Starting phenix.real_space_refine on Mon Nov 18 18:44:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnc_29308/11_2024/8fnc_29308.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnc_29308/11_2024/8fnc_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnc_29308/11_2024/8fnc_29308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnc_29308/11_2024/8fnc_29308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnc_29308/11_2024/8fnc_29308.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnc_29308/11_2024/8fnc_29308.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 8.94, per 1000 atoms: 0.53 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: 4.39 Conformation dependent library (CDL) restraints added in 2.2 seconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3918 Finding SS restraints... Secondary structure from input PDB file: 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: 5.86 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: 5.76 Time building geometry restraints manager: 5.07 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: 2.300 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.810 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.040 ------------------------------------------------------------------------------- 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= 0.178 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 : 6.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (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 TRP 0.010 0.001 TRP14 175 HIS 0.004 0.001 HIS 5 214 PHE 0.030 0.001 PHE 8 83 TYR 0.011 0.001 TYR14 176 ARG 0.009 0.000 ARG 8 469 *********************** 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 : 1.892 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: 0.3529 time to fit residues: 126.6686 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 : 1.918 ------------------------------------------------------------------------------- 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 173 optimal weight: 4.9990 chunk 156 optimal weight: 0.0270 chunk 86 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 161 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- 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 10 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17428 Z= 0.188 Angle : 0.510 10.397 23759 Z= 0.265 Chirality : 0.039 0.175 2717 Planarity : 0.004 0.058 2956 Dihedral : 13.694 167.108 2725 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.92 % Allowed : 12.27 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.19), residues: 2047 helix: 1.55 (0.15), residues: 1282 sheet: 0.08 (0.54), residues: 93 loop : -0.60 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP14 175 HIS 0.005 0.001 HIS 5 151 PHE 0.028 0.001 PHE 8 83 TYR 0.012 0.001 TYR 6 307 ARG 0.006 0.000 ARG 8 403 *********************** 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 262 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7211 (mtp-110) cc_final: 0.6911 (mtp-110) REVERT: 6 61 LEU cc_start: 0.7848 (mt) cc_final: 0.7648 (mt) REVERT: 6 105 ASP cc_start: 0.8529 (m-30) cc_final: 0.8237 (m-30) REVERT: 8 73 ARG cc_start: 0.8347 (mtp85) cc_final: 0.8107 (mtp180) REVERT: 8 306 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.7945 (t80) REVERT: 10 173 MET cc_start: 0.8570 (mmm) cc_final: 0.8142 (tpt) REVERT: 10 174 THR cc_start: 0.8554 (m) cc_final: 0.8319 (p) REVERT: 10 276 MET cc_start: 0.8921 (tpp) cc_final: 0.8333 (ttp) REVERT: 10 335 ASP cc_start: 0.8688 (p0) cc_final: 0.8466 (p0) REVERT: 10 381 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8365 (mp) REVERT: 10 466 LYS cc_start: 0.7911 (tttm) cc_final: 0.7641 (ptmm) REVERT: 14 107 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8253 (mm-30) outliers start: 34 outliers final: 12 residues processed: 254 average time/residue: 0.3488 time to fit residues: 128.1059 Evaluate side-chains 223 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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 7 residue 86 MET Chi-restraints excluded: chain 8 residue 123 ASN 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 10 residue 321 LEU Chi-restraints excluded: chain 10 residue 381 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 103 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 10 419 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17428 Z= 0.200 Angle : 0.495 9.211 23759 Z= 0.254 Chirality : 0.038 0.178 2717 Planarity : 0.004 0.049 2956 Dihedral : 13.519 166.973 2717 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 : 1.87 % Allowed : 13.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 2047 helix: 1.69 (0.15), residues: 1284 sheet: 0.01 (0.53), residues: 94 loop : -0.58 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 PHE 0.024 0.001 PHE 8 83 TYR 0.012 0.001 TYR 6 307 ARG 0.005 0.000 ARG 5 145 *********************** 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 245 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7267 (mtp-110) cc_final: 0.6935 (mtp-110) REVERT: 8 251 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7709 (mt-10) REVERT: 8 306 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.7810 (t80) REVERT: 8 313 ARG cc_start: 0.8702 (mmt90) cc_final: 0.7952 (mtm110) REVERT: 8 382 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8859 (mp) REVERT: 8 475 ILE cc_start: 0.8776 (mm) cc_final: 0.8552 (mt) REVERT: 10 140 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6338 (tp) REVERT: 10 173 MET cc_start: 0.8739 (mmm) cc_final: 0.8267 (tpt) REVERT: 10 276 MET cc_start: 0.8891 (tpp) cc_final: 0.8286 (ttp) REVERT: 10 335 ASP cc_start: 0.8735 (p0) cc_final: 0.8455 (p0) REVERT: 10 381 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8414 (mp) outliers start: 33 outliers final: 19 residues processed: 233 average time/residue: 0.3278 time to fit residues: 113.0957 Evaluate side-chains 225 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 96 THR 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 381 LEU 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 226 LEU Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17428 Z= 0.200 Angle : 0.489 8.960 23759 Z= 0.252 Chirality : 0.038 0.183 2717 Planarity : 0.004 0.048 2956 Dihedral : 13.402 166.286 2715 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.09 % Allowed : 14.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 2047 helix: 1.77 (0.15), residues: 1285 sheet: -0.21 (0.52), residues: 96 loop : -0.59 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 PHE 0.021 0.001 PHE 8 83 TYR 0.013 0.001 TYR10 200 ARG 0.006 0.000 ARG 6 281 *********************** 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 248 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 1.844 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7296 (mtp-110) cc_final: 0.6768 (mtm110) REVERT: 6 281 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.6275 (ttp-110) REVERT: 8 251 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7676 (mt-10) REVERT: 8 306 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.7639 (t80) REVERT: 8 313 ARG cc_start: 0.8713 (mmt90) cc_final: 0.7946 (mtm110) REVERT: 8 345 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8755 (mp) REVERT: 8 382 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8854 (mp) REVERT: 8 475 ILE cc_start: 0.8838 (mm) cc_final: 0.8636 (mt) REVERT: 8 495 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7609 (mmp80) REVERT: 10 140 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5920 (tp) REVERT: 10 173 MET cc_start: 0.8663 (mmm) cc_final: 0.8167 (tpt) REVERT: 10 276 MET cc_start: 0.8869 (tpp) cc_final: 0.8302 (ttp) REVERT: 10 335 ASP cc_start: 0.8753 (p0) cc_final: 0.8377 (p0) REVERT: 10 381 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8395 (mp) outliers start: 37 outliers final: 16 residues processed: 235 average time/residue: 0.3428 time to fit residues: 117.6380 Evaluate side-chains 223 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 6 residue 281 ARG 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 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 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 183 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 10 residue 519 ASP Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17428 Z= 0.352 Angle : 0.574 7.444 23759 Z= 0.294 Chirality : 0.042 0.211 2717 Planarity : 0.005 0.051 2956 Dihedral : 13.455 166.799 2715 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.26 % Allowed : 14.13 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 2047 helix: 1.59 (0.15), residues: 1276 sheet: -0.34 (0.51), residues: 96 loop : -0.70 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 8 447 HIS 0.006 0.001 HIS14 201 PHE 0.020 0.002 PHE 8 83 TYR 0.018 0.002 TYR10 200 ARG 0.004 0.000 ARG 8 93 *********************** 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 242 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 1.919 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7356 (mtp-110) cc_final: 0.6830 (mtm110) REVERT: 6 80 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7828 (mmt180) REVERT: 6 250 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.6295 (mtm) REVERT: 8 251 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7753 (mt-10) REVERT: 8 306 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.7634 (t80) REVERT: 8 313 ARG cc_start: 0.8718 (mmt90) cc_final: 0.7908 (mtm110) REVERT: 8 345 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8810 (mp) REVERT: 8 382 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8877 (mp) REVERT: 8 495 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7654 (mmp80) REVERT: 10 173 MET cc_start: 0.8805 (mmm) cc_final: 0.8081 (tpt) REVERT: 10 276 MET cc_start: 0.8898 (tpp) cc_final: 0.8377 (ttp) REVERT: 10 335 ASP cc_start: 0.8859 (p0) cc_final: 0.8590 (p0) REVERT: 10 356 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8296 (p) REVERT: 10 381 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8456 (mp) REVERT: 14 107 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8338 (mm-30) outliers start: 40 outliers final: 24 residues processed: 230 average time/residue: 0.3383 time to fit residues: 115.2249 Evaluate side-chains 227 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 134 LEU Chi-restraints excluded: chain 6 residue 80 ARG Chi-restraints excluded: chain 6 residue 250 MET Chi-restraints excluded: chain 6 residue 419 THR Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 453 LEU Chi-restraints excluded: chain 6 residue 493 ASP Chi-restraints excluded: chain 7 residue 80 THR Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 8 residue 48 THR 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 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 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 183 THR Chi-restraints excluded: chain 10 residue 333 VAL 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 Chi-restraints excluded: chain 14 residue 329 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17428 Z= 0.191 Angle : 0.487 8.394 23759 Z= 0.252 Chirality : 0.038 0.195 2717 Planarity : 0.004 0.049 2956 Dihedral : 13.265 166.353 2715 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.64 % Allowed : 14.81 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 2047 helix: 1.76 (0.15), residues: 1278 sheet: -0.42 (0.50), residues: 96 loop : -0.65 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 PHE 0.017 0.001 PHE 8 83 TYR 0.014 0.001 TYR10 200 ARG 0.006 0.000 ARG 5 21 *********************** 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 223 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 1.884 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.6899 (mtm110) REVERT: 6 340 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8566 (t0) REVERT: 7 122 GLN cc_start: 0.7748 (mp10) cc_final: 0.7358 (mm-40) REVERT: 8 251 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7678 (mt-10) REVERT: 8 306 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.7576 (t80) REVERT: 8 313 ARG cc_start: 0.8707 (mmt90) cc_final: 0.7891 (mtm110) REVERT: 8 345 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8723 (mp) REVERT: 8 382 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8844 (mp) REVERT: 8 495 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7516 (mmp80) REVERT: 10 173 MET cc_start: 0.8675 (mmm) cc_final: 0.8109 (tpt) REVERT: 10 276 MET cc_start: 0.8821 (tpp) cc_final: 0.8331 (ttp) REVERT: 10 335 ASP cc_start: 0.8829 (p0) cc_final: 0.8347 (p0) REVERT: 10 356 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8260 (p) REVERT: 10 381 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8396 (mp) outliers start: 29 outliers final: 17 residues processed: 215 average time/residue: 0.3374 time to fit residues: 106.1013 Evaluate side-chains 214 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 220 MET Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 334 MET 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 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 10 residue 457 VAL Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17428 Z= 0.290 Angle : 0.530 7.027 23759 Z= 0.273 Chirality : 0.040 0.175 2717 Planarity : 0.004 0.050 2956 Dihedral : 13.244 166.820 2715 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.70 % Allowed : 15.43 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 2047 helix: 1.66 (0.15), residues: 1278 sheet: -0.46 (0.50), residues: 96 loop : -0.66 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 PHE 0.017 0.002 PHE 8 83 TYR 0.017 0.001 TYR10 200 ARG 0.005 0.000 ARG 5 145 *********************** 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 221 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 1.934 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7410 (mtp-110) cc_final: 0.6918 (mtm110) REVERT: 6 80 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7425 (mtm-85) REVERT: 6 250 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.6773 (mtm) REVERT: 6 301 MET cc_start: 0.9086 (mmm) cc_final: 0.8851 (mmm) REVERT: 7 122 GLN cc_start: 0.7808 (mp10) cc_final: 0.7425 (mm-40) REVERT: 7 143 LYS cc_start: 0.7863 (mttm) cc_final: 0.7584 (ttpp) REVERT: 8 251 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7737 (mt-10) REVERT: 8 306 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.7564 (t80) REVERT: 8 313 ARG cc_start: 0.8713 (mmt90) cc_final: 0.7881 (mtm110) REVERT: 8 345 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8756 (mp) REVERT: 8 382 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8870 (mp) REVERT: 8 495 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7559 (mmp80) REVERT: 10 173 MET cc_start: 0.8648 (mmm) cc_final: 0.7831 (tpt) REVERT: 10 276 MET cc_start: 0.8836 (tpp) cc_final: 0.8351 (ttp) REVERT: 10 356 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8326 (p) REVERT: 10 381 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8420 (mp) outliers start: 30 outliers final: 21 residues processed: 214 average time/residue: 0.3386 time to fit residues: 107.3864 Evaluate side-chains 220 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 80 ARG Chi-restraints excluded: chain 6 residue 250 MET Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 453 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 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 334 MET 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 333 VAL 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 10 residue 457 VAL Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 59 optimal weight: 0.0870 chunk 39 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 126 optimal weight: 0.0170 chunk 135 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.3734 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17428 Z= 0.130 Angle : 0.453 9.292 23759 Z= 0.235 Chirality : 0.037 0.173 2717 Planarity : 0.004 0.049 2956 Dihedral : 13.052 165.536 2715 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.70 % Allowed : 15.43 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.19), residues: 2047 helix: 1.93 (0.15), residues: 1279 sheet: -0.40 (0.53), residues: 91 loop : -0.57 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 PHE 0.014 0.001 PHE 8 83 TYR 0.010 0.001 TYR10 200 ARG 0.004 0.000 ARG 5 145 *********************** 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 233 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 1.904 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7369 (mtp-110) cc_final: 0.6933 (mtm110) REVERT: 5 292 MET cc_start: 0.8805 (tpp) cc_final: 0.8541 (mmm) REVERT: 6 80 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7184 (mtm-85) REVERT: 6 250 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6755 (mtm) REVERT: 6 340 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8473 (t0) REVERT: 7 122 GLN cc_start: 0.7720 (mp10) cc_final: 0.7336 (mm-40) REVERT: 7 143 LYS cc_start: 0.7847 (mttm) cc_final: 0.7542 (ttpp) REVERT: 8 251 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7625 (mt-10) REVERT: 8 306 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.7617 (t80) REVERT: 8 345 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8696 (mp) REVERT: 8 382 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8810 (mp) REVERT: 8 495 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7510 (mmp80) REVERT: 10 276 MET cc_start: 0.8775 (tpp) cc_final: 0.8305 (ttp) REVERT: 10 335 ASP cc_start: 0.8782 (p0) cc_final: 0.8377 (p0) REVERT: 10 356 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8281 (p) REVERT: 10 381 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8376 (mp) REVERT: 14 217 MET cc_start: 0.9035 (mtt) cc_final: 0.8667 (mtt) outliers start: 30 outliers final: 16 residues processed: 226 average time/residue: 0.3233 time to fit residues: 108.3574 Evaluate side-chains 219 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 57 LYS Chi-restraints excluded: chain 5 residue 96 THR 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 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 334 MET 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 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 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 180 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17428 Z= 0.172 Angle : 0.470 8.375 23759 Z= 0.241 Chirality : 0.038 0.173 2717 Planarity : 0.004 0.049 2956 Dihedral : 13.034 166.118 2715 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.41 % Allowed : 16.00 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.19), residues: 2047 helix: 1.94 (0.15), residues: 1280 sheet: -0.30 (0.53), residues: 91 loop : -0.53 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 PHE 0.014 0.001 PHE 8 83 TYR 0.013 0.001 TYR10 200 ARG 0.004 0.000 ARG 5 145 *********************** 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 222 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 2.176 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7384 (mtp-110) cc_final: 0.6942 (mtm110) REVERT: 6 80 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7234 (mtm-85) REVERT: 6 250 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6509 (mtm) REVERT: 6 340 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8517 (t0) REVERT: 7 122 GLN cc_start: 0.7712 (mp10) cc_final: 0.7333 (mm-40) REVERT: 7 143 LYS cc_start: 0.7859 (mttm) cc_final: 0.7548 (ttpp) REVERT: 8 251 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7666 (mt-10) REVERT: 8 306 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.7552 (t80) REVERT: 8 345 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8703 (mp) REVERT: 8 382 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8799 (mp) REVERT: 8 495 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7559 (mmp80) REVERT: 10 276 MET cc_start: 0.8798 (tpp) cc_final: 0.8323 (ttp) REVERT: 10 335 ASP cc_start: 0.8825 (p0) cc_final: 0.8386 (p0) REVERT: 10 356 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8316 (p) REVERT: 10 381 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8380 (mp) outliers start: 25 outliers final: 15 residues processed: 216 average time/residue: 0.3427 time to fit residues: 110.8437 Evaluate side-chains 216 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 334 MET 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 269 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 275 VAL Chi-restraints excluded: chain 14 residue 329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 0.5980 chunk 195 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 16 optimal weight: 0.0050 chunk 126 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17428 Z= 0.139 Angle : 0.456 9.187 23759 Z= 0.235 Chirality : 0.037 0.172 2717 Planarity : 0.004 0.049 2956 Dihedral : 12.980 166.214 2715 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.36 % Allowed : 16.51 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.19), residues: 2047 helix: 2.00 (0.15), residues: 1283 sheet: -0.28 (0.50), residues: 96 loop : -0.49 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 PHE 0.013 0.001 PHE 8 83 TYR 0.011 0.001 TYR10 200 ARG 0.004 0.000 ARG 5 145 ********************** 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 216 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 2.043 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7398 (mtp-110) cc_final: 0.6933 (mtm110) REVERT: 6 80 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7098 (mtm-85) REVERT: 6 250 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.6582 (mtm) REVERT: 6 340 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8497 (t0) REVERT: 7 122 GLN cc_start: 0.7695 (mp10) cc_final: 0.7303 (mm-40) REVERT: 7 143 LYS cc_start: 0.7857 (mttm) cc_final: 0.7551 (ttpp) REVERT: 8 251 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7630 (mt-10) REVERT: 8 306 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7610 (t80) REVERT: 8 345 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8674 (mp) REVERT: 8 382 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8798 (mp) REVERT: 8 495 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7515 (mmp80) REVERT: 10 276 MET cc_start: 0.8771 (tpp) cc_final: 0.8303 (ttp) REVERT: 10 335 ASP cc_start: 0.8786 (p0) cc_final: 0.8374 (p0) REVERT: 10 356 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8345 (p) REVERT: 10 381 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8380 (mp) outliers start: 24 outliers final: 13 residues processed: 211 average time/residue: 0.3173 time to fit residues: 99.6220 Evaluate side-chains 212 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 129 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 168 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 = 0.133245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.110209 restraints weight = 20013.596| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.05 r_work: 0.2953 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2733 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= 0.153 Angle : 0.460 8.708 23759 Z= 0.236 Chirality : 0.037 0.172 2717 Planarity : 0.004 0.049 2956 Dihedral : 12.970 166.788 2715 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.41 % Allowed : 16.45 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 2047 helix: 2.05 (0.15), residues: 1274 sheet: -0.39 (0.50), residues: 98 loop : -0.42 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 PHE 0.012 0.001 PHE 8 83 TYR 0.012 0.001 TYR10 200 ARG 0.005 0.000 ARG10 527 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3455.30 seconds wall clock time: 63 minutes 58.49 seconds (3838.49 seconds total)