p0) cc_final: 0.6808 (t0) REVERT: 8 323 MET cc_start: 0.8243 (mmm) cc_final: 0.7895 (mmt) REVERT: 8 335 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6442 (t0) REVERT: 8 409 MET cc_start: 0.8554 (mtt) cc_final: 0.8187 (mtp) REVERT: 10 276 MET cc_start: 0.7007 (mmm) cc_final: 0.6253 (tmm) REVERT: 10 308 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8121 (ptp) REVERT: 10 400 MET cc_start: 0.7603 (mmt) cc_final: 0.7289 (mmt) REVERT: 10 412 ASP cc_start: 0.8235 (t0) cc_final: 0.7857 (t0) REVERT: 14 85 GLN cc_start: 0.6891 (tp-100) cc_final: 0.5904 (tt0) REVERT: 14 181 MET cc_start: 0.8579 (tmm) cc_final: 0.8206 (ttt) REVERT: 14 217 MET cc_start: 0.8313 (mtm) cc_final: 0.8027 (mtm) REVERT: 14 283 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7421 (mt-10) REVERT: 14 330 LYS cc_start: 0.7641 (ptpt) cc_final: 0.7252 (ptpp) outliers start: 58 outliers final: 37 residues processed: 281 average time/residue: 0.3081 time to fit residues: 127.4313 Evaluate side-chains 256 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 5 residue 270 LYS 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 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 152 THR Chi-restraints excluded: chain 8 residue 175 LEU Chi-restraints excluded: chain 8 residue 215 ILE Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 271 CYS Chi-restraints excluded: chain 8 residue 335 ASP Chi-restraints excluded: chain 8 residue 372 THR Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 8 residue 494 LEU Chi-restraints excluded: chain 8 residue 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 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 209 THR Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 277 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 155 optimal weight: 0.4980 chunk 139 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.173654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135492 restraints weight = 20185.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136789 restraints weight = 17827.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138157 restraints weight = 15302.732| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17499 Z= 0.139 Angle : 0.513 10.736 23869 Z= 0.265 Chirality : 0.038 0.185 2732 Planarity : 0.004 0.050 2959 Dihedral : 12.437 163.008 2752 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.67 % Allowed : 20.63 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.19), residues: 2047 helix: 2.03 (0.15), residues: 1244 sheet: -0.20 (0.49), residues: 98 loop : -0.69 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 175 HIS 0.004 0.001 HIS 5 214 PHE 0.020 0.001 PHE 8 83 TYR 0.012 0.001 TYR 8 330 ARG 0.018 0.000 ARG 8 329 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 897) hydrogen bonds : angle 3.56565 ( 2658) covalent geometry : bond 0.00329 (17499) covalent geometry : angle 0.51305 (23869) *********************** 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 293 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 228 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: 5 99 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7124 (mtp) REVERT: 5 102 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8305 (tpp) REVERT: 5 149 VAL cc_start: 0.8048 (t) cc_final: 0.7774 (t) REVERT: 6 136 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8520 (tt) REVERT: 6 213 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8267 (mm) REVERT: 8 197 SER cc_start: 0.8516 (m) cc_final: 0.8229 (t) REVERT: 8 207 ASN cc_start: 0.7155 (t0) cc_final: 0.6870 (t0) REVERT: 8 212 MET cc_start: 0.8429 (mmm) cc_final: 0.8037 (tpt) REVERT: 8 317 ASP cc_start: 0.7656 (p0) cc_final: 0.6901 (t0) REVERT: 8 335 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.6442 (t0) REVERT: 8 409 MET cc_start: 0.8552 (mtt) cc_final: 0.8190 (mtp) REVERT: 8 428 ASP cc_start: 0.7174 (t0) cc_final: 0.6703 (t0) REVERT: 8 474 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.8268 (m-70) REVERT: 10 276 MET cc_start: 0.7013 (mmm) cc_final: 0.6342 (tmm) REVERT: 10 308 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8156 (ptp) REVERT: 10 400 MET cc_start: 0.7758 (mmt) cc_final: 0.7449 (mmt) REVERT: 10 412 ASP cc_start: 0.8262 (t0) cc_final: 0.7831 (t0) REVERT: 10 518 ASN cc_start: 0.7797 (p0) cc_final: 0.7244 (m110) REVERT: 14 85 GLN cc_start: 0.6936 (tp-100) cc_final: 0.6169 (tt0) REVERT: 14 181 MET cc_start: 0.8607 (tmm) cc_final: 0.8275 (ttt) REVERT: 14 283 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7505 (mt-10) REVERT: 14 330 LYS cc_start: 0.7630 (ptpt) cc_final: 0.7236 (ptpp) outliers start: 65 outliers final: 39 residues processed: 274 average time/residue: 0.3064 time to fit residues: 123.9244 Evaluate side-chains 261 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 91 MET Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 5 residue 102 MET Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 251 SER Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 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 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 326 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 474 HIS 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 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 201 HIS Chi-restraints excluded: chain 14 residue 277 VAL 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 176 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.174406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137509 restraints weight = 20046.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.138484 restraints weight = 19329.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140403 restraints weight = 16979.702| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17499 Z= 0.111 Angle : 0.487 8.255 23869 Z= 0.251 Chirality : 0.037 0.182 2732 Planarity : 0.004 0.046 2959 Dihedral : 12.399 162.547 2752 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.77 % Allowed : 21.76 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.19), residues: 2047 helix: 2.13 (0.15), residues: 1239 sheet: -0.05 (0.49), residues: 98 loop : -0.64 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP14 175 HIS 0.003 0.001 HIS 7 95 PHE 0.024 0.001 PHE10 339 TYR 0.011 0.001 TYR10 200 ARG 0.008 0.000 ARG 8 329 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 897) hydrogen bonds : angle 3.46854 ( 2658) covalent geometry : bond 0.00254 (17499) covalent geometry : angle 0.48688 (23869) *********************** 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 266 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 1.730 Fit side-chains revert: symmetry clash REVERT: 5 99 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.6944 (mtp) REVERT: 5 102 MET cc_start: 0.8533 (tpt) cc_final: 0.8286 (tpp) REVERT: 5 149 VAL cc_start: 0.8121 (t) cc_final: 0.7874 (t) REVERT: 6 136 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8494 (tt) REVERT: 6 213 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8158 (mm) REVERT: 8 207 ASN cc_start: 0.7106 (t0) cc_final: 0.6816 (t0) REVERT: 8 212 MET cc_start: 0.8398 (mmm) cc_final: 0.8018 (tpt) REVERT: 8 304 MET cc_start: 0.6167 (mmm) cc_final: 0.5964 (mtt) REVERT: 8 317 ASP cc_start: 0.7660 (p0) cc_final: 0.6885 (t0) REVERT: 8 335 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6199 (t0) REVERT: 10 276 MET cc_start: 0.6896 (mmm) cc_final: 0.6271 (tmm) REVERT: 10 308 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8086 (ptp) REVERT: 10 351 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.6474 (t-90) REVERT: 10 400 MET cc_start: 0.7838 (mmt) cc_final: 0.7560 (mmt) REVERT: 10 412 ASP cc_start: 0.8331 (t0) cc_final: 0.7922 (t0) REVERT: 10 518 ASN cc_start: 0.7726 (p0) cc_final: 0.7272 (m110) REVERT: 14 85 GLN cc_start: 0.6874 (tp-100) cc_final: 0.6309 (tt0) REVERT: 14 104 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7826 (mp) REVERT: 14 181 MET cc_start: 0.8585 (tmm) cc_final: 0.8301 (ttt) REVERT: 14 283 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7431 (mt-10) REVERT: 14 330 LYS cc_start: 0.7610 (ptpt) cc_final: 0.7216 (ptpp) outliers start: 49 outliers final: 31 residues processed: 252 average time/residue: 0.2991 time to fit residues: 111.1795 Evaluate side-chains 248 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 195 THR Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 434 SER Chi-restraints excluded: chain 6 residue 464 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 215 ILE Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 271 CYS Chi-restraints excluded: chain 8 residue 335 ASP Chi-restraints excluded: chain 8 residue 372 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 8 residue 485 MET Chi-restraints excluded: chain 8 residue 494 LEU Chi-restraints excluded: chain 8 residue 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 261 MET Chi-restraints excluded: chain 10 residue 308 MET Chi-restraints excluded: chain 10 residue 351 HIS Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 14 residue 63 THR Chi-restraints excluded: chain 14 residue 104 LEU Chi-restraints excluded: chain 14 residue 316 THR 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 11 optimal weight: 2.9990 chunk 136 optimal weight: 0.2980 chunk 149 optimal weight: 0.4980 chunk 184 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 194 optimal weight: 3.9990 chunk 134 optimal weight: 0.1980 chunk 34 optimal weight: 0.0170 overall best weight: 0.1334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.178334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141969 restraints weight = 19845.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142250 restraints weight = 18593.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.145311 restraints weight = 16392.776| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17499 Z= 0.091 Angle : 0.468 10.266 23869 Z= 0.238 Chirality : 0.036 0.182 2732 Planarity : 0.004 0.047 2959 Dihedral : 12.316 162.861 2752 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.04 % Allowed : 23.12 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 2047 helix: 2.32 (0.15), residues: 1241 sheet: 0.09 (0.47), residues: 108 loop : -0.55 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP14 175 HIS 0.003 0.000 HIS14 118 PHE 0.016 0.001 PHE10 339 TYR 0.009 0.001 TYR10 200 ARG 0.008 0.000 ARG 8 329 Details of bonding type rmsd hydrogen bonds : bond 0.02731 ( 897) hydrogen bonds : angle 3.30556 ( 2658) covalent geometry : bond 0.00191 (17499) covalent geometry : angle 0.46804 (23869) *********************** 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 280 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 1.879 Fit side-chains REVERT: 5 99 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7047 (mtp) REVERT: 5 134 LEU cc_start: 0.7901 (pp) cc_final: 0.7624 (pp) REVERT: 5 149 VAL cc_start: 0.8171 (t) cc_final: 0.7951 (t) REVERT: 6 98 SER cc_start: 0.8565 (t) cc_final: 0.8353 (p) REVERT: 6 136 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8725 (tt) REVERT: 8 207 ASN cc_start: 0.6955 (t0) cc_final: 0.6710 (t0) REVERT: 8 212 MET cc_start: 0.8454 (mmm) cc_final: 0.7967 (tpt) REVERT: 8 260 MET cc_start: 0.7053 (mtt) cc_final: 0.6349 (mtp) REVERT: 8 304 MET cc_start: 0.6512 (mmm) cc_final: 0.6197 (mtt) REVERT: 8 317 ASP cc_start: 0.7177 (p0) cc_final: 0.6714 (t0) REVERT: 8 335 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.6275 (t0) REVERT: 10 276 MET cc_start: 0.6655 (mmm) cc_final: 0.6163 (tmm) REVERT: 10 351 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.6435 (t-90) REVERT: 10 400 MET cc_start: 0.7852 (mmt) cc_final: 0.7534 (mmt) REVERT: 10 412 ASP cc_start: 0.8123 (t0) cc_final: 0.7744 (t0) REVERT: 10 483 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6929 (ttt) REVERT: 10 518 ASN cc_start: 0.7672 (p0) cc_final: 0.7427 (m110) REVERT: 14 85 GLN cc_start: 0.6662 (tp-100) cc_final: 0.6396 (tt0) REVERT: 14 181 MET cc_start: 0.8397 (tmm) cc_final: 0.8169 (ttt) REVERT: 14 283 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7304 (mt-10) REVERT: 14 330 LYS cc_start: 0.7604 (ptpt) cc_final: 0.7216 (ptpp) outliers start: 36 outliers final: 22 residues processed: 269 average time/residue: 0.3140 time to fit residues: 125.0320 Evaluate side-chains 251 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 405 ASP Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 472 LEU Chi-restraints excluded: chain 6 residue 508 ILE Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 175 LEU Chi-restraints excluded: chain 8 residue 189 LEU Chi-restraints excluded: chain 8 residue 215 ILE Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 335 ASP 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 351 HIS Chi-restraints excluded: chain 10 residue 440 GLU Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 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 5 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 182 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 424 GLN 8 256 HIS 10 485 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.173708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.137279 restraints weight = 19858.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.137533 restraints weight = 19528.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.139551 restraints weight = 16996.514| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17499 Z= 0.123 Angle : 0.509 10.786 23869 Z= 0.257 Chirality : 0.037 0.186 2732 Planarity : 0.004 0.046 2959 Dihedral : 12.319 162.806 2752 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.26 % Allowed : 22.89 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 2047 helix: 2.28 (0.15), residues: 1242 sheet: 0.14 (0.47), residues: 108 loop : -0.60 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 175 HIS 0.004 0.001 HIS 8 256 PHE 0.016 0.001 PHE 8 83 TYR 0.011 0.001 TYR10 215 ARG 0.011 0.000 ARG 7 113 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 897) hydrogen bonds : angle 3.37561 ( 2658) covalent geometry : bond 0.00291 (17499) covalent geometry : angle 0.50907 (23869) *********************** 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 259 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 2.027 Fit side-chains revert: symmetry clash REVERT: 5 37 MET cc_start: 0.7486 (mmm) cc_final: 0.6676 (mmm) REVERT: 5 99 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.6969 (mtp) REVERT: 5 149 VAL cc_start: 0.8201 (t) cc_final: 0.7987 (t) REVERT: 5 270 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8399 (mttt) REVERT: 6 98 SER cc_start: 0.8760 (t) cc_final: 0.8529 (p) REVERT: 6 136 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8523 (tt) REVERT: 6 264 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6936 (tt) REVERT: 7 113 ARG cc_start: 0.6894 (ttp-110) cc_final: 0.6586 (mtm110) REVERT: 8 207 ASN cc_start: 0.7090 (t0) cc_final: 0.6788 (t0) REVERT: 8 212 MET cc_start: 0.8390 (mmm) cc_final: 0.7831 (tpt) REVERT: 8 317 ASP cc_start: 0.7607 (p0) cc_final: 0.6863 (t0) REVERT: 8 335 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.6261 (t0) REVERT: 8 428 ASP cc_start: 0.7138 (t0) cc_final: 0.6675 (t0) REVERT: 10 188 ARG cc_start: 0.8579 (tpp80) cc_final: 0.7939 (mmp80) REVERT: 10 272 GLU cc_start: 0.8048 (tp30) cc_final: 0.7817 (tp30) REVERT: 10 276 MET cc_start: 0.6899 (mmm) cc_final: 0.6311 (tmm) REVERT: 10 339 PHE cc_start: 0.7735 (t80) cc_final: 0.7522 (t80) REVERT: 10 351 HIS cc_start: 0.7845 (OUTLIER) cc_final: 0.6521 (t-90) REVERT: 10 400 MET cc_start: 0.7817 (mmt) cc_final: 0.7553 (mmt) REVERT: 10 412 ASP cc_start: 0.8374 (t0) cc_final: 0.7922 (t0) REVERT: 10 483 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6969 (ttt) REVERT: 14 85 GLN cc_start: 0.6790 (tp-100) cc_final: 0.6381 (tt0) REVERT: 14 181 MET cc_start: 0.8538 (tmm) cc_final: 0.8334 (ttt) REVERT: 14 283 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7543 (mt-10) REVERT: 14 330 LYS cc_start: 0.7706 (ptpt) cc_final: 0.7244 (ptpp) outliers start: 40 outliers final: 32 residues processed: 249 average time/residue: 0.3256 time to fit residues: 120.0909 Evaluate side-chains 253 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 91 MET Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 5 residue 270 LYS Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 251 SER Chi-restraints excluded: chain 6 residue 264 LEU 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 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 152 THR Chi-restraints excluded: chain 8 residue 175 LEU Chi-restraints excluded: chain 8 residue 189 LEU Chi-restraints excluded: chain 8 residue 215 ILE Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 271 CYS Chi-restraints excluded: chain 8 residue 335 ASP Chi-restraints excluded: chain 8 residue 468 VAL 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 306 LEU Chi-restraints excluded: chain 10 residue 351 HIS Chi-restraints excluded: chain 10 residue 440 GLU Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 111 LEU Chi-restraints excluded: chain 14 residue 201 HIS 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 99 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 169 optimal weight: 0.2980 chunk 167 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 4 optimal weight: 0.0770 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 424 GLN 8 256 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.176628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139985 restraints weight = 20027.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.140731 restraints weight = 17285.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142709 restraints weight = 14462.314| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17499 Z= 0.090 Angle : 0.476 10.321 23869 Z= 0.239 Chirality : 0.036 0.184 2732 Planarity : 0.004 0.047 2959 Dihedral : 12.246 162.700 2752 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.92 % Allowed : 23.01 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.19), residues: 2047 helix: 2.36 (0.15), residues: 1239 sheet: 0.20 (0.47), residues: 108 loop : -0.57 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 175 HIS 0.003 0.000 HIS 8 256 PHE 0.013 0.001 PHE 8 83 TYR 0.010 0.001 TYR10 200 ARG 0.006 0.000 ARG 7 113 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 897) hydrogen bonds : angle 3.28104 ( 2658) covalent geometry : bond 0.00198 (17499) covalent geometry : angle 0.47611 (23869) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 1.867 Fit side-chains revert: symmetry clash REVERT: 5 37 MET cc_start: 0.7329 (mmm) cc_final: 0.6567 (mmm) REVERT: 5 99 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.6964 (mtp) REVERT: 5 134 LEU cc_start: 0.7738 (pp) cc_final: 0.7403 (pp) REVERT: 5 149 VAL cc_start: 0.8170 (t) cc_final: 0.7960 (t) REVERT: 6 98 SER cc_start: 0.8793 (t) cc_final: 0.8560 (p) REVERT: 6 136 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8526 (tt) REVERT: 8 207 ASN cc_start: 0.6973 (t0) cc_final: 0.6703 (t0) REVERT: 8 317 ASP cc_start: 0.7487 (p0) cc_final: 0.6789 (t0) REVERT: 8 335 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.6115 (t0) REVERT: 10 188 ARG cc_start: 0.8574 (tpp80) cc_final: 0.7943 (mmp80) REVERT: 10 272 GLU cc_start: 0.8037 (tp30) cc_final: 0.7792 (mm-30) REVERT: 10 276 MET cc_start: 0.6829 (mmm) cc_final: 0.6407 (tmm) REVERT: 10 339 PHE cc_start: 0.7709 (t80) cc_final: 0.7499 (t80) REVERT: 10 351 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.6535 (t-90) REVERT: 10 400 MET cc_start: 0.7825 (mmt) cc_final: 0.7525 (mmt) REVERT: 10 412 ASP cc_start: 0.8357 (t0) cc_final: 0.7918 (t0) REVERT: 10 483 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6996 (ttt) REVERT: 14 85 GLN cc_start: 0.6735 (tp-100) cc_final: 0.6439 (tt0) REVERT: 14 330 LYS cc_start: 0.7734 (ptpt) cc_final: 0.7282 (ptpp) outliers start: 34 outliers final: 26 residues processed: 247 average time/residue: 0.3166 time to fit residues: 117.1962 Evaluate side-chains 248 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 251 SER Chi-restraints excluded: chain 6 residue 405 ASP Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 472 LEU Chi-restraints excluded: chain 6 residue 508 ILE Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 119 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 335 ASP 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 351 HIS Chi-restraints excluded: chain 10 residue 440 GLU Chi-restraints excluded: chain 10 residue 463 VAL Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 111 LEU Chi-restraints excluded: chain 14 residue 201 HIS 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 6 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 0.0470 chunk 45 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 100 optimal weight: 0.0050 chunk 133 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 overall best weight: 0.4892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 424 GLN 8 256 HIS 10 485 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.176505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140626 restraints weight = 19940.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141140 restraints weight = 18865.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142681 restraints weight = 17061.900| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17499 Z= 0.092 Angle : 0.481 10.789 23869 Z= 0.241 Chirality : 0.036 0.186 2732 Planarity : 0.004 0.047 2959 Dihedral : 12.160 162.759 2752 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.04 % Allowed : 23.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.19), residues: 2047 helix: 2.39 (0.15), residues: 1240 sheet: 0.35 (0.48), residues: 107 loop : -0.54 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP14 175 HIS 0.004 0.000 HIS 8 256 PHE 0.014 0.001 PHE 8 83 TYR 0.009 0.001 TYR10 200 ARG 0.009 0.000 ARG 7 113 Details of bonding type rmsd hydrogen bonds : bond 0.02942 ( 897) hydrogen bonds : angle 3.25357 ( 2658) covalent geometry : bond 0.00206 (17499) covalent geometry : angle 0.48092 (23869) ********************** 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 262 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 1.920 Fit side-chains revert: symmetry clash REVERT: 5 37 MET cc_start: 0.7390 (mmm) cc_final: 0.6580 (mmm) REVERT: 5 99 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6933 (mtp) REVERT: 6 136 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8525 (tt) REVERT: 7 113 ARG cc_start: 0.7405 (ttp-110) cc_final: 0.6968 (mtm110) REVERT: 8 182 TYR cc_start: 0.6352 (m-10) cc_final: 0.6116 (m-10) REVERT: 8 207 ASN cc_start: 0.7011 (t0) cc_final: 0.6751 (t0) REVERT: 8 212 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7923 (tpt) REVERT: 8 260 MET cc_start: 0.7073 (mtt) cc_final: 0.6280 (mtp) REVERT: 8 317 ASP cc_start: 0.7532 (p0) cc_final: 0.6803 (t0) REVERT: 8 335 ASP cc_start: 0.6587 (OUTLIER) cc_final: 0.6097 (t0) REVERT: 10 188 ARG cc_start: 0.8595 (tpp80) cc_final: 0.7944 (mmp80) REVERT: 10 272 GLU cc_start: 0.8058 (tp30) cc_final: 0.7829 (mm-30) REVERT: 10 276 MET cc_start: 0.6764 (mmm) cc_final: 0.6271 (tmm) REVERT: 10 351 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.6409 (t-90) REVERT: 10 354 ASP cc_start: 0.8795 (m-30) cc_final: 0.8336 (m-30) REVERT: 10 400 MET cc_start: 0.7770 (mmt) cc_final: 0.7520 (mmt) REVERT: 10 412 ASP cc_start: 0.8360 (t0) cc_final: 0.7894 (t0) REVERT: 10 483 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6997 (ttt) REVERT: 10 534 GLU cc_start: 0.7021 (tp30) cc_final: 0.6783 (tp30) REVERT: 14 85 GLN cc_start: 0.6732 (tp-100) cc_final: 0.6441 (tt0) REVERT: 14 330 LYS cc_start: 0.7750 (ptpt) cc_final: 0.7283 (ptpp) outliers start: 36 outliers final: 23 residues processed: 247 average time/residue: 0.3522 time to fit residues: 131.2411 Evaluate side-chains 248 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 91 MET Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 251 SER Chi-restraints excluded: chain 6 residue 464 LEU Chi-restraints excluded: chain 6 residue 472 LEU Chi-restraints excluded: chain 6 residue 508 ILE Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 212 MET Chi-restraints excluded: chain 8 residue 215 ILE Chi-restraints excluded: chain 8 residue 335 ASP 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 261 MET Chi-restraints excluded: chain 10 residue 306 LEU Chi-restraints excluded: chain 10 residue 351 HIS Chi-restraints excluded: chain 10 residue 440 GLU Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 14 residue 38 VAL Chi-restraints excluded: chain 14 residue 111 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 52 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 184 optimal weight: 0.0870 chunk 128 optimal weight: 0.0770 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 256 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.176222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140627 restraints weight = 19871.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141142 restraints weight = 19245.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142665 restraints weight = 17136.607| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17499 Z= 0.094 Angle : 0.484 10.890 23869 Z= 0.242 Chirality : 0.036 0.188 2732 Planarity : 0.004 0.047 2959 Dihedral : 12.091 162.817 2750 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.04 % Allowed : 23.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.19), residues: 2047 helix: 2.42 (0.15), residues: 1240 sheet: 0.38 (0.48), residues: 107 loop : -0.47 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 175 HIS 0.004 0.000 HIS 8 256 PHE 0.029 0.001 PHE10 339 TYR 0.009 0.001 TYR10 200 ARG 0.010 0.000 ARG 7 113 Details of bonding type rmsd hydrogen bonds : bond 0.02904 ( 897) hydrogen bonds : angle 3.25084 ( 2658) covalent geometry : bond 0.00213 (17499) covalent geometry : angle 0.48369 (23869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5226.90 seconds wall clock time: 92 minutes 32.51 seconds (5552.51 seconds total)