Starting phenix.real_space_refine on Sun Aug 24 05:10:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fnc_29308/08_2025/8fnc_29308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fnc_29308/08_2025/8fnc_29308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fnc_29308/08_2025/8fnc_29308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fnc_29308/08_2025/8fnc_29308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fnc_29308/08_2025/8fnc_29308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fnc_29308/08_2025/8fnc_29308.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 33 5.49 5 S 116 5.16 5 C 10655 2.51 5 N 2969 2.21 5 O 3244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17017 Number of models: 1 Model: "" Number of chains: 8 Chain: "m" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 369 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 13, 'rna3p': 3} 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': 5, 'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna2p': 8, 'rna3p': 7} Chain: "5" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2327 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain: "6" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3582 Classifications: {'peptide': 452} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 440} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "7" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 547 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "8" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4076 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 25, 'TRANS': 490} Chain: "10" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3290 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 14, 'TRANS': 401} Chain breaks: 3 Chain: "14" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2496 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 24, 'TRANS': 289} Time building chain proxies: 3.29, per 1000 atoms: 0.19 Number of scatterers: 17017 At special positions: 0 Unit cell: (112.572, 130.626, 136.998, 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 33 15.00 O 3244 8.00 N 2969 7.00 C 10655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 716.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 112 helices and 8 sheets defined 67.2% alpha, 5.8% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain '5' and resid 27 through 31 removed outlier: 3.638A pdb=" N ILE 5 31 " --> pdb=" O PRO 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 34 through 52 Processing helix chain '5' and resid 66 through 74 removed outlier: 4.126A pdb=" N VAL 5 72 " --> pdb=" O ALA 5 69 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA 5 73 " --> pdb=" O LEU 5 70 " (cutoff:3.500A) removed outlier: 3.633A 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 removed outlier: 3.862A pdb=" N TYR 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) Processing helix chain '5' and resid 116 through 121 removed outlier: 3.666A pdb=" N THR 5 121 " --> pdb=" O TYR 5 117 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 159 Processing helix chain '5' and resid 180 through 183 Processing helix chain '5' and resid 198 through 212 Processing helix chain '5' and resid 246 through 256 removed outlier: 3.735A pdb=" N MET 5 250 " --> pdb=" O TYR 5 246 " (cutoff:3.500A) Processing helix chain '5' and resid 265 through 271 Processing helix chain '6' and resid 62 through 79 Processing helix chain '6' and resid 83 through 95 Processing helix chain '6' and resid 105 through 119 removed outlier: 3.504A 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: 4.529A pdb=" N THR 6 156 " --> pdb=" O THR 6 152 " (cutoff:3.500A) removed outlier: 4.243A 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: 3.769A pdb=" N THR 6 186 " --> pdb=" O ALA 6 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR 6 195 " --> pdb=" O ALA 6 191 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 216 removed outlier: 3.987A pdb=" N VAL 6 216 " --> pdb=" O THR 6 212 " (cutoff:3.500A) Processing helix chain '6' and resid 220 through 234 Processing helix chain '6' and resid 238 through 253 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: 3.815A pdb=" N GLY 6 272 " --> pdb=" O PHE 6 268 " (cutoff:3.500A) Processing helix chain '6' and resid 275 through 288 removed outlier: 3.751A pdb=" N SER 6 279 " --> pdb=" O ASP 6 275 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS 6 280 " --> pdb=" O PRO 6 276 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG 6 281 " --> pdb=" O LYS 6 277 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU 6 288 " --> pdb=" O THR 6 284 " (cutoff:3.500A) Processing helix chain '6' and resid 294 through 309 removed outlier: 3.692A pdb=" N GLY 6 309 " --> pdb=" O PHE 6 305 " (cutoff:3.500A) Processing helix chain '6' and resid 312 through 326 removed outlier: 4.066A pdb=" N VAL 6 318 " --> pdb=" O GLN 6 314 " (cutoff:3.500A) Processing helix chain '6' and resid 331 through 346 Processing helix chain '6' and resid 349 through 361 removed outlier: 3.796A pdb=" N ASN 6 355 " --> pdb=" O GLU 6 351 " (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: 3.534A 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: 3.772A pdb=" N VAL 6 410 " --> pdb=" O ALA 6 406 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR 6 419 " --> pdb=" O ALA 6 415 " (cutoff:3.500A) Processing helix chain '6' and resid 423 through 434 removed outlier: 3.544A pdb=" N ALA 6 429 " --> pdb=" O ASP 6 425 " (cutoff:3.500A) Processing helix chain '6' and resid 435 through 441 removed outlier: 3.659A pdb=" N CYS 6 438 " --> pdb=" O VAL 6 435 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ARG 6 439 " --> pdb=" O TYR 6 436 " (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 496 removed outlier: 3.639A pdb=" N ASP 6 493 " --> pdb=" O GLU 6 489 " (cutoff:3.500A) 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 117 Processing helix chain '7' and resid 119 through 124 Processing helix chain '7' and resid 127 through 145 removed outlier: 3.757A pdb=" N LYS 7 143 " --> pdb=" O ALA 7 139 " (cutoff:3.500A) removed outlier: 4.146A 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: 3.645A pdb=" N GLY 8 67 " --> pdb=" O ASP 8 63 " (cutoff:3.500A) Processing helix chain '8' and resid 81 through 96 removed outlier: 3.684A pdb=" N VAL 8 95 " --> pdb=" O THR 8 91 " (cutoff:3.500A) Processing helix chain '8' and resid 108 through 112 removed outlier: 3.782A pdb=" N ILE 8 112 " --> pdb=" O GLU 8 109 " (cutoff:3.500A) Processing helix chain '8' and resid 113 through 127 removed outlier: 3.685A pdb=" N LEU 8 121 " --> pdb=" O LEU 8 117 " (cutoff:3.500A) Processing helix chain '8' and resid 131 through 143 Processing helix chain '8' and resid 145 through 149 removed outlier: 3.622A pdb=" N PHE 8 149 " --> pdb=" O LEU 8 146 " (cutoff:3.500A) Processing helix chain '8' and resid 150 through 164 removed outlier: 3.575A pdb=" N SER 8 155 " --> pdb=" O PRO 8 151 " (cutoff:3.500A) Processing helix chain '8' and resid 168 through 182 removed outlier: 3.748A pdb=" N TYR 8 182 " --> pdb=" O ARG 8 178 " (cutoff:3.500A) Processing helix chain '8' and resid 187 through 201 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 261 through 276 Processing helix chain '8' and resid 279 through 294 removed outlier: 3.694A pdb=" N ILE 8 283 " --> pdb=" O GLN 8 279 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU 8 292 " --> pdb=" O ASP 8 288 " (cutoff:3.500A) removed outlier: 3.960A 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 332 removed outlier: 4.145A pdb=" N ARG 8 329 " --> pdb=" O SER 8 325 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR 8 330 " --> pdb=" O CYS 8 326 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA 8 332 " --> pdb=" O ILE 8 328 " (cutoff:3.500A) Processing helix chain '8' and resid 335 through 347 removed outlier: 4.561A 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 384 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: 4.072A pdb=" N TYR 8 442 " --> pdb=" O THR 8 438 " (cutoff:3.500A) Processing helix chain '8' and resid 446 through 461 Proline residue: 8 452 - end of helix removed outlier: 3.634A pdb=" N ILE 8 459 " --> pdb=" O MET 8 455 " (cutoff:3.500A) removed outlier: 4.389A 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: 4.135A pdb=" N TYR 8 505 " --> pdb=" O ASP 8 501 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN 8 514 " --> pdb=" O SER 8 510 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE 8 515 " --> pdb=" O ARG 8 511 " (cutoff:3.500A) Processing helix chain '8' and resid 524 through 532 removed outlier: 3.538A pdb=" N VAL 8 529 " --> pdb=" O GLU 8 525 " (cutoff:3.500A) Processing helix chain '10' and resid 117 through 141 removed outlier: 4.166A pdb=" N ALA10 121 " --> pdb=" O THR10 117 " (cutoff:3.500A) removed outlier: 4.025A 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 184 through 189 removed outlier: 3.861A pdb=" N ARG10 188 " --> pdb=" O PRO10 184 " (cutoff:3.500A) Processing helix chain '10' and resid 191 through 207 removed outlier: 3.767A pdb=" N LYS10 205 " --> pdb=" O THR10 201 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU10 206 " --> pdb=" O THR10 202 " (cutoff:3.500A) Processing helix chain '10' and resid 211 through 233 removed outlier: 3.724A pdb=" N MET10 221 " --> pdb=" O ALA10 217 " (cutoff:3.500A) Processing helix chain '10' and resid 236 through 249 removed outlier: 4.064A pdb=" N LEU10 241 " --> pdb=" O ALA10 237 " (cutoff:3.500A) Processing helix chain '10' and resid 254 through 265 Processing helix chain '10' and resid 275 through 289 removed outlier: 3.788A pdb=" N THR10 289 " --> pdb=" O ARG10 285 " (cutoff:3.500A) Processing helix chain '10' and resid 294 through 296 No H-bonds generated for 'chain '10' and resid 294 through 296' Processing helix chain '10' and resid 297 through 308 removed outlier: 3.747A pdb=" N MET10 308 " --> pdb=" O VAL10 304 " (cutoff:3.500A) Processing helix chain '10' and resid 308 through 315 Processing helix chain '10' and resid 320 through 334 removed outlier: 3.507A pdb=" N LEU10 325 " --> pdb=" O LEU10 321 " (cutoff:3.500A) removed outlier: 3.612A 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 350 removed outlier: 3.670A pdb=" N ALA10 348 " --> pdb=" O LEU10 344 " (cutoff:3.500A) Processing helix chain '10' and resid 356 through 370 removed outlier: 3.909A pdb=" N ALA10 361 " --> pdb=" O PRO10 357 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR10 362 " --> pdb=" O HIS10 358 " (cutoff:3.500A) Processing helix chain '10' and resid 374 through 387 removed outlier: 3.932A pdb=" N ARG10 380 " --> pdb=" O GLU10 376 " (cutoff:3.500A) Processing helix chain '10' and resid 392 through 408 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: 3.634A pdb=" N ILE10 434 " --> pdb=" O MET10 430 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG10 437 " --> pdb=" O GLN10 433 " (cutoff:3.500A) Processing helix chain '10' and resid 445 through 459 removed outlier: 3.883A pdb=" N ILE10 449 " --> pdb=" O ALA10 445 " (cutoff:3.500A) Processing helix chain '10' and resid 464 through 486 removed outlier: 3.781A pdb=" N ASP10 477 " --> pdb=" O SER10 473 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET10 478 " --> pdb=" O GLN10 474 " (cutoff:3.500A) Processing helix chain '10' and resid 502 through 517 Processing helix chain '10' and resid 521 through 535 removed outlier: 3.579A pdb=" N SER10 525 " --> pdb=" O ALA10 521 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN10 526 " --> pdb=" O PRO10 522 " (cutoff:3.500A) Processing helix chain '14' and resid 49 through 53 Processing helix chain '14' and resid 66 through 70 removed outlier: 4.054A pdb=" N PHE14 70 " --> pdb=" O VAL14 67 " (cutoff:3.500A) Processing helix chain '14' and resid 76 through 87 removed outlier: 3.571A 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: 3.622A pdb=" N ILE14 154 " --> pdb=" O MET14 150 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR14 155 " --> pdb=" O HIS14 151 " (cutoff:3.500A) Processing helix chain '14' and resid 156 through 167 removed outlier: 4.030A pdb=" N ALA14 162 " --> pdb=" O THR14 158 " (cutoff:3.500A) Processing helix chain '14' and resid 194 through 199 Processing helix chain '14' and resid 249 through 255 Processing helix chain '14' and resid 256 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 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: 5.976A pdb=" N LEU 5 193 " --> pdb=" O VAL 5 220 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU 5 222 " --> pdb=" O LEU 5 193 " (cutoff:3.500A) removed outlier: 6.493A 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: 6.518A pdb=" N VAL 5 240 " --> pdb=" O ILE 5 261 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL 5 263 " --> pdb=" O VAL 5 240 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL 5 242 " --> pdb=" O VAL 5 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '14' and resid 88 through 90 removed outlier: 6.318A pdb=" N VAL14 304 " --> pdb=" O MET14 181 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET14 181 " --> pdb=" O VAL14 304 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS14 306 " --> pdb=" O VAL14 179 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL14 179 " --> pdb=" O CYS14 306 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE14 308 " --> pdb=" O ASP14 177 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP14 177 " --> pdb=" O PHE14 308 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N HIS14 310 " --> pdb=" O TRP14 175 " (cutoff:3.500A) removed outlier: 3.895A 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: 6.318A pdb=" N VAL14 304 " --> pdb=" O MET14 181 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET14 181 " --> pdb=" O VAL14 304 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS14 306 " --> pdb=" O VAL14 179 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL14 179 " --> pdb=" O CYS14 306 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE14 308 " --> pdb=" O ASP14 177 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP14 177 " --> pdb=" O PHE14 308 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N HIS14 310 " --> pdb=" O TRP14 175 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL14 172 " --> pdb=" O VAL14 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '14' and resid 190 through 193 removed outlier: 4.372A pdb=" N TRP14 192 " --> pdb=" O PHE14 293 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE14 293 " --> pdb=" O TRP14 192 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4397 1.33 - 1.46: 3466 1.46 - 1.58: 9306 1.58 - 1.70: 64 1.70 - 1.82: 195 Bond restraints: 17428 Sorted by residual: bond pdb=" N PRO 8 521 " pdb=" CD PRO 8 521 " ideal model delta sigma weight residual 1.473 1.542 -0.069 1.40e-02 5.10e+03 2.46e+01 bond pdb=" N PRO 8 524 " pdb=" CD PRO 8 524 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.15e+01 bond pdb=" N VAL14 38 " pdb=" CA VAL14 38 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.10e-02 8.26e+03 7.94e+00 bond pdb=" CA ASN14 206 " pdb=" C ASN14 206 " ideal model delta sigma weight residual 1.531 1.501 0.030 1.15e-02 7.56e+03 6.99e+00 bond pdb=" CA ASP14 66 " pdb=" C ASP14 66 " ideal model delta sigma weight residual 1.528 1.493 0.036 1.38e-02 5.25e+03 6.70e+00 ... (remaining 17423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 23484 2.15 - 4.29: 240 4.29 - 6.44: 32 6.44 - 8.58: 2 8.58 - 10.73: 1 Bond angle restraints: 23759 Sorted by residual: angle pdb=" N VAL14 205 " pdb=" CA VAL14 205 " pdb=" C VAL14 205 " ideal model delta sigma weight residual 107.37 102.20 5.17 1.42e+00 4.96e-01 1.32e+01 angle pdb=" N GLN 5 75 " pdb=" CA GLN 5 75 " pdb=" C GLN 5 75 " ideal model delta sigma weight residual 111.14 114.94 -3.80 1.08e+00 8.57e-01 1.24e+01 angle pdb=" N VAL 5 72 " pdb=" CA VAL 5 72 " pdb=" C VAL 5 72 " ideal model delta sigma weight residual 111.09 115.35 -4.26 1.25e+00 6.40e-01 1.16e+01 angle pdb=" C3' U g -2 " pdb=" O3' U g -2 " pdb=" P U g -1 " ideal model delta sigma weight residual 120.20 125.31 -5.11 1.50e+00 4.44e-01 1.16e+01 angle pdb=" N MET 5 76 " pdb=" CA MET 5 76 " pdb=" C MET 5 76 " ideal model delta sigma weight residual 108.96 113.96 -5.00 1.49e+00 4.50e-01 1.13e+01 ... (remaining 23754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 10191 35.40 - 70.79: 356 70.79 - 106.19: 25 106.19 - 141.58: 1 141.58 - 176.98: 5 Dihedral angle restraints: 10578 sinusoidal: 4542 harmonic: 6036 Sorted by residual: dihedral pdb=" O4' U g -16 " pdb=" C1' U g -16 " pdb=" N1 U g -16 " pdb=" C2 U g -16 " ideal model delta sinusoidal sigma weight residual 200.00 41.85 158.15 1 1.50e+01 4.44e-03 8.23e+01 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 64.45 167.55 1 1.70e+01 3.46e-03 6.57e+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 -60.14 -99.86 1 1.50e+01 4.44e-03 5.00e+01 ... (remaining 10575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1939 0.035 - 0.071: 604 0.071 - 0.106: 135 0.106 - 0.141: 32 0.141 - 0.177: 7 Chirality restraints: 2717 Sorted by residual: chirality pdb=" C3' A m 120 " pdb=" C4' A m 120 " pdb=" O3' A m 120 " pdb=" C2' A m 120 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" C1' U m 105 " pdb=" O4' U m 105 " pdb=" C2' U m 105 " pdb=" N1 U m 105 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.35e-01 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 -2.59 -0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 2714 not shown) Planarity restraints: 2956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU10 421 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO10 422 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO10 422 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO10 422 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR10 372 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C THR10 372 " 0.044 2.00e-02 2.50e+03 pdb=" O THR10 372 " -0.016 2.00e-02 2.50e+03 pdb=" N MET10 373 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR 6 465 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PRO 6 466 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO 6 466 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO 6 466 " 0.035 5.00e-02 4.00e+02 ... (remaining 2953 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 933 2.73 - 3.27: 17095 3.27 - 3.82: 27834 3.82 - 4.36: 33348 4.36 - 4.90: 58429 Nonbonded interactions: 137639 Sorted by model distance: nonbonded pdb=" O ASN10 419 " pdb=" ND2 ASN10 419 " model vdw 2.191 3.120 nonbonded pdb=" O HIS14 118 " pdb=" OG1 THR14 121 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR14 61 " pdb=" O ASP14 152 " model vdw 2.224 3.040 nonbonded pdb=" OP2 U g -13 " pdb=" NH1 ARG 5 21 " model vdw 2.229 3.120 nonbonded pdb=" O4 U g -14 " pdb=" NH2 ARG 6 215 " model vdw 2.243 3.120 ... (remaining 137634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.830 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17428 Z= 0.149 Angle : 0.548 10.727 23759 Z= 0.307 Chirality : 0.037 0.177 2717 Planarity : 0.005 0.065 2956 Dihedral : 17.655 176.977 6660 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.90 % Allowed : 12.38 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.19), residues: 2047 helix: 1.34 (0.15), residues: 1242 sheet: 0.21 (0.55), residues: 93 loop : -0.68 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 8 469 TYR 0.011 0.001 TYR14 176 PHE 0.030 0.001 PHE 8 83 TRP 0.010 0.001 TRP14 175 HIS 0.004 0.001 HIS 5 214 Details of bonding type rmsd covalent geometry : bond 0.00270 (17428) covalent geometry : angle 0.54840 (23759) hydrogen bonds : bond 0.16006 ( 921) hydrogen bonds : angle 5.45320 ( 2718) *********************** 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 253 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 6 195 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8822 (p) REVERT: 6 250 MET cc_start: 0.7141 (mtt) cc_final: 0.6820 (mtp) REVERT: 10 466 LYS cc_start: 0.7940 (tttm) cc_final: 0.7508 (ptmm) REVERT: 14 107 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8320 (mm-30) outliers start: 16 outliers final: 3 residues processed: 245 average time/residue: 0.1453 time to fit residues: 51.7041 Evaluate side-chains 211 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 207 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 76 MET Chi-restraints excluded: chain 6 residue 195 THR Chi-restraints excluded: chain 8 residue 469 ARG Chi-restraints excluded: chain 14 residue 249 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.0050 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 200 HIS ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 138 ASN 6 381 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.136015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112455 restraints weight = 20085.305| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.17 r_work: 0.3014 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17428 Z= 0.115 Angle : 0.493 10.518 23759 Z= 0.257 Chirality : 0.038 0.171 2717 Planarity : 0.004 0.058 2956 Dihedral : 13.693 167.719 2725 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.92 % Allowed : 12.15 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.19), residues: 2047 helix: 1.62 (0.15), residues: 1281 sheet: 0.26 (0.57), residues: 88 loop : -0.60 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 8 403 TYR 0.011 0.001 TYR 6 307 PHE 0.027 0.001 PHE 8 83 TRP 0.009 0.001 TRP14 175 HIS 0.005 0.001 HIS 5 151 Details of bonding type rmsd covalent geometry : bond 0.00246 (17428) covalent geometry : angle 0.49333 (23759) hydrogen bonds : bond 0.04015 ( 921) hydrogen bonds : angle 4.04879 ( 2718) *********************** 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 258 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 76 MET cc_start: 0.8891 (ptp) cc_final: 0.8579 (ptp) REVERT: 5 125 ARG cc_start: 0.7504 (mtp-110) cc_final: 0.7187 (mtp-110) REVERT: 6 105 ASP cc_start: 0.8754 (m-30) cc_final: 0.8510 (m-30) REVERT: 8 73 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8240 (mtp180) REVERT: 10 173 MET cc_start: 0.8575 (mmm) cc_final: 0.8211 (tpt) REVERT: 10 276 MET cc_start: 0.8635 (tpp) cc_final: 0.7945 (ttp) REVERT: 10 278 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8747 (m) REVERT: 10 466 LYS cc_start: 0.8094 (tttm) cc_final: 0.7843 (ptmm) REVERT: 14 107 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8219 (mm-30) outliers start: 34 outliers final: 11 residues processed: 248 average time/residue: 0.1620 time to fit residues: 57.7419 Evaluate side-chains 221 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 97 GLU Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 220 MET Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 10 residue 278 SER Chi-restraints excluded: chain 10 residue 321 LEU Chi-restraints excluded: chain 10 residue 344 LEU Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 249 ASP Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 170 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 35 optimal weight: 0.3980 chunk 104 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 75 GLN ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 138 ASN 10 122 HIS 10 171 ASN 10 419 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.132510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.108766 restraints weight = 20373.639| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.15 r_work: 0.2968 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17428 Z= 0.142 Angle : 0.510 8.997 23759 Z= 0.262 Chirality : 0.039 0.175 2717 Planarity : 0.004 0.051 2956 Dihedral : 13.529 166.832 2717 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.98 % Allowed : 13.23 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.19), residues: 2047 helix: 1.67 (0.14), residues: 1284 sheet: -0.01 (0.53), residues: 94 loop : -0.57 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 8 403 TYR 0.012 0.001 TYR 6 307 PHE 0.025 0.001 PHE 8 83 TRP 0.007 0.001 TRP14 175 HIS 0.005 0.001 HIS 5 214 Details of bonding type rmsd covalent geometry : bond 0.00339 (17428) covalent geometry : angle 0.50978 (23759) hydrogen bonds : bond 0.04125 ( 921) hydrogen bonds : angle 3.85648 ( 2718) *********************** 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 243 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7556 (mtp-110) cc_final: 0.7184 (mtp-110) REVERT: 5 160 VAL cc_start: 0.8975 (p) cc_final: 0.8736 (m) REVERT: 6 388 GLU cc_start: 0.7682 (mp0) cc_final: 0.7447 (tp30) REVERT: 7 122 GLN cc_start: 0.8296 (mp10) cc_final: 0.7720 (mm110) REVERT: 8 251 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7910 (mt-10) REVERT: 8 306 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7607 (t80) REVERT: 8 313 ARG cc_start: 0.8996 (mmt90) cc_final: 0.7935 (mtm110) REVERT: 8 382 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8703 (mp) REVERT: 8 475 ILE cc_start: 0.8677 (mm) cc_final: 0.8449 (mt) REVERT: 10 140 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6209 (tp) REVERT: 10 276 MET cc_start: 0.8578 (tpp) cc_final: 0.7917 (ttp) REVERT: 10 278 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8695 (m) REVERT: 14 107 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8173 (mm-30) REVERT: 14 268 MET cc_start: 0.7757 (mtm) cc_final: 0.7544 (mtm) REVERT: 14 315 LYS cc_start: 0.8907 (mmtp) cc_final: 0.8650 (mmtp) outliers start: 35 outliers final: 19 residues processed: 229 average time/residue: 0.1549 time to fit residues: 52.3098 Evaluate side-chains 222 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 419 THR Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 493 ASP Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 220 MET Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 528 GLN Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 140 LEU Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 278 SER Chi-restraints excluded: chain 10 residue 389 ASP Chi-restraints excluded: chain 10 residue 434 ILE Chi-restraints excluded: chain 10 residue 439 ASP Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 190 VAL Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 312 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 57 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 127 ASN ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 419 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.132687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.109114 restraints weight = 20201.489| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.11 r_work: 0.2949 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17428 Z= 0.126 Angle : 0.485 9.194 23759 Z= 0.249 Chirality : 0.038 0.176 2717 Planarity : 0.004 0.048 2956 Dihedral : 13.432 166.447 2715 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.98 % Allowed : 13.68 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.19), residues: 2047 helix: 1.77 (0.15), residues: 1285 sheet: -0.20 (0.52), residues: 96 loop : -0.58 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 8 403 TYR 0.012 0.001 TYR10 200 PHE 0.021 0.001 PHE 8 83 TRP 0.008 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 Details of bonding type rmsd covalent geometry : bond 0.00298 (17428) covalent geometry : angle 0.48522 (23759) hydrogen bonds : bond 0.03648 ( 921) hydrogen bonds : angle 3.72447 ( 2718) *********************** 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 240 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 160 VAL cc_start: 0.8994 (p) cc_final: 0.8760 (m) REVERT: 6 388 GLU cc_start: 0.7751 (mp0) cc_final: 0.7496 (tp30) REVERT: 8 251 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7952 (mt-10) REVERT: 8 306 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7501 (t80) REVERT: 8 313 ARG cc_start: 0.8992 (mmt90) cc_final: 0.7970 (mtm110) REVERT: 8 327 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8602 (p) REVERT: 8 345 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8718 (mp) REVERT: 8 382 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8742 (mp) REVERT: 8 475 ILE cc_start: 0.8734 (mm) cc_final: 0.8512 (mt) REVERT: 8 495 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7784 (mmp80) REVERT: 10 140 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6127 (tp) REVERT: 10 276 MET cc_start: 0.8525 (tpp) cc_final: 0.7859 (ttp) REVERT: 10 278 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8670 (m) REVERT: 10 381 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8355 (mp) REVERT: 14 268 MET cc_start: 0.7882 (mtm) cc_final: 0.7660 (mtm) REVERT: 14 292 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8450 (mp) outliers start: 35 outliers final: 17 residues processed: 232 average time/residue: 0.1563 time to fit residues: 52.9617 Evaluate side-chains 221 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 97 GLU Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 493 ASP Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 180 MET Chi-restraints excluded: chain 8 residue 220 MET Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 327 VAL Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 8 residue 528 GLN Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 140 LEU Chi-restraints excluded: chain 10 residue 278 SER Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 434 ILE Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 10 residue 519 ASP Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 292 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 95 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 58 optimal weight: 0.0370 chunk 106 optimal weight: 0.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.131213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.107633 restraints weight = 20103.868| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.09 r_work: 0.2928 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17428 Z= 0.144 Angle : 0.502 8.424 23759 Z= 0.258 Chirality : 0.039 0.179 2717 Planarity : 0.004 0.049 2956 Dihedral : 13.383 166.307 2715 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.92 % Allowed : 14.19 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.19), residues: 2047 helix: 1.78 (0.15), residues: 1284 sheet: -0.12 (0.52), residues: 94 loop : -0.60 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 8 403 TYR 0.014 0.001 TYR10 200 PHE 0.019 0.001 PHE 8 83 TRP 0.008 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 Details of bonding type rmsd covalent geometry : bond 0.00348 (17428) covalent geometry : angle 0.50219 (23759) hydrogen bonds : bond 0.03921 ( 921) hydrogen bonds : angle 3.73054 ( 2718) *********************** 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 236 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7698 (mtp-110) cc_final: 0.6851 (mtm110) REVERT: 5 127 ASN cc_start: 0.8906 (t0) cc_final: 0.8699 (t0) REVERT: 5 160 VAL cc_start: 0.8994 (p) cc_final: 0.8762 (m) REVERT: 6 250 MET cc_start: 0.7479 (mmp) cc_final: 0.6420 (mtm) REVERT: 6 388 GLU cc_start: 0.7677 (mp0) cc_final: 0.7471 (tp30) REVERT: 7 122 GLN cc_start: 0.8255 (mp10) cc_final: 0.7686 (mm-40) REVERT: 8 251 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7962 (mt-10) REVERT: 8 306 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.7481 (t80) REVERT: 8 313 ARG cc_start: 0.8942 (mmt90) cc_final: 0.7891 (mtm110) REVERT: 8 345 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8731 (mp) REVERT: 8 382 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8738 (mp) REVERT: 8 495 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7777 (mmp80) REVERT: 10 140 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6044 (tp) REVERT: 10 276 MET cc_start: 0.8569 (tpp) cc_final: 0.7935 (ttp) REVERT: 10 278 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8674 (m) REVERT: 10 356 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8345 (p) REVERT: 10 381 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8416 (mp) REVERT: 14 268 MET cc_start: 0.7899 (mtm) cc_final: 0.7686 (mtm) outliers start: 34 outliers final: 19 residues processed: 226 average time/residue: 0.1576 time to fit residues: 51.9653 Evaluate side-chains 223 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 97 GLU Chi-restraints excluded: chain 6 residue 419 THR Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 493 ASP Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 167 THR Chi-restraints excluded: chain 8 residue 180 MET Chi-restraints excluded: chain 8 residue 220 MET Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 140 LEU Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 278 SER Chi-restraints excluded: chain 10 residue 356 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 434 ILE Chi-restraints excluded: chain 10 residue 439 ASP Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 99 optimal weight: 0.0370 chunk 126 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.133447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.109564 restraints weight = 19969.750| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.09 r_work: 0.2979 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17428 Z= 0.100 Angle : 0.458 9.184 23759 Z= 0.236 Chirality : 0.037 0.196 2717 Planarity : 0.004 0.048 2956 Dihedral : 13.240 165.934 2715 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.98 % Allowed : 14.58 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.19), residues: 2047 helix: 1.95 (0.15), residues: 1281 sheet: -0.31 (0.50), residues: 96 loop : -0.52 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 5 21 TYR 0.012 0.001 TYR10 200 PHE 0.016 0.001 PHE 8 83 TRP 0.009 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 Details of bonding type rmsd covalent geometry : bond 0.00224 (17428) covalent geometry : angle 0.45806 (23759) hydrogen bonds : bond 0.03201 ( 921) hydrogen bonds : angle 3.59911 ( 2718) *********************** 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 234 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.7021 (mtm110) REVERT: 5 160 VAL cc_start: 0.8952 (p) cc_final: 0.8719 (m) REVERT: 6 250 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6562 (mtm) REVERT: 6 340 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8488 (t0) REVERT: 6 388 GLU cc_start: 0.7584 (mp0) cc_final: 0.7363 (tp30) REVERT: 8 251 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7812 (mt-10) REVERT: 8 306 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.7472 (t80) REVERT: 8 313 ARG cc_start: 0.8873 (mmt90) cc_final: 0.7818 (mtm110) REVERT: 8 345 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8662 (mp) REVERT: 8 382 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8692 (mp) REVERT: 8 495 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7667 (mmp80) REVERT: 10 140 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5866 (tp) REVERT: 10 276 MET cc_start: 0.8474 (tpp) cc_final: 0.7850 (ttp) REVERT: 10 278 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8561 (m) REVERT: 10 356 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8219 (p) REVERT: 10 381 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8313 (mp) REVERT: 14 268 MET cc_start: 0.7810 (mtm) cc_final: 0.7556 (mtm) REVERT: 14 292 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8451 (mp) outliers start: 35 outliers final: 18 residues processed: 226 average time/residue: 0.1564 time to fit residues: 51.7100 Evaluate side-chains 222 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 6 residue 250 MET Chi-restraints excluded: chain 6 residue 340 ASN Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 453 LEU Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 180 MET Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 140 LEU Chi-restraints excluded: chain 10 residue 278 SER Chi-restraints excluded: chain 10 residue 356 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 434 ILE Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 292 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 97 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 109 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.133648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.111928 restraints weight = 19922.215| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.04 r_work: 0.2998 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17428 Z= 0.099 Angle : 0.455 8.780 23759 Z= 0.235 Chirality : 0.037 0.174 2717 Planarity : 0.004 0.048 2956 Dihedral : 13.161 165.589 2715 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.58 % Allowed : 15.04 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.19), residues: 2047 helix: 2.04 (0.15), residues: 1280 sheet: -0.30 (0.53), residues: 91 loop : -0.47 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 6 281 TYR 0.012 0.001 TYR10 200 PHE 0.015 0.001 PHE 8 83 TRP 0.010 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 Details of bonding type rmsd covalent geometry : bond 0.00224 (17428) covalent geometry : angle 0.45503 (23759) hydrogen bonds : bond 0.03181 ( 921) hydrogen bonds : angle 3.53507 ( 2718) *********************** 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 230 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.7040 (mtm110) REVERT: 5 160 VAL cc_start: 0.8958 (p) cc_final: 0.8697 (m) REVERT: 6 250 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6303 (mtm) REVERT: 6 340 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8436 (t0) REVERT: 7 122 GLN cc_start: 0.8077 (mp10) cc_final: 0.7544 (mm-40) REVERT: 8 251 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7768 (mt-10) REVERT: 8 306 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7624 (t80) REVERT: 8 313 ARG cc_start: 0.8854 (mmt90) cc_final: 0.7818 (mtm110) REVERT: 8 345 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8663 (mp) REVERT: 8 382 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8685 (mp) REVERT: 8 495 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7617 (mmp80) REVERT: 10 276 MET cc_start: 0.8447 (tpp) cc_final: 0.7810 (ttp) REVERT: 10 278 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8506 (m) REVERT: 10 356 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8228 (p) REVERT: 10 381 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8306 (mp) REVERT: 10 530 GLU cc_start: 0.7946 (tt0) cc_final: 0.7746 (mt-10) REVERT: 14 268 MET cc_start: 0.7810 (mtm) cc_final: 0.7609 (mtm) REVERT: 14 292 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8428 (mp) outliers start: 28 outliers final: 15 residues processed: 224 average time/residue: 0.1565 time to fit residues: 50.8347 Evaluate side-chains 218 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 6 residue 250 MET Chi-restraints excluded: chain 6 residue 340 ASN Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 180 MET Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 278 SER Chi-restraints excluded: chain 10 residue 356 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 292 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 160 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 181 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 137 optimal weight: 0.0770 chunk 116 optimal weight: 3.9990 chunk 8 optimal weight: 0.0010 chunk 14 optimal weight: 3.9990 overall best weight: 0.5946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.134109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.110213 restraints weight = 20118.928| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.10 r_work: 0.2988 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17428 Z= 0.096 Angle : 0.450 8.201 23759 Z= 0.232 Chirality : 0.037 0.172 2717 Planarity : 0.004 0.048 2956 Dihedral : 13.091 165.481 2715 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.58 % Allowed : 15.32 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.19), residues: 2047 helix: 2.07 (0.15), residues: 1282 sheet: -0.17 (0.53), residues: 89 loop : -0.43 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 5 145 TYR 0.012 0.001 TYR10 200 PHE 0.014 0.001 PHE 8 83 TRP 0.010 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 Details of bonding type rmsd covalent geometry : bond 0.00215 (17428) covalent geometry : angle 0.44992 (23759) hydrogen bonds : bond 0.03090 ( 921) hydrogen bonds : angle 3.50388 ( 2718) *********************** 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 222 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7693 (mtp-110) cc_final: 0.6841 (mtm110) REVERT: 5 160 VAL cc_start: 0.8873 (p) cc_final: 0.8622 (m) REVERT: 6 80 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7812 (mmt180) REVERT: 6 250 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.6595 (mtm) REVERT: 6 340 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8433 (t0) REVERT: 7 122 GLN cc_start: 0.8067 (mp10) cc_final: 0.7562 (mm-40) REVERT: 8 214 GLN cc_start: 0.8343 (tt0) cc_final: 0.8128 (mt0) REVERT: 8 251 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7788 (mt-10) REVERT: 8 306 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7653 (t80) REVERT: 8 313 ARG cc_start: 0.8877 (mmt90) cc_final: 0.7838 (mtm110) REVERT: 8 345 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8677 (mp) REVERT: 8 382 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8689 (mp) REVERT: 8 495 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7628 (mmp80) REVERT: 10 276 MET cc_start: 0.8461 (tpp) cc_final: 0.7831 (ttp) REVERT: 10 278 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8506 (m) REVERT: 10 356 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8289 (p) REVERT: 10 381 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8315 (mp) REVERT: 14 292 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8445 (mp) outliers start: 28 outliers final: 16 residues processed: 215 average time/residue: 0.1557 time to fit residues: 48.5109 Evaluate side-chains 220 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 6 residue 80 ARG Chi-restraints excluded: chain 6 residue 250 MET Chi-restraints excluded: chain 6 residue 340 ASN Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 180 MET Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 278 SER Chi-restraints excluded: chain 10 residue 356 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 434 ILE Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 292 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 166 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.0670 chunk 17 optimal weight: 0.0000 chunk 130 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 171 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 overall best weight: 0.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.135116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.111566 restraints weight = 20075.068| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.06 r_work: 0.2990 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17428 Z= 0.090 Angle : 0.443 8.120 23759 Z= 0.229 Chirality : 0.036 0.172 2717 Planarity : 0.004 0.048 2956 Dihedral : 13.014 165.958 2715 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.70 % Allowed : 15.15 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.19), residues: 2047 helix: 2.12 (0.15), residues: 1281 sheet: -0.16 (0.53), residues: 89 loop : -0.42 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 145 TYR 0.011 0.001 TYR10 200 PHE 0.013 0.001 PHE 8 83 TRP 0.011 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 Details of bonding type rmsd covalent geometry : bond 0.00198 (17428) covalent geometry : angle 0.44331 (23759) hydrogen bonds : bond 0.02928 ( 921) hydrogen bonds : angle 3.45971 ( 2718) *********************** 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 229 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7789 (mtp-110) cc_final: 0.7049 (mtm110) REVERT: 5 160 VAL cc_start: 0.8881 (p) cc_final: 0.8603 (m) REVERT: 6 80 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7696 (mmt180) REVERT: 6 250 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.6686 (mtm) REVERT: 6 340 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8469 (t0) REVERT: 7 122 GLN cc_start: 0.8065 (mp10) cc_final: 0.7548 (mm-40) REVERT: 8 251 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7816 (mt-10) REVERT: 8 306 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.7669 (t80) REVERT: 8 313 ARG cc_start: 0.8902 (mmt90) cc_final: 0.7884 (mtm110) REVERT: 8 345 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8723 (mp) REVERT: 8 382 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8719 (mp) REVERT: 8 495 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7685 (mmp80) REVERT: 10 276 MET cc_start: 0.8428 (tpp) cc_final: 0.7819 (ttp) REVERT: 10 278 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8501 (m) REVERT: 10 344 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8646 (mp) REVERT: 10 356 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8373 (p) REVERT: 10 381 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8347 (mp) REVERT: 14 259 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6804 (mt-10) REVERT: 14 268 MET cc_start: 0.7690 (mtm) cc_final: 0.7446 (mtm) REVERT: 14 292 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8585 (mp) outliers start: 30 outliers final: 15 residues processed: 221 average time/residue: 0.1658 time to fit residues: 52.8632 Evaluate side-chains 218 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 6 residue 80 ARG Chi-restraints excluded: chain 6 residue 250 MET Chi-restraints excluded: chain 6 residue 340 ASN Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 180 MET Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 278 SER Chi-restraints excluded: chain 10 residue 344 LEU Chi-restraints excluded: chain 10 residue 356 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 434 ILE Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 292 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 174 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 193 optimal weight: 0.0060 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.145297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.123575 restraints weight = 19577.123| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 0.94 r_work: 0.3031 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17428 Z= 0.103 Angle : 0.453 7.853 23759 Z= 0.233 Chirality : 0.037 0.172 2717 Planarity : 0.004 0.047 2956 Dihedral : 13.003 165.788 2715 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.75 % Allowed : 15.21 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.19), residues: 2047 helix: 2.12 (0.15), residues: 1280 sheet: -0.13 (0.53), residues: 89 loop : -0.41 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 145 TYR 0.012 0.001 TYR10 200 PHE 0.019 0.001 PHE10 532 TRP 0.009 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 Details of bonding type rmsd covalent geometry : bond 0.00237 (17428) covalent geometry : angle 0.45325 (23759) hydrogen bonds : bond 0.03122 ( 921) hydrogen bonds : angle 3.48076 ( 2718) ********************** 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 224 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.679 Fit side-chains REVERT: 5 125 ARG cc_start: 0.7660 (mtp-110) cc_final: 0.6977 (mtm110) REVERT: 5 160 VAL cc_start: 0.8843 (p) cc_final: 0.8606 (m) REVERT: 6 80 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7340 (mtm-85) REVERT: 6 250 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.6881 (mtp) REVERT: 6 340 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8386 (t0) REVERT: 7 122 GLN cc_start: 0.8003 (mp10) cc_final: 0.7489 (mm-40) REVERT: 8 251 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7745 (mt-10) REVERT: 8 306 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.7491 (t80) REVERT: 8 313 ARG cc_start: 0.8825 (mmt90) cc_final: 0.7838 (mtm110) REVERT: 8 345 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8651 (mp) REVERT: 8 382 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8706 (mp) REVERT: 8 495 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7659 (mmp80) REVERT: 10 276 MET cc_start: 0.8448 (tpp) cc_final: 0.7805 (ttp) REVERT: 10 278 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8460 (m) REVERT: 10 344 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8639 (mp) REVERT: 10 356 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8346 (p) REVERT: 10 381 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8344 (mp) REVERT: 14 248 LYS cc_start: 0.7714 (mttp) cc_final: 0.7379 (mttp) REVERT: 14 292 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8496 (mp) outliers start: 31 outliers final: 15 residues processed: 216 average time/residue: 0.1481 time to fit residues: 46.5855 Evaluate side-chains 218 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 6 residue 80 ARG Chi-restraints excluded: chain 6 residue 250 MET Chi-restraints excluded: chain 6 residue 340 ASN Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 180 MET Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 278 SER Chi-restraints excluded: chain 10 residue 344 LEU Chi-restraints excluded: chain 10 residue 356 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 434 ILE Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 292 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 163 optimal weight: 0.0980 chunk 102 optimal weight: 0.0020 chunk 44 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 15 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.146356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.125144 restraints weight = 19365.257| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 0.94 r_work: 0.3036 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17428 Z= 0.091 Angle : 0.442 7.877 23759 Z= 0.227 Chirality : 0.037 0.171 2717 Planarity : 0.004 0.048 2956 Dihedral : 12.960 166.271 2715 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.53 % Allowed : 15.55 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.19), residues: 2047 helix: 2.21 (0.15), residues: 1278 sheet: -0.11 (0.49), residues: 99 loop : -0.40 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 145 TYR 0.011 0.001 TYR10 200 PHE 0.012 0.001 PHE 8 83 TRP 0.010 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 Details of bonding type rmsd covalent geometry : bond 0.00202 (17428) covalent geometry : angle 0.44250 (23759) hydrogen bonds : bond 0.02918 ( 921) hydrogen bonds : angle 3.43501 ( 2718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4071.42 seconds wall clock time: 70 minutes 29.86 seconds (4229.86 seconds total)