Starting phenix.real_space_refine on Sun Jun 15 10:00:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fnc_29308/06_2025/8fnc_29308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fnc_29308/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fnc_29308/06_2025/8fnc_29308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fnc_29308/06_2025/8fnc_29308.map" model { file = "/net/cci-nas-00/data/ceres_data/8fnc_29308/06_2025/8fnc_29308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fnc_29308/06_2025/8fnc_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.59, per 1000 atoms: 0.56 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: 4.13 Conformation dependent library (CDL) restraints added in 2.1 seconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3918 Finding SS restraints... Secondary structure from input PDB file: 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: 5.01 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: 5.30 Time building geometry restraints manager: 4.91 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: 0.740 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 40.770 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.470 ------------------------------------------------------------------------------- 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 : 6.51 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 Details of bonding type rmsd hydrogen bonds : bond 0.16006 ( 921) hydrogen bonds : angle 5.45320 ( 2718) covalent geometry : bond 0.00270 (17428) covalent geometry : angle 0.54840 (23759) *********************** 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 : 1.702 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: 0.3109 time to fit residues: 110.7800 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 : 1.679 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.145053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119801 restraints weight = 19738.764| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.23 r_work: 0.3069 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1032 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= 0.126 Angle : 0.510 10.398 23759 Z= 0.265 Chirality : 0.039 0.175 2717 Planarity : 0.004 0.058 2956 Dihedral : 13.695 167.118 2725 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.17 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 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 921) hydrogen bonds : angle 4.01880 ( 2718) covalent geometry : bond 0.00286 (17428) covalent geometry : angle 0.50997 (23759) *********************** 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 : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7373 (mtp-110) cc_final: 0.7043 (mtp-110) REVERT: 5 160 VAL cc_start: 0.8927 (p) cc_final: 0.8684 (m) REVERT: 6 105 ASP cc_start: 0.8715 (m-30) cc_final: 0.8458 (m-30) REVERT: 8 73 ARG cc_start: 0.8382 (mtp85) cc_final: 0.8180 (mtp180) REVERT: 8 306 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7807 (t80) REVERT: 8 345 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8775 (mp) REVERT: 10 173 MET cc_start: 0.8498 (mmm) cc_final: 0.8098 (tpt) REVERT: 10 174 THR cc_start: 0.8509 (m) cc_final: 0.8301 (p) REVERT: 10 276 MET cc_start: 0.8605 (tpp) cc_final: 0.7923 (ttp) REVERT: 10 278 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8749 (m) REVERT: 10 335 ASP cc_start: 0.8563 (p0) cc_final: 0.8288 (p0) REVERT: 10 381 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8390 (mp) REVERT: 10 466 LYS cc_start: 0.8058 (tttm) cc_final: 0.7830 (ptmm) REVERT: 14 107 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8154 (mm-30) outliers start: 34 outliers final: 12 residues processed: 254 average time/residue: 0.3359 time to fit residues: 122.8450 Evaluate side-chains 226 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 1.752 ------------------------------------------------------------------------------- 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 8 residue 345 ILE Chi-restraints excluded: chain 10 residue 278 SER 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 126 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** 10 122 HIS 10 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.129651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.105862 restraints weight = 20145.782| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.17 r_work: 0.2918 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17428 Z= 0.198 Angle : 0.575 8.234 23759 Z= 0.294 Chirality : 0.041 0.188 2717 Planarity : 0.005 0.051 2956 Dihedral : 13.631 167.550 2717 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.26 % Allowed : 13.68 % Favored : 84.06 % 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: 1.03 (0.19), residues: 2047 helix: 1.47 (0.14), residues: 1279 sheet: -0.06 (0.53), residues: 94 loop : -0.69 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 8 447 HIS 0.006 0.001 HIS 5 214 PHE 0.026 0.002 PHE 8 83 TYR 0.014 0.002 TYR14 176 ARG 0.009 0.001 ARG 6 281 Details of bonding type rmsd hydrogen bonds : bond 0.04954 ( 921) hydrogen bonds : angle 3.99723 ( 2718) covalent geometry : bond 0.00492 (17428) covalent geometry : angle 0.57476 (23759) *********************** 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: 40 poor density : 205 time to evaluate : 1.766 Fit side-chains revert: symmetry clash REVERT: 5 160 VAL cc_start: 0.8987 (p) cc_final: 0.8757 (m) REVERT: 6 370 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.8075 (ttm170) REVERT: 6 388 GLU cc_start: 0.7676 (mp0) cc_final: 0.7395 (tp30) REVERT: 8 251 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8024 (mt-10) REVERT: 8 306 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7567 (t80) REVERT: 8 313 ARG cc_start: 0.9014 (mmt90) cc_final: 0.7946 (mtm110) REVERT: 8 345 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8754 (mp) REVERT: 8 382 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8757 (mp) REVERT: 8 495 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7777 (mmp80) REVERT: 10 173 MET cc_start: 0.8787 (mmm) cc_final: 0.8233 (tpt) REVERT: 10 276 MET cc_start: 0.8617 (tpp) cc_final: 0.8024 (ttp) REVERT: 10 278 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8728 (m) REVERT: 10 381 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8464 (mp) outliers start: 40 outliers final: 20 residues processed: 233 average time/residue: 0.3229 time to fit residues: 110.1742 Evaluate side-chains 225 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 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 278 SER 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 190 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 124 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 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** 6 138 ASN 10 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.131531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.108177 restraints weight = 20052.428| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.14 r_work: 0.2931 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1997 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= 0.126 Angle : 0.493 8.815 23759 Z= 0.253 Chirality : 0.038 0.178 2717 Planarity : 0.004 0.050 2956 Dihedral : 13.467 166.779 2715 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.98 % Allowed : 14.19 % Favored : 83.83 % 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: 1.23 (0.19), residues: 2047 helix: 1.66 (0.15), residues: 1284 sheet: -0.21 (0.52), residues: 94 loop : -0.64 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP14 175 HIS 0.007 0.001 HIS 5 214 PHE 0.021 0.001 PHE 8 83 TYR 0.013 0.001 TYR10 200 ARG 0.003 0.000 ARG 8 403 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 921) hydrogen bonds : angle 3.77808 ( 2718) covalent geometry : bond 0.00298 (17428) covalent geometry : angle 0.49280 (23759) *********************** 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 244 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 1.777 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7672 (mtp-110) cc_final: 0.6798 (mtm110) REVERT: 5 160 VAL cc_start: 0.8992 (p) cc_final: 0.8761 (m) REVERT: 6 388 GLU cc_start: 0.7727 (mp0) cc_final: 0.7430 (tp30) REVERT: 6 453 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8964 (mp) REVERT: 8 251 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7959 (mt-10) REVERT: 8 306 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7551 (t80) REVERT: 8 313 ARG cc_start: 0.9005 (mmt90) cc_final: 0.7950 (mtm110) REVERT: 8 345 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8749 (mp) REVERT: 8 382 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8733 (mp) REVERT: 8 437 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7816 (mt-10) REVERT: 10 140 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6094 (tp) REVERT: 10 173 MET cc_start: 0.8752 (mmm) cc_final: 0.8332 (tpt) REVERT: 10 276 MET cc_start: 0.8550 (tpp) cc_final: 0.7972 (ttp) REVERT: 10 278 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8712 (m) REVERT: 10 356 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8303 (p) REVERT: 10 381 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8429 (mp) outliers start: 35 outliers final: 22 residues processed: 235 average time/residue: 0.3122 time to fit residues: 107.6577 Evaluate side-chains 228 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 97 GLU Chi-restraints excluded: chain 6 residue 121 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 48 THR Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 132 GLU 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 327 VAL Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE 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 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 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 124 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 176 optimal weight: 0.0060 chunk 183 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.132660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.109179 restraints weight = 20361.865| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.06 r_work: 0.2942 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2134 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= 0.106 Angle : 0.470 8.920 23759 Z= 0.242 Chirality : 0.037 0.177 2717 Planarity : 0.004 0.048 2956 Dihedral : 13.337 166.502 2715 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.92 % Allowed : 14.25 % Favored : 83.83 % 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: 1.43 (0.19), residues: 2047 helix: 1.85 (0.15), residues: 1282 sheet: -0.39 (0.50), residues: 96 loop : -0.60 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 PHE 0.018 0.001 PHE 8 83 TYR 0.012 0.001 TYR10 200 ARG 0.006 0.000 ARG 5 145 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 921) hydrogen bonds : angle 3.65567 ( 2718) covalent geometry : bond 0.00241 (17428) covalent geometry : angle 0.47002 (23759) *********************** 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 238 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7731 (mtp-110) cc_final: 0.6878 (mtm110) REVERT: 5 160 VAL cc_start: 0.8991 (p) cc_final: 0.8753 (m) REVERT: 6 388 GLU cc_start: 0.7649 (mp0) cc_final: 0.7428 (tp30) REVERT: 7 122 GLN cc_start: 0.8265 (mp10) cc_final: 0.7724 (mm-40) REVERT: 8 251 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7942 (mt-10) REVERT: 8 306 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7482 (t80) REVERT: 8 313 ARG cc_start: 0.8987 (mmt90) cc_final: 0.7924 (mtm110) REVERT: 8 345 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8729 (mp) REVERT: 8 382 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8733 (mp) REVERT: 8 495 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7731 (mmp80) REVERT: 10 140 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.6053 (tp) REVERT: 10 173 MET cc_start: 0.8731 (mmm) cc_final: 0.8325 (tpt) REVERT: 10 276 MET cc_start: 0.8492 (tpp) cc_final: 0.7911 (ttp) REVERT: 10 278 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8622 (m) REVERT: 10 381 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8428 (mp) outliers start: 34 outliers final: 17 residues processed: 231 average time/residue: 0.3129 time to fit residues: 106.2058 Evaluate side-chains 219 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 132 GLU 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 327 VAL 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 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 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 329 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 177 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 187 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.133822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.109894 restraints weight = 20197.520| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.09 r_work: 0.2982 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2271 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= 0.096 Angle : 0.455 9.182 23759 Z= 0.234 Chirality : 0.037 0.175 2717 Planarity : 0.004 0.048 2956 Dihedral : 13.208 165.932 2715 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.04 % Allowed : 14.87 % 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 (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: 1.58 (0.19), residues: 2047 helix: 1.97 (0.15), residues: 1283 sheet: -0.39 (0.52), residues: 91 loop : -0.53 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 PHE 0.016 0.001 PHE 8 83 TYR 0.011 0.001 TYR10 200 ARG 0.003 0.000 ARG 5 145 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 921) hydrogen bonds : angle 3.56347 ( 2718) covalent geometry : bond 0.00215 (17428) covalent geometry : angle 0.45524 (23759) *********************** 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 239 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 3.767 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7648 (mtp-110) cc_final: 0.7025 (mtm110) REVERT: 5 160 VAL cc_start: 0.8956 (p) cc_final: 0.8704 (m) REVERT: 6 80 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7814 (mmt180) REVERT: 6 340 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8483 (t0) REVERT: 6 388 GLU cc_start: 0.7581 (mp0) cc_final: 0.7357 (tp30) REVERT: 8 251 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7786 (mt-10) REVERT: 8 306 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7526 (t80) REVERT: 8 313 ARG cc_start: 0.8895 (mmt90) cc_final: 0.7838 (mtm110) REVERT: 8 345 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8664 (mp) REVERT: 8 382 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8695 (mp) REVERT: 8 495 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7629 (mmp80) REVERT: 10 140 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5942 (tp) REVERT: 10 276 MET cc_start: 0.8431 (tpp) cc_final: 0.7827 (ttp) REVERT: 10 278 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8516 (m) REVERT: 10 356 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8253 (p) REVERT: 10 381 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8386 (mp) REVERT: 10 530 GLU cc_start: 0.7995 (tt0) cc_final: 0.7779 (mt-10) REVERT: 14 292 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8373 (mp) outliers start: 36 outliers final: 18 residues processed: 230 average time/residue: 0.3309 time to fit residues: 112.8606 Evaluate side-chains 226 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 57 LYS Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 6 residue 80 ARG 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 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 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 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 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 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 Chi-restraints excluded: chain 14 residue 329 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 30 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 190 optimal weight: 0.0060 chunk 32 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 80 optimal weight: 0.0770 chunk 161 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.7956 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.133240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.109530 restraints weight = 20127.402| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.05 r_work: 0.2936 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2364 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= 0.104 Angle : 0.458 8.232 23759 Z= 0.236 Chirality : 0.037 0.174 2717 Planarity : 0.004 0.048 2956 Dihedral : 13.155 165.747 2715 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.98 % Allowed : 15.09 % 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 (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: 1.62 (0.19), residues: 2047 helix: 1.99 (0.15), residues: 1282 sheet: -0.34 (0.52), residues: 91 loop : -0.49 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 PHE 0.015 0.001 PHE 8 83 TYR 0.012 0.001 TYR10 200 ARG 0.002 0.000 ARG 5 145 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 921) hydrogen bonds : angle 3.55003 ( 2718) covalent geometry : bond 0.00241 (17428) covalent geometry : angle 0.45810 (23759) *********************** 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 237 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7801 (mtp-110) cc_final: 0.7190 (mtm110) REVERT: 5 160 VAL cc_start: 0.8985 (p) cc_final: 0.8734 (m) REVERT: 6 80 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7934 (mmt180) REVERT: 6 340 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8548 (t0) REVERT: 6 388 GLU cc_start: 0.7632 (mp0) cc_final: 0.7381 (tp30) REVERT: 7 122 GLN cc_start: 0.8167 (mp10) cc_final: 0.7652 (mm-40) REVERT: 8 251 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7897 (mt-10) REVERT: 8 306 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.7532 (t80) REVERT: 8 313 ARG cc_start: 0.8948 (mmt90) cc_final: 0.7907 (mtm110) REVERT: 8 345 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8737 (mp) REVERT: 8 382 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8758 (mp) REVERT: 8 495 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7714 (mmp80) REVERT: 10 140 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5825 (tp) REVERT: 10 276 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7877 (ttp) REVERT: 10 278 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8589 (m) REVERT: 10 356 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8392 (p) REVERT: 10 381 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8440 (mp) REVERT: 10 530 GLU cc_start: 0.8178 (tt0) cc_final: 0.7955 (mt-10) REVERT: 14 259 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6820 (mt-10) REVERT: 14 292 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8492 (mp) outliers start: 35 outliers final: 20 residues processed: 229 average time/residue: 0.3479 time to fit residues: 118.5419 Evaluate side-chains 228 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 96 THR Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 6 residue 80 ARG 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 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 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 140 LEU Chi-restraints excluded: chain 10 residue 276 MET Chi-restraints excluded: chain 10 residue 278 SER 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 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 Chi-restraints excluded: chain 14 residue 329 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 25 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 81 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.129261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.105536 restraints weight = 20166.283| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.14 r_work: 0.2910 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17428 Z= 0.177 Angle : 0.531 6.830 23759 Z= 0.273 Chirality : 0.040 0.174 2717 Planarity : 0.004 0.048 2956 Dihedral : 13.161 166.505 2715 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.32 % Allowed : 14.87 % Favored : 82.82 % 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: 1.32 (0.19), residues: 2047 helix: 1.73 (0.15), residues: 1285 sheet: -0.37 (0.50), residues: 96 loop : -0.57 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 8 447 HIS 0.006 0.001 HIS 5 214 PHE 0.016 0.002 PHE 6 305 TYR 0.018 0.001 TYR10 200 ARG 0.007 0.000 ARG 6 281 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 921) hydrogen bonds : angle 3.76253 ( 2718) covalent geometry : bond 0.00438 (17428) covalent geometry : angle 0.53083 (23759) *********************** 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 239 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 1.743 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7688 (mtp-110) cc_final: 0.7132 (mtm110) REVERT: 5 160 VAL cc_start: 0.8989 (p) cc_final: 0.8787 (m) REVERT: 6 80 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7490 (mtm-85) REVERT: 6 340 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8588 (t0) REVERT: 6 388 GLU cc_start: 0.7604 (mp0) cc_final: 0.7332 (tp30) REVERT: 7 122 GLN cc_start: 0.8141 (mp10) cc_final: 0.7680 (mm-40) REVERT: 8 125 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8322 (m-40) REVERT: 8 251 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7918 (mt-10) REVERT: 8 306 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.7534 (t80) REVERT: 8 345 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8731 (mp) REVERT: 8 382 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8740 (mp) REVERT: 8 495 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7715 (mmp80) REVERT: 10 161 PHE cc_start: 0.6810 (m-10) cc_final: 0.6594 (m-80) REVERT: 10 276 MET cc_start: 0.8568 (tpp) cc_final: 0.7928 (ttp) REVERT: 10 278 SER cc_start: 0.8988 (OUTLIER) cc_final: 0.8685 (m) REVERT: 10 356 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8289 (p) REVERT: 10 381 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8424 (mp) REVERT: 14 259 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6716 (mt-10) outliers start: 41 outliers final: 24 residues processed: 230 average time/residue: 0.3190 time to fit residues: 106.9286 Evaluate side-chains 229 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 96 THR Chi-restraints excluded: chain 6 residue 80 ARG 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 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 48 THR Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 125 ASN Chi-restraints excluded: chain 8 residue 142 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 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 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 Chi-restraints excluded: chain 14 residue 329 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 107 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.130056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.106927 restraints weight = 20226.057| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.14 r_work: 0.2932 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17428 Z= 0.148 Angle : 0.503 8.162 23759 Z= 0.259 Chirality : 0.039 0.175 2717 Planarity : 0.004 0.048 2956 Dihedral : 13.079 166.219 2715 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.92 % Allowed : 15.43 % Favored : 82.65 % 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: 1.32 (0.19), residues: 2047 helix: 1.73 (0.15), residues: 1287 sheet: -0.33 (0.53), residues: 91 loop : -0.60 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP14 175 HIS 0.006 0.001 HIS 5 214 PHE 0.016 0.001 PHE 6 382 TYR 0.015 0.001 TYR10 200 ARG 0.002 0.000 ARG 8 496 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 921) hydrogen bonds : angle 3.70857 ( 2718) covalent geometry : bond 0.00360 (17428) covalent geometry : angle 0.50311 (23759) *********************** 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 230 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 2.085 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7716 (mtp-110) cc_final: 0.7132 (mtm110) REVERT: 6 80 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7476 (mtm-85) REVERT: 6 340 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8543 (t0) REVERT: 6 388 GLU cc_start: 0.7564 (mp0) cc_final: 0.7272 (tp30) REVERT: 7 122 GLN cc_start: 0.8166 (mp10) cc_final: 0.7718 (mm-40) REVERT: 8 251 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7880 (mt-10) REVERT: 8 306 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7673 (t80) REVERT: 8 345 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8741 (mp) REVERT: 8 382 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8740 (mp) REVERT: 8 495 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7654 (mmp80) REVERT: 10 276 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7906 (ttp) REVERT: 10 278 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8671 (m) REVERT: 10 356 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8296 (p) REVERT: 10 381 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8423 (mp) REVERT: 14 217 MET cc_start: 0.9116 (mtt) cc_final: 0.8560 (mtt) REVERT: 14 259 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6696 (mt-10) outliers start: 34 outliers final: 24 residues processed: 222 average time/residue: 0.3102 time to fit residues: 102.8781 Evaluate side-chains 228 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 96 THR Chi-restraints excluded: chain 6 residue 80 ARG 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 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 48 THR 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 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 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 276 MET Chi-restraints excluded: chain 10 residue 278 SER 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 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 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 184 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 127 optimal weight: 0.0980 chunk 167 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.132364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.109067 restraints weight = 20194.183| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.05 r_work: 0.2945 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2651 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= 0.103 Angle : 0.468 8.619 23759 Z= 0.243 Chirality : 0.037 0.173 2717 Planarity : 0.004 0.048 2956 Dihedral : 12.969 165.364 2715 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.87 % Allowed : 15.72 % Favored : 82.42 % 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: 1.53 (0.19), residues: 2047 helix: 1.91 (0.15), residues: 1284 sheet: -0.31 (0.52), residues: 91 loop : -0.53 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP14 175 HIS 0.007 0.001 HIS 5 214 PHE 0.022 0.001 PHE10 161 TYR 0.012 0.001 TYR10 200 ARG 0.002 0.000 ARG 5 145 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 921) hydrogen bonds : angle 3.62420 ( 2718) covalent geometry : bond 0.00235 (17428) covalent geometry : angle 0.46845 (23759) ********************** 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 233 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 1.898 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7266 (mtm110) REVERT: 6 80 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7440 (mtm-85) REVERT: 6 340 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8495 (t0) REVERT: 6 388 GLU cc_start: 0.7472 (mp0) cc_final: 0.7212 (tp30) REVERT: 7 122 GLN cc_start: 0.8168 (mp10) cc_final: 0.7715 (mm-40) REVERT: 8 251 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7882 (mt-10) REVERT: 8 306 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7648 (t80) REVERT: 8 345 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8730 (mp) REVERT: 8 382 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8768 (mp) REVERT: 8 495 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7694 (mmp80) REVERT: 10 276 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7915 (ttp) REVERT: 10 278 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8607 (m) REVERT: 10 356 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8388 (p) REVERT: 10 381 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8454 (mp) REVERT: 10 530 GLU cc_start: 0.8110 (tt0) cc_final: 0.7892 (mt-10) REVERT: 14 217 MET cc_start: 0.9038 (mtt) cc_final: 0.8660 (mtt) outliers start: 33 outliers final: 21 residues processed: 224 average time/residue: 0.3200 time to fit residues: 106.2080 Evaluate side-chains 226 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 96 THR Chi-restraints excluded: chain 6 residue 80 ARG 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 48 THR 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 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 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 276 MET Chi-restraints excluded: chain 10 residue 278 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.149148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.132559 restraints weight = 19071.140| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 0.72 r_work: 0.3016 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2696 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= 0.119 Angle : 0.480 8.833 23759 Z= 0.246 Chirality : 0.038 0.173 2717 Planarity : 0.004 0.048 2956 Dihedral : 12.951 165.854 2715 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.75 % Allowed : 16.05 % Favored : 82.19 % 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: 1.89 (0.15), residues: 1284 sheet: -0.31 (0.53), residues: 91 loop : -0.50 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 175 HIS 0.007 0.001 HIS 5 214 PHE 0.012 0.001 PHE 8 83 TYR 0.014 0.001 TYR10 200 ARG 0.004 0.000 ARG10 527 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 921) hydrogen bonds : angle 3.62646 ( 2718) covalent geometry : bond 0.00281 (17428) covalent geometry : angle 0.47994 (23759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8711.64 seconds wall clock time: 150 minutes 31.83 seconds (9031.83 seconds total)