Starting phenix.real_space_refine on Sat Oct 31 10:27:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36bd_77350/10_2026/36bd_77350.cif Found real_map, /net/cci-nas-00/data/ceres_data/36bd_77350/10_2026/36bd_77350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/36bd_77350/10_2026/36bd_77350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36bd_77350/10_2026/36bd_77350.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/36bd_77350/10_2026/36bd_77350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36bd_77350/10_2026/36bd_77350.map" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 18 5.49 5 S 179 5.16 5 C 26280 2.51 5 N 7081 2.21 5 O 8064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41622 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3071 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain breaks: 1 Chain: "B" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3028 Classifications: {'peptide': 386} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 366} Chain: "C" Number of atoms: 6584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6584 Classifications: {'peptide': 848} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 818} Chain breaks: 2 Chain: "D" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3756 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 445} Chain: "I" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3013 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 367} Chain: "J" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2989 Classifications: {'peptide': 379} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 361} Chain breaks: 1 Chain: "L" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1061 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 9, 'TRANS': 121} Chain: "M" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3267 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 405} Chain: "N" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1808 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "Z" Number of atoms: 6776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 6776 Classifications: {'peptide': 880} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 854} Chain breaks: 2 Chain: "K" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3029 Classifications: {'peptide': 382} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 363} Chain: "P" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3054 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.53, per 1000 atoms: 0.20 Number of scatterers: 41622 At special positions: 0 Unit cell: (220.08, 230.56, 214.84, 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 179 16.00 P 18 15.00 O 8064 8.00 N 7081 7.00 C 26280 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: 3.43 Conformation dependent library (CDL) restraints added in 2.0 seconds 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9894 Finding SS restraints... Secondary structure from input PDB file: 265 helices and 22 sheets defined 59.7% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 30 through 40 removed outlier: 3.687A pdb=" N SER A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 68 removed outlier: 3.737A pdb=" N ASP A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.844A pdb=" N ILE A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.811A pdb=" N VAL A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 231 through 239 removed outlier: 4.244A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.823A pdb=" N VAL A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 276 through 280' Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.672A pdb=" N VAL A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 327 through 343 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 415 through 434 Processing helix chain 'A' and resid 439 through 450 Processing helix chain 'B' and resid 55 through 82 Processing helix chain 'B' and resid 85 through 101 removed outlier: 4.651A pdb=" N GLN B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.737A pdb=" N VAL B 170 " --> pdb=" O PRO B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.895A pdb=" N TYR B 208 " --> pdb=" O HIS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 241 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 292 removed outlier: 3.529A pdb=" N GLY B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 316 removed outlier: 3.573A pdb=" N GLU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 354 through 367 Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'B' and resid 412 through 431 Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 60 through 62 No H-bonds generated for 'chain 'C' and resid 60 through 62' Processing helix chain 'C' and resid 63 through 80 Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 95 through 106 Processing helix chain 'C' and resid 108 through 127 removed outlier: 3.827A pdb=" N ILE C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 146 through 149 Processing helix chain 'C' and resid 150 through 178 Processing helix chain 'C' and resid 196 through 214 Proline residue: C 209 - end of helix Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 229 through 237 Proline residue: C 234 - end of helix Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 259 through 275 Processing helix chain 'C' and resid 277 through 289 removed outlier: 3.695A pdb=" N ALA C 283 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.584A pdb=" N ILE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 318 Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 334 through 347 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 360 through 363 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.682A pdb=" N PHE C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 391 Processing helix chain 'C' and resid 403 through 411 removed outlier: 3.575A pdb=" N TRP C 406 " --> pdb=" O ASN C 403 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS C 411 " --> pdb=" O TYR C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 426 removed outlier: 4.272A pdb=" N THR C 416 " --> pdb=" O GLY C 412 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY C 423 " --> pdb=" O VAL C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 438 removed outlier: 3.923A pdb=" N GLN C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS C 438 " --> pdb=" O GLN C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 442 Processing helix chain 'C' and resid 444 through 459 Processing helix chain 'C' and resid 468 through 479 removed outlier: 4.648A pdb=" N ASP C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 497 Processing helix chain 'C' and resid 502 through 515 Proline residue: C 511 - end of helix Processing helix chain 'C' and resid 519 through 534 Processing helix chain 'C' and resid 539 through 553 removed outlier: 3.536A pdb=" N ILE C 546 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 547 " --> pdb=" O THR C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 559 Processing helix chain 'C' and resid 561 through 574 removed outlier: 3.906A pdb=" N PHE C 565 " --> pdb=" O ASP C 561 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR C 574 " --> pdb=" O LEU C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 580 Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 594 through 608 removed outlier: 4.594A pdb=" N ALA C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 625 Processing helix chain 'C' and resid 724 through 748 removed outlier: 3.914A pdb=" N ALA C 744 " --> pdb=" O VAL C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 768 removed outlier: 3.510A pdb=" N LEU C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG C 759 " --> pdb=" O GLU C 755 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS C 766 " --> pdb=" O GLY C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 784 Proline residue: C 777 - end of helix Processing helix chain 'C' and resid 789 through 800 removed outlier: 3.985A pdb=" N THR C 795 " --> pdb=" O LYS C 791 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 798 " --> pdb=" O ASP C 794 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 799 " --> pdb=" O THR C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 819 Processing helix chain 'C' and resid 824 through 838 Processing helix chain 'C' and resid 841 through 856 Processing helix chain 'C' and resid 857 through 860 Processing helix chain 'C' and resid 874 through 888 Processing helix chain 'C' and resid 890 through 895 removed outlier: 3.619A pdb=" N MET C 894 " --> pdb=" O SER C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 removed outlier: 3.703A pdb=" N LEU C 900 " --> pdb=" O HIS C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 908 removed outlier: 4.020A pdb=" N GLY C 907 " --> pdb=" O MET C 903 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 28 through 43 removed outlier: 4.055A pdb=" N THR D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 72 through 82 Processing helix chain 'D' and resid 88 through 96 Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 109 through 122 Processing helix chain 'D' and resid 125 through 130 removed outlier: 4.480A pdb=" N PHE D 129 " --> pdb=" O LYS D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 166 through 175 Processing helix chain 'D' and resid 177 through 188 Processing helix chain 'D' and resid 189 through 207 removed outlier: 4.557A pdb=" N GLN D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE D 206 " --> pdb=" O ILE D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 220 through 228 Processing helix chain 'D' and resid 230 through 252 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 262 removed outlier: 3.591A pdb=" N VAL D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 273 removed outlier: 3.716A pdb=" N PHE D 267 " --> pdb=" O ILE D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 removed outlier: 4.121A pdb=" N ARG D 281 " --> pdb=" O TYR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 296 Processing helix chain 'D' and resid 303 through 313 Processing helix chain 'D' and resid 319 through 330 removed outlier: 3.928A pdb=" N ILE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLU D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 347 removed outlier: 3.805A pdb=" N LYS D 340 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASP D 341 " --> pdb=" O LYS D 337 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL D 342 " --> pdb=" O TYR D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'D' and resid 375 through 382 removed outlier: 4.235A pdb=" N LEU D 382 " --> pdb=" O ILE D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 395 Processing helix chain 'D' and resid 397 through 408 Processing helix chain 'D' and resid 408 through 417 removed outlier: 4.257A pdb=" N MET D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 442 Processing helix chain 'D' and resid 444 through 449 Processing helix chain 'D' and resid 451 through 465 Processing helix chain 'I' and resid 18 through 67 Processing helix chain 'I' and resid 103 through 107 removed outlier: 3.510A pdb=" N LEU I 107 " --> pdb=" O VAL I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 164 through 170 Processing helix chain 'I' and resid 171 through 178 Processing helix chain 'I' and resid 194 through 206 Processing helix chain 'I' and resid 216 through 219 Processing helix chain 'I' and resid 225 through 240 removed outlier: 4.221A pdb=" N MET I 229 " --> pdb=" O GLU I 225 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL I 230 " --> pdb=" O GLY I 226 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG I 238 " --> pdb=" O PHE I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 255 Processing helix chain 'I' and resid 262 through 265 removed outlier: 3.528A pdb=" N ASP I 265 " --> pdb=" O GLY I 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 262 through 265' Processing helix chain 'I' and resid 266 through 281 removed outlier: 3.695A pdb=" N LEU I 276 " --> pdb=" O MET I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 306 removed outlier: 3.895A pdb=" N LEU I 305 " --> pdb=" O ASP I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 332 Processing helix chain 'I' and resid 342 through 350 removed outlier: 3.914A pdb=" N VAL I 346 " --> pdb=" O ASN I 342 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET I 350 " --> pdb=" O VAL I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 372 removed outlier: 3.580A pdb=" N VAL I 358 " --> pdb=" O SER I 354 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS I 359 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU I 372 " --> pdb=" O TYR I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 378 through 396 removed outlier: 4.132A pdb=" N ASN I 391 " --> pdb=" O GLY I 387 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS I 392 " --> pdb=" O LYS I 388 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 399 No H-bonds generated for 'chain 'I' and resid 397 through 399' Processing helix chain 'J' and resid 47 through 91 Processing helix chain 'J' and resid 127 through 131 Processing helix chain 'J' and resid 151 through 156 removed outlier: 4.462A pdb=" N SER J 154 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP J 155 " --> pdb=" O PRO J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 174 Processing helix chain 'J' and resid 177 through 188 Processing helix chain 'J' and resid 188 through 194 Processing helix chain 'J' and resid 194 through 202 removed outlier: 3.622A pdb=" N TYR J 198 " --> pdb=" O GLN J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 230 removed outlier: 3.641A pdb=" N VAL J 223 " --> pdb=" O LYS J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 243 Processing helix chain 'J' and resid 248 through 264 removed outlier: 3.503A pdb=" N MET J 253 " --> pdb=" O GLU J 249 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL J 254 " --> pdb=" O GLY J 250 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU J 263 " --> pdb=" O ARG J 259 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN J 264 " --> pdb=" O LEU J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 277 Processing helix chain 'J' and resid 286 through 304 Processing helix chain 'J' and resid 325 through 330 Processing helix chain 'J' and resid 345 through 358 Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.676A pdb=" N ILE J 372 " --> pdb=" O LEU J 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 397 Processing helix chain 'J' and resid 403 through 417 removed outlier: 3.818A pdb=" N THR J 417 " --> pdb=" O THR J 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 44 Processing helix chain 'L' and resid 115 through 127 removed outlier: 3.510A pdb=" N TYR L 122 " --> pdb=" O ASP L 118 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET L 125 " --> pdb=" O ILE L 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 20 removed outlier: 3.710A pdb=" N VAL M 17 " --> pdb=" O ASP M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 51 Processing helix chain 'M' and resid 88 through 90 No H-bonds generated for 'chain 'M' and resid 88 through 90' Processing helix chain 'N' and resid 4 through 12 Processing helix chain 'N' and resid 14 through 25 Processing helix chain 'N' and resid 26 through 31 removed outlier: 3.908A pdb=" N LEU N 30 " --> pdb=" O SER N 27 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN N 31 " --> pdb=" O LEU N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 46 removed outlier: 3.666A pdb=" N TRP N 42 " --> pdb=" O ILE N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 57 removed outlier: 3.949A pdb=" N SER N 57 " --> pdb=" O SER N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 74 through 83 removed outlier: 3.573A pdb=" N ILE N 78 " --> pdb=" O THR N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 91 Processing helix chain 'N' and resid 109 through 117 Processing helix chain 'N' and resid 119 through 129 Processing helix chain 'N' and resid 142 through 151 removed outlier: 3.631A pdb=" N ARG N 146 " --> pdb=" O ILE N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 162 removed outlier: 3.876A pdb=" N GLU N 157 " --> pdb=" O LEU N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 184 removed outlier: 3.552A pdb=" N HIS N 180 " --> pdb=" O THR N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 198 Processing helix chain 'N' and resid 211 through 215 Processing helix chain 'N' and resid 217 through 227 removed outlier: 3.629A pdb=" N ASN N 227 " --> pdb=" O PHE N 223 " (cutoff:3.500A) Processing helix chain 'Z' and resid 6 through 14 removed outlier: 3.517A pdb=" N LEU Z 13 " --> pdb=" O LEU Z 9 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG Z 14 " --> pdb=" O LEU Z 10 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 30 Processing helix chain 'Z' and resid 31 through 40 removed outlier: 7.177A pdb=" N SER Z 37 " --> pdb=" O ASP Z 33 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU Z 38 " --> pdb=" O GLN Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 52 Processing helix chain 'Z' and resid 57 through 73 Processing helix chain 'Z' and resid 74 through 86 removed outlier: 3.701A pdb=" N LYS Z 86 " --> pdb=" O ALA Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 89 No H-bonds generated for 'chain 'Z' and resid 87 through 89' Processing helix chain 'Z' and resid 95 through 118 removed outlier: 3.509A pdb=" N TYR Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 122 through 127 removed outlier: 3.855A pdb=" N ASP Z 127 " --> pdb=" O TYR Z 124 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 147 Processing helix chain 'Z' and resid 149 through 160 Processing helix chain 'Z' and resid 162 through 175 Processing helix chain 'Z' and resid 178 through 196 Processing helix chain 'Z' and resid 199 through 217 Processing helix chain 'Z' and resid 221 through 233 removed outlier: 3.573A pdb=" N VAL Z 230 " --> pdb=" O ASN Z 226 " (cutoff:3.500A) Processing helix chain 'Z' and resid 234 through 249 removed outlier: 3.869A pdb=" N ALA Z 238 " --> pdb=" O ASP Z 234 " (cutoff:3.500A) Processing helix chain 'Z' and resid 250 through 265 Processing helix chain 'Z' and resid 266 through 280 Processing helix chain 'Z' and resid 283 through 291 Processing helix chain 'Z' and resid 292 through 306 Processing helix chain 'Z' and resid 310 through 321 Processing helix chain 'Z' and resid 325 through 340 removed outlier: 3.525A pdb=" N PHE Z 338 " --> pdb=" O VAL Z 334 " (cutoff:3.500A) Processing helix chain 'Z' and resid 346 through 352 Processing helix chain 'Z' and resid 352 through 358 Processing helix chain 'Z' and resid 361 through 375 removed outlier: 3.809A pdb=" N LEU Z 371 " --> pdb=" O ALA Z 367 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY Z 372 " --> pdb=" O THR Z 368 " (cutoff:3.500A) Processing helix chain 'Z' and resid 381 through 387 Processing helix chain 'Z' and resid 388 through 390 No H-bonds generated for 'chain 'Z' and resid 388 through 390' Processing helix chain 'Z' and resid 397 through 412 Processing helix chain 'Z' and resid 416 through 432 removed outlier: 4.094A pdb=" N ASP Z 421 " --> pdb=" O ARG Z 417 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR Z 422 " --> pdb=" O ASP Z 418 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE Z 426 " --> pdb=" O TYR Z 422 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY Z 432 " --> pdb=" O VAL Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 436 through 454 Processing helix chain 'Z' and resid 459 through 472 removed outlier: 3.582A pdb=" N VAL Z 469 " --> pdb=" O ALA Z 465 " (cutoff:3.500A) Processing helix chain 'Z' and resid 474 through 489 removed outlier: 3.997A pdb=" N GLU Z 479 " --> pdb=" O ALA Z 475 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA Z 480 " --> pdb=" O THR Z 476 " (cutoff:3.500A) Processing helix chain 'Z' and resid 494 through 508 removed outlier: 3.644A pdb=" N GLN Z 506 " --> pdb=" O PHE Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 510 through 525 Processing helix chain 'Z' and resid 528 through 531 Processing helix chain 'Z' and resid 532 through 542 removed outlier: 3.638A pdb=" N LYS Z 538 " --> pdb=" O ASP Z 534 " (cutoff:3.500A) Processing helix chain 'Z' and resid 544 through 559 removed outlier: 3.642A pdb=" N ALA Z 556 " --> pdb=" O ALA Z 552 " (cutoff:3.500A) Processing helix chain 'Z' and resid 564 through 578 Processing helix chain 'Z' and resid 580 through 595 removed outlier: 3.766A pdb=" N LEU Z 591 " --> pdb=" O ALA Z 587 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY Z 592 " --> pdb=" O VAL Z 588 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE Z 593 " --> pdb=" O ILE Z 589 " (cutoff:3.500A) Processing helix chain 'Z' and resid 598 through 600 No H-bonds generated for 'chain 'Z' and resid 598 through 600' Processing helix chain 'Z' and resid 601 through 611 removed outlier: 4.555A pdb=" N LEU Z 608 " --> pdb=" O ARG Z 604 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU Z 609 " --> pdb=" O ILE Z 605 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS Z 611 " --> pdb=" O GLN Z 607 " (cutoff:3.500A) Processing helix chain 'Z' and resid 614 through 629 removed outlier: 3.617A pdb=" N PHE Z 623 " --> pdb=" O CYS Z 619 " (cutoff:3.500A) Processing helix chain 'Z' and resid 634 through 646 removed outlier: 3.935A pdb=" N VAL Z 640 " --> pdb=" O SER Z 636 " (cutoff:3.500A) Proline residue: Z 643 - end of helix removed outlier: 3.731A pdb=" N LYS Z 646 " --> pdb=" O ASP Z 642 " (cutoff:3.500A) Processing helix chain 'Z' and resid 649 through 664 Processing helix chain 'Z' and resid 673 through 688 removed outlier: 4.141A pdb=" N ASP Z 677 " --> pdb=" O PRO Z 673 " (cutoff:3.500A) Processing helix chain 'Z' and resid 692 through 707 Processing helix chain 'Z' and resid 726 through 738 removed outlier: 3.511A pdb=" N GLN Z 738 " --> pdb=" O VAL Z 734 " (cutoff:3.500A) Processing helix chain 'Z' and resid 739 through 741 No H-bonds generated for 'chain 'Z' and resid 739 through 741' Processing helix chain 'Z' and resid 742 through 751 removed outlier: 3.632A pdb=" N HIS Z 747 " --> pdb=" O PRO Z 744 " (cutoff:3.500A) Processing helix chain 'Z' and resid 804 through 821 removed outlier: 4.338A pdb=" N ALA Z 808 " --> pdb=" O LEU Z 804 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG Z 809 " --> pdb=" O SER Z 805 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS Z 816 " --> pdb=" O ALA Z 812 " (cutoff:3.500A) Processing helix chain 'Z' and resid 875 through 880 removed outlier: 3.838A pdb=" N ARG Z 880 " --> pdb=" O PRO Z 876 " (cutoff:3.500A) Processing helix chain 'Z' and resid 919 through 925 Processing helix chain 'Z' and resid 937 through 942 Processing helix chain 'K' and resid 47 through 99 Processing helix chain 'K' and resid 136 through 140 Processing helix chain 'K' and resid 165 through 170 Processing helix chain 'K' and resid 179 through 183 Processing helix chain 'K' and resid 186 through 203 removed outlier: 3.600A pdb=" N GLU K 192 " --> pdb=" O GLU K 188 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU K 199 " --> pdb=" O GLU K 195 " (cutoff:3.500A) Proline residue: K 200 - end of helix Processing helix chain 'K' and resid 204 through 211 Processing helix chain 'K' and resid 227 through 240 removed outlier: 3.705A pdb=" N GLY K 240 " --> pdb=" O ALA K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 252 removed outlier: 3.593A pdb=" N ILE K 251 " --> pdb=" O PRO K 247 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL K 252 " --> pdb=" O ALA K 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 247 through 252' Processing helix chain 'K' and resid 257 through 273 Processing helix chain 'K' and resid 282 through 286 Processing helix chain 'K' and resid 295 through 315 Processing helix chain 'K' and resid 329 through 333 Processing helix chain 'K' and resid 353 through 367 removed outlier: 4.114A pdb=" N LYS K 367 " --> pdb=" O ILE K 363 " (cutoff:3.500A) Processing helix chain 'K' and resid 375 through 383 Processing helix chain 'K' and resid 387 through 405 Processing helix chain 'K' and resid 411 through 427 removed outlier: 3.597A pdb=" N LEU K 415 " --> pdb=" O ASN K 411 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 25 Processing helix chain 'P' and resid 26 through 73 Processing helix chain 'P' and resid 136 through 140 Processing helix chain 'P' and resid 164 through 169 removed outlier: 3.928A pdb=" N LYS P 168 " --> pdb=" O ASP P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 183 Processing helix chain 'P' and resid 186 through 197 Processing helix chain 'P' and resid 197 through 203 removed outlier: 3.590A pdb=" N MET P 201 " --> pdb=" O ILE P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 210 Processing helix chain 'P' and resid 227 through 239 Processing helix chain 'P' and resid 249 through 252 Processing helix chain 'P' and resid 257 through 273 Processing helix chain 'P' and resid 282 through 286 Processing helix chain 'P' and resid 295 through 315 removed outlier: 3.634A pdb=" N ARG P 299 " --> pdb=" O LYS P 295 " (cutoff:3.500A) Processing helix chain 'P' and resid 334 through 339 Processing helix chain 'P' and resid 353 through 365 Processing helix chain 'P' and resid 375 through 383 Processing helix chain 'P' and resid 387 through 406 Processing helix chain 'P' and resid 411 through 428 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 107 removed outlier: 5.480A pdb=" N CYS A 102 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASN A 148 " --> pdb=" O CYS A 102 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 154 through 157 current: chain 'A' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 183 through 186 current: chain 'B' and resid 117 through 121 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 128 through 131 current: chain 'B' and resid 156 through 159 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 156 through 159 current: chain 'I' and resid 83 through 88 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 92 through 97 current: chain 'I' and resid 122 through 125 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 122 through 125 current: chain 'J' and resid 107 through 112 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 117 through 121 current: chain 'J' and resid 146 through 149 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 146 through 149 current: chain 'K' and resid 117 through 121 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 126 through 129 current: chain 'K' and resid 155 through 158 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 155 through 158 current: chain 'P' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 126 through 129 current: chain 'P' and resid 155 through 158 Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 201 removed outlier: 6.014A pdb=" N THR A 270 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE A 307 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 272 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP A 309 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL A 274 " --> pdb=" O ASP A 309 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N CYS A 304 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N MET A 352 " --> pdb=" O CYS A 304 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE A 306 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA A 354 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE A 308 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY A 245 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL A 375 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU A 247 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 174 removed outlier: 6.212A pdb=" N THR B 243 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N PHE B 280 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU B 245 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP B 282 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE B 247 " --> pdb=" O ASP B 282 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET B 326 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N ILE B 348 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 220 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE B 350 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR B 222 " --> pdb=" O PHE B 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 862 through 863 Processing sheet with id=AA5, first strand: chain 'C' and resid 912 through 916 removed outlier: 4.515A pdb=" N ALA C 915 " --> pdb=" O ILE C 923 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 922 through 923 current: chain 'C' and resid 979 through 985 Processing sheet with id=AA6, first strand: chain 'C' and resid 945 through 952 removed outlier: 6.039A pdb=" N GLY C 947 " --> pdb=" O GLN C 931 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLN C 931 " --> pdb=" O GLY C 947 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 209 through 214 removed outlier: 6.721A pdb=" N LYS I 209 " --> pdb=" O ILE I 244 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N PHE I 246 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE I 211 " --> pdb=" O PHE I 246 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASP I 248 " --> pdb=" O ILE I 211 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL I 213 " --> pdb=" O ASP I 248 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER I 243 " --> pdb=" O LYS I 289 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE I 291 " --> pdb=" O SER I 243 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE I 245 " --> pdb=" O ILE I 291 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA I 293 " --> pdb=" O ILE I 245 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N MET I 247 " --> pdb=" O ALA I 293 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY I 184 " --> pdb=" O ARG I 312 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE I 314 " --> pdb=" O GLY I 184 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE I 186 " --> pdb=" O ILE I 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 233 through 238 removed outlier: 6.357A pdb=" N ALA J 233 " --> pdb=" O ILE J 268 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE J 270 " --> pdb=" O ALA J 233 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE J 235 " --> pdb=" O PHE J 270 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASP J 272 " --> pdb=" O ILE J 235 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL J 237 " --> pdb=" O ASP J 272 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER J 267 " --> pdb=" O LYS J 313 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE J 315 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE J 269 " --> pdb=" O ILE J 315 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA J 317 " --> pdb=" O ILE J 269 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE J 271 " --> pdb=" O ALA J 317 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL J 209 " --> pdb=" O MET J 316 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N THR J 318 " --> pdb=" O VAL J 209 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU J 211 " --> pdb=" O THR J 318 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR J 212 " --> pdb=" O ILE J 338 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 8 through 17 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 23 through 26 current: chain 'L' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 65 through 68 current: chain 'L' and resid 86 through 91 Processing sheet with id=AB1, first strand: chain 'M' and resid 2 through 5 removed outlier: 6.740A pdb=" N LYS M 3 " --> pdb=" O LEU M 328 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY M 325 " --> pdb=" O GLN M 314 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N MET M 311 " --> pdb=" O TYR M 307 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER M 292 " --> pdb=" O GLY M 306 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 8 through 10 removed outlier: 4.535A pdb=" N GLY M 52 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 60 through 63 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 76 through 81 current: chain 'M' and resid 344 through 349 Processing sheet with id=AB4, first strand: chain 'M' and resid 85 through 86 removed outlier: 3.803A pdb=" N ARG M 85 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE M 408 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL M 403 " --> pdb=" O GLN M 387 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN M 387 " --> pdb=" O VAL M 403 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 96 through 102 removed outlier: 3.771A pdb=" N ALA M 98 " --> pdb=" O GLY M 112 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG M 129 " --> pdb=" O VAL M 120 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 141 through 144 removed outlier: 3.617A pdb=" N LYS M 141 " --> pdb=" O SER M 154 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG M 172 " --> pdb=" O ILE M 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 181 through 187 removed outlier: 3.962A pdb=" N ASP M 183 " --> pdb=" O ALA M 196 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN M 192 " --> pdb=" O ILE M 187 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR M 201 " --> pdb=" O SER M 197 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE M 202 " --> pdb=" O THR M 215 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR M 215 " --> pdb=" O ILE M 202 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU M 204 " --> pdb=" O ILE M 213 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR M 211 " --> pdb=" O GLU M 206 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 226 through 233 removed outlier: 3.891A pdb=" N SER M 228 " --> pdb=" O GLY M 262 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE M 280 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN M 272 " --> pdb=" O GLN M 278 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLN M 278 " --> pdb=" O ASN M 272 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Z' and resid 713 through 715 Processing sheet with id=AC1, first strand: chain 'Z' and resid 758 through 762 removed outlier: 6.179A pdb=" N ILE Z 759 " --> pdb=" O VAL Z 903 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU Z 905 " --> pdb=" O ILE Z 759 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE Z 761 " --> pdb=" O LEU Z 905 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP Z 907 " --> pdb=" O ILE Z 761 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Z' and resid 867 through 869 Processing sheet with id=AC3, first strand: chain 'K' and resid 242 through 245 removed outlier: 6.456A pdb=" N VAL K 218 " --> pdb=" O MET K 325 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR K 327 " --> pdb=" O VAL K 218 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU K 220 " --> pdb=" O THR K 327 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG K 345 " --> pdb=" O GLY K 217 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 171 through 172 removed outlier: 4.500A pdb=" N PHE P 243 " --> pdb=" O VAL P 172 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR P 276 " --> pdb=" O LYS P 322 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU P 324 " --> pdb=" O THR P 276 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE P 278 " --> pdb=" O LEU P 324 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA P 326 " --> pdb=" O ILE P 278 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE P 280 " --> pdb=" O ALA P 326 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLY P 217 " --> pdb=" O ARG P 345 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE P 347 " --> pdb=" O GLY P 217 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU P 219 " --> pdb=" O ILE P 347 " (cutoff:3.500A) 2182 hydrogen bonds defined for protein. 6285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.61 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13888 1.34 - 1.46: 8522 1.46 - 1.58: 19568 1.58 - 1.70: 20 1.70 - 1.82: 308 Bond restraints: 42306 Sorted by residual: bond pdb=" CA PRO I 190 " pdb=" C PRO I 190 " ideal model delta sigma weight residual 1.514 1.490 0.025 5.50e-03 3.31e+04 2.02e+01 bond pdb=" C ILE K 158 " pdb=" N LEU K 159 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.47e-02 4.63e+03 6.73e+00 bond pdb=" CA PRO A 251 " pdb=" C PRO A 251 " ideal model delta sigma weight residual 1.514 1.503 0.011 5.50e-03 3.31e+04 3.98e+00 bond pdb=" CA GLY B 260 " pdb=" C GLY B 260 " ideal model delta sigma weight residual 1.511 1.524 -0.013 6.90e-03 2.10e+04 3.52e+00 bond pdb=" CB MET P 58 " pdb=" CG MET P 58 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.35e+00 ... (remaining 42301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 56465 2.37 - 4.75: 624 4.75 - 7.12: 81 7.12 - 9.49: 24 9.49 - 11.87: 10 Bond angle restraints: 57204 Sorted by residual: angle pdb=" C SER D 449 " pdb=" CA SER D 449 " pdb=" CB SER D 449 " ideal model delta sigma weight residual 117.23 110.48 6.75 1.36e+00 5.41e-01 2.46e+01 angle pdb=" CA MET I 149 " pdb=" CB MET I 149 " pdb=" CG MET I 149 " ideal model delta sigma weight residual 114.10 123.87 -9.77 2.00e+00 2.50e-01 2.39e+01 angle pdb=" N ILE I 253 " pdb=" CA ILE I 253 " pdb=" C ILE I 253 " ideal model delta sigma weight residual 113.53 108.76 4.77 9.80e-01 1.04e+00 2.37e+01 angle pdb=" CA LYS N 154 " pdb=" CB LYS N 154 " pdb=" CG LYS N 154 " ideal model delta sigma weight residual 114.10 123.10 -9.00 2.00e+00 2.50e-01 2.02e+01 angle pdb=" CA SER D 449 " pdb=" C SER D 449 " pdb=" N VAL D 450 " ideal model delta sigma weight residual 119.98 116.32 3.66 8.50e-01 1.38e+00 1.85e+01 ... (remaining 57199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 23417 17.97 - 35.94: 2132 35.94 - 53.90: 412 53.90 - 71.87: 65 71.87 - 89.84: 37 Dihedral angle restraints: 26063 sinusoidal: 10759 harmonic: 15304 Sorted by residual: dihedral pdb=" CA ALA P 169 " pdb=" C ALA P 169 " pdb=" N MET P 170 " pdb=" CA MET P 170 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA PRO D 47 " pdb=" C PRO D 47 " pdb=" N ASP D 48 " pdb=" CA ASP D 48 " ideal model delta harmonic sigma weight residual -180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA LEU J 130 " pdb=" C LEU J 130 " pdb=" N LEU J 131 " pdb=" CA LEU J 131 " ideal model delta harmonic sigma weight residual -180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 26060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 5303 0.051 - 0.102: 1077 0.102 - 0.152: 176 0.152 - 0.203: 1 0.203 - 0.254: 2 Chirality restraints: 6559 Sorted by residual: chirality pdb=" CG LEU N 158 " pdb=" CB LEU N 158 " pdb=" CD1 LEU N 158 " pdb=" CD2 LEU N 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU I 65 " pdb=" CB LEU I 65 " pdb=" CD1 LEU I 65 " pdb=" CD2 LEU I 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA MET K 280 " pdb=" N MET K 280 " pdb=" C MET K 280 " pdb=" CB MET K 280 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 6556 not shown) Planarity restraints: 7376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN I 89 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.38e+00 pdb=" N PRO I 90 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO I 90 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO I 90 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 270 " 0.014 2.00e-02 2.50e+03 1.68e-02 4.94e+00 pdb=" CG PHE J 270 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE J 270 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE J 270 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE J 270 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE J 270 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE J 270 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET Z 386 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.52e+00 pdb=" C MET Z 386 " 0.037 2.00e-02 2.50e+03 pdb=" O MET Z 386 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA Z 387 " -0.013 2.00e-02 2.50e+03 ... (remaining 7373 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 21101 2.97 - 3.45: 46545 3.45 - 3.94: 72218 3.94 - 4.42: 84499 4.42 - 4.90: 128581 Nonbonded interactions: 352944 Sorted by model distance: nonbonded pdb=" O ARG J 259 " pdb=" OE1 GLU J 263 " model vdw 2.490 3.040 nonbonded pdb=" N ASP A 205 " pdb=" OD1 ASP A 205 " model vdw 2.507 3.120 nonbonded pdb=" N GLN D 205 " pdb=" OE1 GLN D 205 " model vdw 2.510 3.120 nonbonded pdb=" N GLU J 263 " pdb=" OE1 GLU J 263 " model vdw 2.514 3.120 nonbonded pdb=" O ASN M 381 " pdb=" OD1 ASP M 382 " model vdw 2.519 3.040 ... (remaining 352939 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.400 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: 0.050 Extract box with map and model: 0.920 Check model and map are aligned: 0.160 Set scattering table: 0.130 Process input model: 40.240 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 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:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 42306 Z= 0.178 Angle : 0.664 11.865 57204 Z= 0.358 Chirality : 0.041 0.254 6559 Planarity : 0.004 0.072 7376 Dihedral : 14.245 89.839 16169 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.73 % Favored : 97.25 % Rotamer: Outliers : 0.94 % Allowed : 13.18 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.12), residues: 5242 helix: 0.95 (0.10), residues: 2744 sheet: 0.06 (0.21), residues: 601 loop : 0.88 (0.16), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 178 TYR 0.015 0.001 TYR P 255 PHE 0.039 0.002 PHE J 270 TRP 0.032 0.002 TRP Z 740 HIS 0.008 0.001 HIS D 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (42306) covalent geometry : angle 0.66427 / 0.36 (57204) hydrogen bonds : bond 0.20083 / 13.37 ( 2182) hydrogen bonds : angle 7.35813 / 5.27 ( 6285) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 260 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.9110 (mt) cc_final: 0.8877 (pp) REVERT: A 172 MET cc_start: 0.7557 (ttm) cc_final: 0.6640 (ptm) REVERT: A 268 ASP cc_start: 0.8911 (m-30) cc_final: 0.8545 (m-30) REVERT: A 289 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8764 (ptt-90) REVERT: A 396 MET cc_start: 0.8719 (mmm) cc_final: 0.8354 (mmm) REVERT: A 428 MET cc_start: 0.8922 (tpt) cc_final: 0.8313 (mmt) REVERT: B 62 MET cc_start: 0.9152 (ptp) cc_final: 0.8861 (mpp) REVERT: B 167 MET cc_start: 0.8246 (mmm) cc_final: 0.7801 (mmt) REVERT: B 209 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8774 (mm-30) REVERT: B 369 MET cc_start: 0.2127 (mtm) cc_final: -0.1224 (tpt) REVERT: B 395 MET cc_start: 0.1928 (ttt) cc_final: 0.1588 (ttp) REVERT: B 424 MET cc_start: 0.9081 (mmt) cc_final: 0.8689 (mmm) REVERT: C 249 MET cc_start: 0.8903 (ptt) cc_final: 0.8451 (ptt) REVERT: C 525 MET cc_start: 0.9359 (mtm) cc_final: 0.8520 (ptp) REVERT: C 575 MET cc_start: 0.8686 (tpp) cc_final: 0.8466 (tpt) REVERT: C 748 LEU cc_start: 0.8933 (tp) cc_final: 0.8639 (pp) REVERT: C 775 MET cc_start: 0.7627 (mmt) cc_final: 0.7331 (mmt) REVERT: C 813 PHE cc_start: 0.9513 (t80) cc_final: 0.9166 (t80) REVERT: C 864 MET cc_start: 0.8116 (mtt) cc_final: 0.7460 (mmm) REVERT: C 894 MET cc_start: 0.9066 (mmm) cc_final: 0.8714 (mmm) REVERT: C 903 MET cc_start: 0.8642 (tpp) cc_final: 0.8233 (tpp) REVERT: D 24 ASN cc_start: 0.9253 (t0) cc_final: 0.8868 (p0) REVERT: D 197 ILE cc_start: 0.9222 (mm) cc_final: 0.8751 (tt) REVERT: D 356 MET cc_start: 0.8968 (mmt) cc_final: 0.8763 (mmt) REVERT: I 121 MET cc_start: 0.8928 (tpp) cc_final: 0.8467 (tpp) REVERT: I 335 MET cc_start: 0.4108 (tpp) cc_final: 0.3819 (tpp) REVERT: I 350 MET cc_start: 0.8463 (ptm) cc_final: 0.7685 (ppp) REVERT: J 134 SER cc_start: 0.9259 (m) cc_final: 0.9002 (p) REVERT: J 242 PHE cc_start: 0.9081 (m-80) cc_final: 0.8805 (m-10) REVERT: J 281 ARG cc_start: 0.8010 (mtm180) cc_final: 0.7371 (ppt170) REVERT: J 298 GLU cc_start: 0.9507 (tp30) cc_final: 0.8990 (tm-30) REVERT: J 328 LEU cc_start: 0.9694 (tp) cc_final: 0.9142 (pp) REVERT: N 11 MET cc_start: 0.9551 (mtt) cc_final: 0.9151 (mmm) REVERT: N 67 TYR cc_start: 0.9017 (m-80) cc_final: 0.8711 (m-80) REVERT: N 117 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7471 (mmtm) REVERT: N 119 TRP cc_start: 0.6407 (m100) cc_final: 0.6150 (m100) REVERT: N 124 GLN cc_start: 0.9633 (OUTLIER) cc_final: 0.9301 (pt0) REVERT: N 125 PHE cc_start: 0.9319 (m-80) cc_final: 0.8952 (m-80) REVERT: N 180 HIS cc_start: 0.8468 (m170) cc_final: 0.8116 (m-70) REVERT: Z 210 SER cc_start: 0.9226 (m) cc_final: 0.8807 (p) REVERT: Z 217 MET cc_start: 0.7706 (tpp) cc_final: 0.6920 (tpp) REVERT: Z 571 LEU cc_start: 0.9153 (mt) cc_final: 0.8824 (tp) REVERT: K 382 MET cc_start: 0.2075 (tpt) cc_final: 0.1791 (tmm) REVERT: K 409 HIS cc_start: 0.9427 (m-70) cc_final: 0.9076 (m-70) REVERT: P 86 MET cc_start: 0.8707 (pmm) cc_final: 0.8381 (pmm) REVERT: P 131 MET cc_start: 0.8532 (tpp) cc_final: 0.7977 (tpp) REVERT: P 170 MET cc_start: 0.4487 (mmt) cc_final: 0.4209 (tpp) REVERT: P 210 MET cc_start: 0.1545 (ptp) cc_final: 0.0648 (pmm) REVERT: P 254 MET cc_start: 0.5472 (tmm) cc_final: 0.4635 (tmm) REVERT: P 255 TYR cc_start: 0.6217 (m-80) cc_final: 0.5373 (m-10) REVERT: P 256 ILE cc_start: 0.2534 (OUTLIER) cc_final: 0.2163 (mt) REVERT: P 400 MET cc_start: 0.6715 (mtp) cc_final: 0.6458 (ptp) outliers start: 43 outliers final: 31 residues processed: 295 average time/residue: 0.2436 time to fit residues: 121.0278 Evaluate side-chains 281 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 854 LEU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 120 PHE Chi-restraints excluded: chain N residue 124 GLN Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain Z residue 296 CYS Chi-restraints excluded: chain Z residue 427 ILE Chi-restraints excluded: chain Z residue 737 SER Chi-restraints excluded: chain Z residue 868 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 305 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: [394, 430, 41, 265, 497, 414, 310, 488, 366, 223, 516] chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 497 optimal weight: 8.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 1.9990 chunk 516 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 GLN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.089492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.068567 restraints weight = 368385.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.068592 restraints weight = 210578.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.068668 restraints weight = 144057.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.068664 restraints weight = 130917.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.068722 restraints weight = 124417.954| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 42306 Z= 0.149 Angle : 0.586 11.162 57204 Z= 0.304 Chirality : 0.042 0.343 6559 Planarity : 0.004 0.055 7376 Dihedral : 7.378 89.370 5955 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.59 % Favored : 97.39 % Rotamer: Outliers : 1.66 % Allowed : 12.05 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.12), residues: 5242 helix: 1.35 (0.10), residues: 2808 sheet: -0.03 (0.20), residues: 612 loop : 0.98 (0.16), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG Z 880 TYR 0.020 0.001 TYR Z 549 PHE 0.019 0.001 PHE C 793 TRP 0.019 0.002 TRP N 73 HIS 0.004 0.001 HIS I 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (42306) covalent geometry : angle 0.58577 / 0.30 (57204) hydrogen bonds : bond 0.05036 / 3.35 ( 2182) hydrogen bonds : angle 5.09134 / 3.63 ( 6285) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 261 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7410 (ttm) cc_final: 0.6575 (ptm) REVERT: A 289 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.7886 (ptt-90) REVERT: A 396 MET cc_start: 0.8698 (mmm) cc_final: 0.8318 (mmm) REVERT: B 50 TYR cc_start: 0.8430 (m-10) cc_final: 0.8216 (m-80) REVERT: B 167 MET cc_start: 0.8162 (mmm) cc_final: 0.7689 (mmt) REVERT: B 369 MET cc_start: 0.1907 (mtm) cc_final: -0.1317 (tpt) REVERT: B 395 MET cc_start: 0.2075 (ttt) cc_final: 0.1613 (ttp) REVERT: B 424 MET cc_start: 0.9088 (mmt) cc_final: 0.8654 (mmm) REVERT: C 405 ASN cc_start: 0.9824 (m-40) cc_final: 0.9577 (t0) REVERT: C 525 MET cc_start: 0.9126 (mtm) cc_final: 0.8793 (ptp) REVERT: C 547 MET cc_start: 0.8888 (pmm) cc_final: 0.8612 (pmm) REVERT: C 813 PHE cc_start: 0.9368 (t80) cc_final: 0.8941 (t80) REVERT: C 894 MET cc_start: 0.8944 (mmm) cc_final: 0.8555 (mmm) REVERT: C 903 MET cc_start: 0.8483 (tpp) cc_final: 0.8109 (tpp) REVERT: D 24 ASN cc_start: 0.9245 (t0) cc_final: 0.8838 (p0) REVERT: D 197 ILE cc_start: 0.9119 (mm) cc_final: 0.8711 (tt) REVERT: D 356 MET cc_start: 0.8838 (mmt) cc_final: 0.8634 (mmt) REVERT: I 121 MET cc_start: 0.8793 (tpp) cc_final: 0.8444 (tpp) REVERT: I 335 MET cc_start: 0.4048 (tpp) cc_final: 0.3572 (tpp) REVERT: I 350 MET cc_start: 0.8540 (ptm) cc_final: 0.7495 (ppp) REVERT: J 134 SER cc_start: 0.9091 (m) cc_final: 0.8836 (p) REVERT: J 139 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7456 (mt) REVERT: J 242 PHE cc_start: 0.9145 (m-80) cc_final: 0.8830 (m-10) REVERT: J 281 ARG cc_start: 0.7663 (mtm180) cc_final: 0.6826 (ppt170) REVERT: J 300 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9349 (mm) REVERT: J 376 ASP cc_start: 0.8337 (m-30) cc_final: 0.8094 (t0) REVERT: J 411 TYR cc_start: 0.7797 (t80) cc_final: 0.7590 (t80) REVERT: L 3 MET cc_start: 0.3642 (mtt) cc_final: 0.0702 (tpp) REVERT: N 67 TYR cc_start: 0.9029 (m-80) cc_final: 0.8683 (m-80) REVERT: N 119 TRP cc_start: 0.6493 (m100) cc_final: 0.6289 (m100) REVERT: N 125 PHE cc_start: 0.9373 (m-80) cc_final: 0.9072 (m-80) REVERT: N 180 HIS cc_start: 0.8482 (m170) cc_final: 0.8213 (m170) REVERT: Z 217 MET cc_start: 0.7730 (tpp) cc_final: 0.6553 (tpp) REVERT: Z 501 MET cc_start: 0.8566 (mtt) cc_final: 0.8290 (mtp) REVERT: Z 707 ASN cc_start: 0.7955 (m-40) cc_final: 0.7560 (t0) REVERT: K 409 HIS cc_start: 0.9414 (m-70) cc_final: 0.9122 (m-70) REVERT: P 58 MET cc_start: 0.9060 (ttt) cc_final: 0.8829 (ttt) REVERT: P 131 MET cc_start: 0.8622 (tpp) cc_final: 0.8115 (tpp) REVERT: P 254 MET cc_start: 0.5554 (tmm) cc_final: 0.4941 (tmm) REVERT: P 255 TYR cc_start: 0.6022 (m-80) cc_final: 0.5121 (m-80) REVERT: P 400 MET cc_start: 0.6673 (mtp) cc_final: 0.6399 (ptp) outliers start: 76 outliers final: 33 residues processed: 330 average time/residue: 0.2321 time to fit residues: 129.5643 Evaluate side-chains 281 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 154 SER Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain M residue 183 ASP Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain Z residue 427 ILE Chi-restraints excluded: chain Z residue 523 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 660 LEU Chi-restraints excluded: chain Z residue 715 ILE Chi-restraints excluded: chain Z residue 737 SER Chi-restraints excluded: chain Z residue 868 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 305 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: [326, 299, 348, 212, 204, 165, 190, 291, 47, 263, 26] chunk 326 optimal weight: 40.0000 chunk 299 optimal weight: 5.9990 chunk 348 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 190 optimal weight: 0.3980 chunk 291 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 263 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 HIS C 771 HIS C 959 HIS ** D 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN I 277 ASN ** I 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 268 GLN Z 679 ASN ** Z 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.086775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.066310 restraints weight = 350306.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.065010 restraints weight = 223577.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.064858 restraints weight = 178422.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.064866 restraints weight = 192464.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.064961 restraints weight = 154682.184| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 42306 Z= 0.278 Angle : 0.696 10.176 57204 Z= 0.363 Chirality : 0.044 0.338 6559 Planarity : 0.004 0.056 7376 Dihedral : 7.490 89.267 5925 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 2.49 % Allowed : 12.26 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.12), residues: 5242 helix: 0.92 (0.10), residues: 2807 sheet: -0.32 (0.20), residues: 626 loop : 0.68 (0.16), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 292 TYR 0.024 0.002 TYR Z 549 PHE 0.033 0.002 PHE D 347 TRP 0.026 0.002 TRP Z 740 HIS 0.006 0.001 HIS Z 573 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.28 (42306) covalent geometry : angle 0.69579 / 0.36 (57204) hydrogen bonds : bond 0.04828 / 3.23 ( 2182) hydrogen bonds : angle 5.08237 / 3.62 ( 6285) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 241 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.9016 (mt) cc_final: 0.8721 (pp) REVERT: A 172 MET cc_start: 0.7435 (ttm) cc_final: 0.6657 (ptm) REVERT: A 221 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7730 (tp) REVERT: A 396 MET cc_start: 0.8683 (mmm) cc_final: 0.7976 (mmm) REVERT: B 167 MET cc_start: 0.8186 (mmm) cc_final: 0.7604 (mmt) REVERT: B 334 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8808 (mm) REVERT: B 369 MET cc_start: 0.1927 (mtm) cc_final: -0.1190 (tpt) REVERT: B 395 MET cc_start: 0.2155 (ttt) cc_final: 0.1650 (ttp) REVERT: C 249 MET cc_start: 0.9070 (ptt) cc_final: 0.7912 (ppp) REVERT: C 298 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8214 (m-80) REVERT: C 406 TRP cc_start: 0.9170 (t-100) cc_final: 0.8668 (t-100) REVERT: C 525 MET cc_start: 0.9086 (mtm) cc_final: 0.8787 (ptp) REVERT: C 595 MET cc_start: 0.8060 (tpp) cc_final: 0.7601 (tpt) REVERT: C 813 PHE cc_start: 0.9280 (t80) cc_final: 0.8903 (t80) REVERT: C 864 MET cc_start: 0.8037 (mtt) cc_final: 0.7067 (mmt) REVERT: C 894 MET cc_start: 0.9001 (mmm) cc_final: 0.8604 (mmm) REVERT: C 903 MET cc_start: 0.8380 (tpp) cc_final: 0.8100 (tpp) REVERT: D 24 ASN cc_start: 0.9262 (t0) cc_final: 0.8878 (p0) REVERT: D 291 LEU cc_start: 0.9324 (tp) cc_final: 0.8912 (tt) REVERT: I 121 MET cc_start: 0.8825 (tpp) cc_final: 0.8554 (tpp) REVERT: I 350 MET cc_start: 0.8602 (ptm) cc_final: 0.7250 (ppp) REVERT: J 67 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7655 (p90) REVERT: J 134 SER cc_start: 0.9305 (m) cc_final: 0.9032 (p) REVERT: J 139 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7795 (mt) REVERT: J 242 PHE cc_start: 0.9127 (m-80) cc_final: 0.8727 (m-80) REVERT: J 253 MET cc_start: 0.9479 (ppp) cc_final: 0.9238 (ppp) REVERT: J 281 ARG cc_start: 0.7664 (mtm180) cc_final: 0.6360 (ppt170) REVERT: J 328 LEU cc_start: 0.9658 (tp) cc_final: 0.9018 (pp) REVERT: J 376 ASP cc_start: 0.8416 (m-30) cc_final: 0.8140 (t0) REVERT: L 3 MET cc_start: 0.3335 (mtt) cc_final: -0.0314 (tpp) REVERT: L 46 TRP cc_start: 0.3500 (m100) cc_final: 0.3100 (m100) REVERT: M 91 LEU cc_start: 0.3913 (OUTLIER) cc_final: 0.3470 (mm) REVERT: N 67 TYR cc_start: 0.9029 (m-80) cc_final: 0.8644 (m-80) REVERT: N 124 GLN cc_start: 0.9633 (OUTLIER) cc_final: 0.9281 (pt0) REVERT: N 125 PHE cc_start: 0.9395 (m-80) cc_final: 0.9067 (m-80) REVERT: N 180 HIS cc_start: 0.8480 (m170) cc_final: 0.8177 (m170) REVERT: Z 217 MET cc_start: 0.7901 (tpp) cc_final: 0.7052 (tpp) REVERT: Z 268 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7759 (pp30) REVERT: Z 501 MET cc_start: 0.8509 (mtt) cc_final: 0.8279 (mtp) REVERT: K 409 HIS cc_start: 0.9367 (m-70) cc_final: 0.9000 (m-70) REVERT: K 420 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8126 (tpm170) REVERT: P 58 MET cc_start: 0.9160 (ttm) cc_final: 0.8924 (ttt) REVERT: P 170 MET cc_start: 0.4761 (tpp) cc_final: 0.4198 (tpp) REVERT: P 256 ILE cc_start: 0.2656 (OUTLIER) cc_final: 0.2311 (mt) REVERT: P 368 MET cc_start: 0.2346 (ptt) cc_final: 0.0826 (pmm) REVERT: P 400 MET cc_start: 0.6815 (mtp) cc_final: 0.6366 (ppp) outliers start: 114 outliers final: 67 residues processed: 342 average time/residue: 0.2401 time to fit residues: 139.9828 Evaluate side-chains 300 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 224 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain C residue 884 THR Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 101 GLU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 154 SER Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 183 ASP Chi-restraints excluded: chain M residue 360 ILE Chi-restraints excluded: chain M residue 361 SER Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 124 GLN Chi-restraints excluded: chain N residue 145 HIS Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 224 PHE Chi-restraints excluded: chain Z residue 268 GLN Chi-restraints excluded: chain Z residue 301 THR Chi-restraints excluded: chain Z residue 419 THR Chi-restraints excluded: chain Z residue 427 ILE Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 523 LEU Chi-restraints excluded: chain Z residue 555 ILE Chi-restraints excluded: chain Z residue 625 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 660 LEU Chi-restraints excluded: chain Z residue 665 ILE Chi-restraints excluded: chain Z residue 715 ILE Chi-restraints excluded: chain Z residue 737 SER Chi-restraints excluded: chain Z residue 752 SER Chi-restraints excluded: chain Z residue 868 VAL Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 325 MET Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 305 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: [126, 405, 460, 191, 200, 233, 56, 176, 1, 474, 109] chunk 126 optimal weight: 4.9990 chunk 405 optimal weight: 1.9990 chunk 460 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 233 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 474 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN ** D 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 375 ASN ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 233 ASN Z 510 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.088319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.068229 restraints weight = 369787.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.068067 restraints weight = 214254.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.068142 restraints weight = 153045.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.068352 restraints weight = 144017.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.068515 restraints weight = 129688.447| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 42306 Z= 0.140 Angle : 0.572 12.530 57204 Z= 0.292 Chirality : 0.042 0.339 6559 Planarity : 0.004 0.055 7376 Dihedral : 7.191 89.361 5920 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.90 % Favored : 97.08 % Rotamer: Outliers : 2.08 % Allowed : 13.03 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.12), residues: 5242 helix: 1.29 (0.10), residues: 2794 sheet: -0.28 (0.20), residues: 614 loop : 0.82 (0.16), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 894 TYR 0.018 0.001 TYR B 50 PHE 0.020 0.001 PHE Z 651 TRP 0.017 0.002 TRP N 42 HIS 0.004 0.001 HIS I 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (42306) covalent geometry : angle 0.57247 / 0.29 (57204) hydrogen bonds : bond 0.03973 / 2.64 ( 2182) hydrogen bonds : angle 4.69062 / 3.35 ( 6285) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 247 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7354 (ttm) cc_final: 0.6521 (ptm) REVERT: A 197 MET cc_start: 0.7080 (tmm) cc_final: 0.6661 (tmm) REVERT: A 289 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8796 (ptt-90) REVERT: A 396 MET cc_start: 0.8552 (mmm) cc_final: 0.8141 (mmm) REVERT: B 167 MET cc_start: 0.8091 (mmm) cc_final: 0.7649 (mmt) REVERT: B 369 MET cc_start: 0.1617 (mtm) cc_final: -0.1178 (tpt) REVERT: B 395 MET cc_start: 0.2020 (ttt) cc_final: 0.1448 (ttp) REVERT: B 424 MET cc_start: 0.9044 (mmt) cc_final: 0.8472 (mmm) REVERT: C 406 TRP cc_start: 0.9130 (t-100) cc_final: 0.8653 (t-100) REVERT: C 525 MET cc_start: 0.9116 (mtm) cc_final: 0.8321 (ptp) REVERT: C 595 MET cc_start: 0.8050 (tpp) cc_final: 0.7687 (tpt) REVERT: C 813 PHE cc_start: 0.9237 (t80) cc_final: 0.8875 (t80) REVERT: C 894 MET cc_start: 0.8939 (mmm) cc_final: 0.8574 (mmm) REVERT: C 903 MET cc_start: 0.8312 (tpp) cc_final: 0.8065 (tpp) REVERT: D 24 ASN cc_start: 0.9249 (t0) cc_final: 0.8852 (p0) REVERT: I 121 MET cc_start: 0.8881 (tpp) cc_final: 0.8664 (tpp) REVERT: I 350 MET cc_start: 0.8334 (ptm) cc_final: 0.7365 (ppp) REVERT: J 134 SER cc_start: 0.9144 (m) cc_final: 0.8738 (p) REVERT: J 139 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7645 (mt) REVERT: J 179 MET cc_start: 0.9521 (tpt) cc_final: 0.8737 (pmm) REVERT: J 242 PHE cc_start: 0.9001 (m-80) cc_final: 0.8704 (m-80) REVERT: J 281 ARG cc_start: 0.7322 (mtm180) cc_final: 0.6570 (ppt170) REVERT: J 328 LEU cc_start: 0.9607 (tp) cc_final: 0.8945 (pp) REVERT: J 376 ASP cc_start: 0.8247 (m-30) cc_final: 0.7957 (t0) REVERT: L 1 MET cc_start: 0.3542 (pmm) cc_final: 0.2939 (pmm) REVERT: L 3 MET cc_start: 0.1900 (mtt) cc_final: -0.1676 (tpp) REVERT: L 46 TRP cc_start: 0.3077 (m100) cc_final: 0.2746 (m100) REVERT: M 91 LEU cc_start: 0.3567 (OUTLIER) cc_final: 0.3063 (mm) REVERT: N 124 GLN cc_start: 0.9662 (OUTLIER) cc_final: 0.9268 (pt0) REVERT: N 125 PHE cc_start: 0.9396 (m-80) cc_final: 0.9047 (m-80) REVERT: N 180 HIS cc_start: 0.8415 (m170) cc_final: 0.8113 (m170) REVERT: Z 217 MET cc_start: 0.7999 (tpp) cc_final: 0.6784 (tpp) REVERT: Z 233 ASN cc_start: 0.9240 (OUTLIER) cc_final: 0.8459 (t0) REVERT: Z 501 MET cc_start: 0.8351 (mtt) cc_final: 0.8144 (mtp) REVERT: Z 657 MET cc_start: 0.8131 (ptp) cc_final: 0.7898 (ptm) REVERT: K 290 ARG cc_start: 0.4915 (OUTLIER) cc_final: 0.4595 (tmt170) REVERT: K 409 HIS cc_start: 0.9300 (m-70) cc_final: 0.8891 (m-70) REVERT: K 420 ARG cc_start: 0.8490 (mtt180) cc_final: 0.8140 (tpm170) REVERT: P 58 MET cc_start: 0.9244 (ttm) cc_final: 0.9021 (ttt) REVERT: P 86 MET cc_start: 0.8883 (pmm) cc_final: 0.8489 (pmm) REVERT: P 131 MET cc_start: 0.8219 (tpp) cc_final: 0.7954 (tpp) REVERT: P 256 ILE cc_start: 0.2600 (OUTLIER) cc_final: 0.2238 (mt) REVERT: P 400 MET cc_start: 0.6836 (mtp) cc_final: 0.6297 (ppp) outliers start: 95 outliers final: 55 residues processed: 332 average time/residue: 0.2254 time to fit residues: 126.1234 Evaluate side-chains 296 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 234 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 183 ASP Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 124 GLN Chi-restraints excluded: chain N residue 145 HIS Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 224 PHE Chi-restraints excluded: chain Z residue 233 ASN Chi-restraints excluded: chain Z residue 427 ILE Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 523 LEU Chi-restraints excluded: chain Z residue 625 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 660 LEU Chi-restraints excluded: chain Z residue 715 ILE Chi-restraints excluded: chain Z residue 737 SER Chi-restraints excluded: chain Z residue 749 LEU Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain K residue 290 ARG Chi-restraints excluded: chain K residue 325 MET Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 305 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: [69, 451, 56, 228, 334, 511, 203, 227, 190, 188, 387] chunk 69 optimal weight: 0.7980 chunk 451 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 334 optimal weight: 10.0000 chunk 511 optimal weight: 0.0770 chunk 203 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 188 optimal weight: 0.7980 chunk 387 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 HIS ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 ASN ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 GLN L 105 ASN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.089189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.068439 restraints weight = 366622.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.068530 restraints weight = 220277.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.068241 restraints weight = 149193.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.068362 restraints weight = 161174.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.068409 restraints weight = 139918.813| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 42306 Z= 0.111 Angle : 0.552 13.247 57204 Z= 0.279 Chirality : 0.042 0.397 6559 Planarity : 0.003 0.053 7376 Dihedral : 6.938 87.681 5919 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.01 % Favored : 96.97 % Rotamer: Outliers : 1.79 % Allowed : 13.42 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.12), residues: 5242 helix: 1.54 (0.10), residues: 2783 sheet: -0.21 (0.20), residues: 624 loop : 0.91 (0.16), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 171 TYR 0.014 0.001 TYR P 255 PHE 0.019 0.001 PHE C 793 TRP 0.016 0.001 TRP M 163 HIS 0.004 0.001 HIS I 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (42306) covalent geometry : angle 0.55228 / 0.28 (57204) hydrogen bonds : bond 0.03632 / 2.40 ( 2182) hydrogen bonds : angle 4.48981 / 3.20 ( 6285) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 264 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7299 (ttm) cc_final: 0.6428 (ptm) REVERT: A 289 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8925 (ptt-90) REVERT: A 290 MET cc_start: 0.9315 (mmm) cc_final: 0.8976 (mmm) REVERT: A 396 MET cc_start: 0.8437 (mmm) cc_final: 0.8128 (mmm) REVERT: B 167 MET cc_start: 0.8128 (mmm) cc_final: 0.7716 (mmt) REVERT: B 209 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8647 (mm-30) REVERT: B 259 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7112 (t0) REVERT: B 334 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8769 (mm) REVERT: B 369 MET cc_start: 0.1731 (mtm) cc_final: -0.1283 (tpt) REVERT: B 424 MET cc_start: 0.9035 (mmt) cc_final: 0.8524 (mmm) REVERT: C 249 MET cc_start: 0.8970 (ptt) cc_final: 0.7806 (ppp) REVERT: C 298 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: C 406 TRP cc_start: 0.9150 (t-100) cc_final: 0.8707 (t-100) REVERT: C 525 MET cc_start: 0.9137 (mtm) cc_final: 0.8660 (ttm) REVERT: C 595 MET cc_start: 0.8012 (tpp) cc_final: 0.7526 (tpt) REVERT: C 813 PHE cc_start: 0.9294 (t80) cc_final: 0.8941 (t80) REVERT: C 815 MET cc_start: 0.9265 (mtp) cc_final: 0.8582 (mmt) REVERT: C 894 MET cc_start: 0.8963 (mmm) cc_final: 0.8619 (mmm) REVERT: C 903 MET cc_start: 0.8403 (tpp) cc_final: 0.8187 (tpp) REVERT: D 24 ASN cc_start: 0.9298 (t0) cc_final: 0.8913 (p0) REVERT: D 197 ILE cc_start: 0.9112 (mm) cc_final: 0.8691 (tt) REVERT: I 121 MET cc_start: 0.9110 (tpp) cc_final: 0.8880 (tpp) REVERT: I 127 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.8236 (tm-30) REVERT: I 335 MET cc_start: 0.4038 (tpp) cc_final: 0.3575 (tpp) REVERT: I 350 MET cc_start: 0.8663 (ptm) cc_final: 0.7677 (ppp) REVERT: J 134 SER cc_start: 0.9068 (m) cc_final: 0.8708 (p) REVERT: J 139 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7434 (mt) REVERT: J 242 PHE cc_start: 0.9156 (m-80) cc_final: 0.8810 (m-10) REVERT: J 281 ARG cc_start: 0.7735 (mtm180) cc_final: 0.6649 (ppt170) REVERT: J 328 LEU cc_start: 0.9576 (tp) cc_final: 0.8946 (pp) REVERT: J 353 PHE cc_start: 0.7724 (m-80) cc_final: 0.7468 (m-10) REVERT: J 376 ASP cc_start: 0.8322 (m-30) cc_final: 0.8107 (t0) REVERT: L 1 MET cc_start: 0.3540 (pmm) cc_final: 0.3025 (pmm) REVERT: L 3 MET cc_start: 0.3255 (mtt) cc_final: -0.0297 (tpp) REVERT: L 46 TRP cc_start: 0.3147 (m100) cc_final: 0.2841 (m100) REVERT: M 91 LEU cc_start: 0.4034 (OUTLIER) cc_final: 0.3601 (mm) REVERT: N 11 MET cc_start: 0.9682 (mtt) cc_final: 0.9260 (mmt) REVERT: N 124 GLN cc_start: 0.9634 (OUTLIER) cc_final: 0.9278 (pt0) REVERT: N 125 PHE cc_start: 0.9392 (m-80) cc_final: 0.9052 (m-10) REVERT: N 180 HIS cc_start: 0.8537 (m170) cc_final: 0.8100 (m170) REVERT: Z 217 MET cc_start: 0.7866 (tpp) cc_final: 0.6809 (tpp) REVERT: K 409 HIS cc_start: 0.9289 (m-70) cc_final: 0.8971 (m-70) REVERT: P 58 MET cc_start: 0.9321 (ttm) cc_final: 0.9104 (ttt) REVERT: P 86 MET cc_start: 0.8926 (pmm) cc_final: 0.8694 (pmm) REVERT: P 254 MET cc_start: 0.5773 (tmm) cc_final: 0.4782 (tmm) REVERT: P 255 TYR cc_start: 0.5981 (m-80) cc_final: 0.5088 (m-80) REVERT: P 256 ILE cc_start: 0.2361 (OUTLIER) cc_final: 0.2069 (mt) REVERT: P 368 MET cc_start: 0.2538 (ptt) cc_final: 0.1196 (pmm) REVERT: P 400 MET cc_start: 0.6765 (mtp) cc_final: 0.6277 (ppp) outliers start: 82 outliers final: 49 residues processed: 338 average time/residue: 0.2218 time to fit residues: 127.0799 Evaluate side-chains 303 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 372 ILE Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 183 ASP Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 124 GLN Chi-restraints excluded: chain N residue 145 HIS Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 224 PHE Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 523 LEU Chi-restraints excluded: chain Z residue 625 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 660 LEU Chi-restraints excluded: chain Z residue 715 ILE Chi-restraints excluded: chain Z residue 749 LEU Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 305 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: [351, 255, 516, 16, 332, 406, 152, 484, 56, 408, 109] chunk 351 optimal weight: 8.9990 chunk 255 optimal weight: 5.9990 chunk 516 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 332 optimal weight: 10.0000 chunk 406 optimal weight: 0.9990 chunk 152 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.4845 > 50:) chunk 484 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 408 optimal weight: 3.9990 chunk 109 optimal weight: 0.0770 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 HIS ** D 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 180 HIS ** Z 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.087624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.066250 restraints weight = 349451.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.066515 restraints weight = 202908.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.065867 restraints weight = 153304.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.066069 restraints weight = 153842.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.066023 restraints weight = 133351.046| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 42306 Z= 0.181 Angle : 0.597 11.949 57204 Z= 0.304 Chirality : 0.042 0.358 6559 Planarity : 0.004 0.054 7376 Dihedral : 6.959 86.913 5916 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.15 % Favored : 96.83 % Rotamer: Outliers : 2.08 % Allowed : 14.04 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.12), residues: 5242 helix: 1.52 (0.10), residues: 2784 sheet: -0.22 (0.20), residues: 623 loop : 0.85 (0.16), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 171 TYR 0.019 0.001 TYR Z 526 PHE 0.022 0.002 PHE Z 651 TRP 0.017 0.002 TRP M 163 HIS 0.005 0.001 HIS J 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (42306) covalent geometry : angle 0.59716 / 0.30 (57204) hydrogen bonds : bond 0.03797 / 2.52 ( 2182) hydrogen bonds : angle 4.58495 / 3.27 ( 6285) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 236 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7294 (ttm) cc_final: 0.6416 (ptm) REVERT: A 261 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8862 (mtm-85) REVERT: A 289 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8903 (ptt-90) REVERT: A 290 MET cc_start: 0.9260 (mmm) cc_final: 0.9058 (mmm) REVERT: A 318 ARG cc_start: 0.4447 (OUTLIER) cc_final: 0.3815 (mmm-85) REVERT: A 396 MET cc_start: 0.8449 (mmm) cc_final: 0.8091 (mmm) REVERT: B 167 MET cc_start: 0.8213 (mmm) cc_final: 0.7756 (mmt) REVERT: B 259 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7146 (t0) REVERT: B 334 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8690 (mm) REVERT: B 369 MET cc_start: 0.1563 (mtm) cc_final: -0.1369 (tpt) REVERT: C 298 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: C 406 TRP cc_start: 0.9173 (t-100) cc_final: 0.8736 (t-100) REVERT: C 525 MET cc_start: 0.9156 (mtm) cc_final: 0.8696 (ptp) REVERT: C 813 PHE cc_start: 0.9307 (t80) cc_final: 0.8830 (t80) REVERT: C 894 MET cc_start: 0.9064 (mmm) cc_final: 0.8700 (mmm) REVERT: C 903 MET cc_start: 0.8366 (tpp) cc_final: 0.8060 (tpp) REVERT: D 24 ASN cc_start: 0.9269 (t0) cc_final: 0.8884 (p0) REVERT: D 197 ILE cc_start: 0.9117 (mm) cc_final: 0.8724 (tt) REVERT: I 121 MET cc_start: 0.9051 (tpp) cc_final: 0.8823 (tpp) REVERT: I 127 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: I 335 MET cc_start: 0.3975 (tpp) cc_final: 0.3540 (tpp) REVERT: I 350 MET cc_start: 0.8746 (ptm) cc_final: 0.7360 (ppp) REVERT: J 242 PHE cc_start: 0.9074 (m-80) cc_final: 0.8724 (m-80) REVERT: J 281 ARG cc_start: 0.7674 (mtm180) cc_final: 0.6695 (ppt170) REVERT: J 299 LEU cc_start: 0.9810 (OUTLIER) cc_final: 0.9601 (tp) REVERT: J 328 LEU cc_start: 0.9642 (tp) cc_final: 0.9068 (pp) REVERT: J 376 ASP cc_start: 0.8378 (m-30) cc_final: 0.8079 (t0) REVERT: L 3 MET cc_start: 0.3693 (mtt) cc_final: 0.0285 (tpp) REVERT: L 46 TRP cc_start: 0.3108 (m100) cc_final: 0.2782 (m100) REVERT: M 91 LEU cc_start: 0.4191 (OUTLIER) cc_final: 0.3812 (mm) REVERT: N 124 GLN cc_start: 0.9578 (OUTLIER) cc_final: 0.9198 (pt0) REVERT: N 125 PHE cc_start: 0.9404 (m-80) cc_final: 0.9090 (m-10) REVERT: N 180 HIS cc_start: 0.8365 (m-70) cc_final: 0.7994 (m-70) REVERT: Z 217 MET cc_start: 0.7979 (tpp) cc_final: 0.6934 (tpp) REVERT: K 109 MET cc_start: 0.7186 (mmm) cc_final: 0.6889 (mmt) REVERT: K 290 ARG cc_start: 0.5253 (OUTLIER) cc_final: 0.4929 (tmt170) REVERT: K 409 HIS cc_start: 0.9296 (m-70) cc_final: 0.8987 (m-70) REVERT: P 58 MET cc_start: 0.9353 (ttm) cc_final: 0.9127 (ttt) REVERT: P 170 MET cc_start: 0.5512 (tpp) cc_final: 0.5262 (tpp) REVERT: P 210 MET cc_start: 0.1158 (ptp) cc_final: -0.0479 (pmm) REVERT: P 256 ILE cc_start: 0.2765 (OUTLIER) cc_final: 0.2500 (mt) REVERT: P 368 MET cc_start: 0.3068 (ptt) cc_final: 0.1589 (pmm) REVERT: P 400 MET cc_start: 0.6666 (mtp) cc_final: 0.6194 (ppp) outliers start: 95 outliers final: 68 residues processed: 320 average time/residue: 0.2232 time to fit residues: 121.0358 Evaluate side-chains 307 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 227 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 372 ILE Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 183 ASP Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 124 GLN Chi-restraints excluded: chain N residue 145 HIS Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 224 PHE Chi-restraints excluded: chain Z residue 427 ILE Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 625 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 660 LEU Chi-restraints excluded: chain Z residue 715 ILE Chi-restraints excluded: chain Z residue 757 THR Chi-restraints excluded: chain Z residue 868 VAL Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain K residue 290 ARG Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 305 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: [238, 165, 230, 400, 119, 77, 499, 342, 454, 198, 61] chunk 238 optimal weight: 20.0000 chunk 165 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 400 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 499 optimal weight: 6.9990 chunk 342 optimal weight: 10.0000 chunk 454 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 900 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.088389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.068132 restraints weight = 368179.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.067361 restraints weight = 217237.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.067160 restraints weight = 167365.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.067167 restraints weight = 174227.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.067260 restraints weight = 141665.258| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42306 Z= 0.131 Angle : 0.570 13.690 57204 Z= 0.286 Chirality : 0.042 0.361 6559 Planarity : 0.003 0.054 7376 Dihedral : 6.838 86.865 5911 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.05 % Favored : 96.93 % Rotamer: Outliers : 1.90 % Allowed : 14.45 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.12), residues: 5242 helix: 1.59 (0.10), residues: 2777 sheet: -0.22 (0.20), residues: 624 loop : 0.88 (0.16), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 346 TYR 0.015 0.001 TYR P 255 PHE 0.019 0.001 PHE A 295 TRP 0.018 0.001 TRP M 163 HIS 0.005 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (42306) covalent geometry : angle 0.57025 / 0.29 (57204) hydrogen bonds : bond 0.03570 / 2.36 ( 2182) hydrogen bonds : angle 4.48052 / 3.19 ( 6285) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 244 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7281 (ttm) cc_final: 0.6403 (ptm) REVERT: A 197 MET cc_start: 0.6899 (tmm) cc_final: 0.6647 (tmm) REVERT: A 289 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8929 (ptt-90) REVERT: A 290 MET cc_start: 0.9339 (mmm) cc_final: 0.9129 (mmm) REVERT: A 396 MET cc_start: 0.8445 (mmm) cc_final: 0.8101 (mmm) REVERT: B 259 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7122 (t0) REVERT: B 334 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8722 (mm) REVERT: B 369 MET cc_start: 0.1602 (mtm) cc_final: -0.1329 (tpt) REVERT: B 424 MET cc_start: 0.9108 (mmt) cc_final: 0.8608 (mmm) REVERT: C 249 MET cc_start: 0.8920 (ptt) cc_final: 0.7806 (ppp) REVERT: C 298 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8198 (m-80) REVERT: C 406 TRP cc_start: 0.9186 (t-100) cc_final: 0.8764 (t-100) REVERT: C 525 MET cc_start: 0.9128 (mtm) cc_final: 0.8660 (ptp) REVERT: C 780 MET cc_start: 0.9086 (mmm) cc_final: 0.8876 (mmm) REVERT: C 813 PHE cc_start: 0.9194 (t80) cc_final: 0.8891 (t80) REVERT: C 894 MET cc_start: 0.8878 (mmm) cc_final: 0.8518 (mmm) REVERT: C 903 MET cc_start: 0.8314 (tpp) cc_final: 0.8029 (tpp) REVERT: D 24 ASN cc_start: 0.9289 (t0) cc_final: 0.8904 (p0) REVERT: D 197 ILE cc_start: 0.9074 (mm) cc_final: 0.8703 (tt) REVERT: I 127 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8115 (tm-30) REVERT: I 335 MET cc_start: 0.3781 (tpp) cc_final: 0.3340 (tpp) REVERT: I 350 MET cc_start: 0.8724 (ptm) cc_final: 0.7336 (ppp) REVERT: J 242 PHE cc_start: 0.9027 (m-80) cc_final: 0.8683 (m-10) REVERT: J 328 LEU cc_start: 0.9589 (tp) cc_final: 0.8974 (pp) REVERT: J 376 ASP cc_start: 0.8368 (m-30) cc_final: 0.8065 (t0) REVERT: L 3 MET cc_start: 0.3662 (mtt) cc_final: 0.0124 (tpp) REVERT: L 46 TRP cc_start: 0.3039 (m100) cc_final: 0.2743 (m100) REVERT: M 91 LEU cc_start: 0.4193 (OUTLIER) cc_final: 0.3782 (mm) REVERT: M 97 THR cc_start: 0.0076 (OUTLIER) cc_final: -0.0179 (p) REVERT: N 121 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8531 (mm-30) REVERT: N 125 PHE cc_start: 0.9405 (m-80) cc_final: 0.9149 (m-10) REVERT: N 180 HIS cc_start: 0.8540 (m-70) cc_final: 0.8101 (m170) REVERT: Z 217 MET cc_start: 0.7808 (tpp) cc_final: 0.6801 (tpp) REVERT: K 109 MET cc_start: 0.7153 (mmm) cc_final: 0.6863 (mmt) REVERT: K 187 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8662 (t) REVERT: K 188 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: K 290 ARG cc_start: 0.5308 (OUTLIER) cc_final: 0.4884 (tmt170) REVERT: K 409 HIS cc_start: 0.9281 (m-70) cc_final: 0.8976 (m-70) REVERT: K 420 ARG cc_start: 0.8415 (mtt180) cc_final: 0.7970 (tpm170) REVERT: P 58 MET cc_start: 0.9368 (ttm) cc_final: 0.9128 (ttt) REVERT: P 131 MET cc_start: 0.8369 (tpp) cc_final: 0.8064 (tpp) REVERT: P 254 MET cc_start: 0.5669 (tmm) cc_final: 0.4706 (tmm) REVERT: P 255 TYR cc_start: 0.5661 (m-80) cc_final: 0.4738 (m-80) REVERT: P 256 ILE cc_start: 0.2416 (OUTLIER) cc_final: 0.2151 (mt) REVERT: P 368 MET cc_start: 0.2850 (ptt) cc_final: 0.1377 (pmm) outliers start: 87 outliers final: 61 residues processed: 322 average time/residue: 0.2280 time to fit residues: 124.1697 Evaluate side-chains 301 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 229 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 183 ASP Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 124 GLN Chi-restraints excluded: chain N residue 145 HIS Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 224 PHE Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 523 LEU Chi-restraints excluded: chain Z residue 608 LEU Chi-restraints excluded: chain Z residue 625 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 660 LEU Chi-restraints excluded: chain Z residue 715 ILE Chi-restraints excluded: chain Z residue 813 ARG Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain K residue 290 ARG Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 305 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: [11, 226, 316, 448, 484, 362, 127, 332, 388, 194, 291] chunk 11 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 316 optimal weight: 50.0000 chunk 448 optimal weight: 10.0000 chunk 484 optimal weight: 7.9990 chunk 362 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 332 optimal weight: 6.9990 chunk 388 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 291 optimal weight: 9.9990 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 GLN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN ** Z 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 364 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.085606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.064548 restraints weight = 372858.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.063901 restraints weight = 253027.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.063657 restraints weight = 192369.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.063807 restraints weight = 206129.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.063726 restraints weight = 180247.366| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 42306 Z= 0.344 Angle : 0.774 12.085 57204 Z= 0.404 Chirality : 0.046 0.287 6559 Planarity : 0.005 0.084 7376 Dihedral : 7.254 88.700 5911 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.20 % Favored : 95.78 % Rotamer: Outliers : 2.47 % Allowed : 14.15 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.12), residues: 5242 helix: 0.87 (0.10), residues: 2788 sheet: -0.34 (0.21), residues: 625 loop : 0.48 (0.16), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 261 TYR 0.034 0.002 TYR Z 549 PHE 0.036 0.003 PHE Z 651 TRP 0.025 0.003 TRP Z 740 HIS 0.008 0.002 HIS Z 573 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.34 (42306) covalent geometry : angle 0.77435 / 0.40 (57204) hydrogen bonds : bond 0.04647 / 3.10 ( 2182) hydrogen bonds : angle 5.05638 / 3.59 ( 6285) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 227 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7602 (ttm) cc_final: 0.6658 (ptm) REVERT: A 197 MET cc_start: 0.7065 (tmm) cc_final: 0.6696 (tmm) REVERT: A 289 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8772 (pmt-80) REVERT: A 290 MET cc_start: 0.9438 (mmm) cc_final: 0.8761 (mmm) REVERT: A 297 MET cc_start: 0.8879 (tpp) cc_final: 0.8633 (tpp) REVERT: A 318 ARG cc_start: 0.5253 (OUTLIER) cc_final: 0.4243 (mmm160) REVERT: A 396 MET cc_start: 0.8322 (mmm) cc_final: 0.7873 (mmm) REVERT: B 259 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7273 (t0) REVERT: B 334 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8774 (mm) REVERT: B 369 MET cc_start: 0.1706 (mtm) cc_final: -0.1309 (tpt) REVERT: B 395 MET cc_start: 0.2232 (ttt) cc_final: 0.1708 (ttp) REVERT: B 405 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8425 (tmm-80) REVERT: B 424 MET cc_start: 0.9016 (mmt) cc_final: 0.8492 (mmm) REVERT: C 406 TRP cc_start: 0.9173 (t-100) cc_final: 0.8731 (t-100) REVERT: C 525 MET cc_start: 0.9134 (mtm) cc_final: 0.8620 (ptp) REVERT: C 575 MET cc_start: 0.8714 (tpt) cc_final: 0.8488 (tpp) REVERT: C 595 MET cc_start: 0.8317 (tpp) cc_final: 0.7810 (tpt) REVERT: C 813 PHE cc_start: 0.9258 (t80) cc_final: 0.8898 (t80) REVERT: C 864 MET cc_start: 0.8092 (mtt) cc_final: 0.7116 (mmt) REVERT: C 894 MET cc_start: 0.9001 (mmm) cc_final: 0.8666 (mmm) REVERT: C 903 MET cc_start: 0.8335 (tpp) cc_final: 0.8007 (tpp) REVERT: D 24 ASN cc_start: 0.9318 (t0) cc_final: 0.8966 (p0) REVERT: D 291 LEU cc_start: 0.9295 (tp) cc_final: 0.8899 (tt) REVERT: D 356 MET cc_start: 0.8747 (mmt) cc_final: 0.8501 (mmm) REVERT: I 121 MET cc_start: 0.8353 (tpp) cc_final: 0.7085 (tpp) REVERT: I 127 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: I 335 MET cc_start: 0.3841 (tpp) cc_final: 0.3407 (tpp) REVERT: I 350 MET cc_start: 0.8797 (ptm) cc_final: 0.8254 (ptm) REVERT: J 67 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7783 (p90) REVERT: J 242 PHE cc_start: 0.8992 (m-80) cc_final: 0.8636 (m-80) REVERT: J 328 LEU cc_start: 0.9693 (tp) cc_final: 0.9160 (pp) REVERT: J 376 ASP cc_start: 0.8398 (m-30) cc_final: 0.8152 (t0) REVERT: L 3 MET cc_start: 0.3583 (mtt) cc_final: -0.0092 (tpp) REVERT: L 46 TRP cc_start: 0.2929 (m100) cc_final: 0.2671 (m100) REVERT: M 91 LEU cc_start: 0.4511 (OUTLIER) cc_final: 0.4096 (mm) REVERT: N 19 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8717 (pm20) REVERT: N 124 GLN cc_start: 0.9582 (OUTLIER) cc_final: 0.9161 (pt0) REVERT: N 125 PHE cc_start: 0.9414 (m-80) cc_final: 0.9156 (m-10) REVERT: N 180 HIS cc_start: 0.8358 (m-70) cc_final: 0.7889 (m170) REVERT: Z 217 MET cc_start: 0.8193 (tpp) cc_final: 0.7125 (tpp) REVERT: Z 657 MET cc_start: 0.8524 (ptt) cc_final: 0.8284 (ptt) REVERT: K 109 MET cc_start: 0.7375 (mmm) cc_final: 0.7117 (mmt) REVERT: K 187 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8861 (t) REVERT: K 188 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: K 290 ARG cc_start: 0.5746 (OUTLIER) cc_final: 0.5453 (tmt170) REVERT: K 409 HIS cc_start: 0.9305 (m-70) cc_final: 0.8966 (m-70) REVERT: P 58 MET cc_start: 0.9405 (ttm) cc_final: 0.9202 (ttt) REVERT: P 210 MET cc_start: 0.1046 (ptp) cc_final: 0.0160 (pmm) REVERT: P 254 MET cc_start: 0.5726 (tmm) cc_final: 0.5129 (tmm) REVERT: P 255 TYR cc_start: 0.5836 (m-80) cc_final: 0.5151 (m-80) REVERT: P 256 ILE cc_start: 0.2678 (OUTLIER) cc_final: 0.2405 (mt) outliers start: 113 outliers final: 77 residues processed: 327 average time/residue: 0.2333 time to fit residues: 128.0403 Evaluate side-chains 311 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 220 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 154 SER Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 220 THR Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 281 ARG Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 183 ASP Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 124 GLN Chi-restraints excluded: chain N residue 145 HIS Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 224 PHE Chi-restraints excluded: chain Z residue 317 SER Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 608 LEU Chi-restraints excluded: chain Z residue 625 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 660 LEU Chi-restraints excluded: chain Z residue 715 ILE Chi-restraints excluded: chain Z residue 757 THR Chi-restraints excluded: chain Z residue 813 ARG Chi-restraints excluded: chain Z residue 868 VAL Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 290 ARG Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 305 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: [368, 356, 34, 203, 45, 349, 237, 245, 343, 396, 293] chunk 368 optimal weight: 1.9990 chunk 356 optimal weight: 2.9990 chunk 34 optimal weight: 0.0040 chunk 203 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 349 optimal weight: 9.9990 chunk 237 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 343 optimal weight: 9.9990 chunk 396 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 549 ASN ** D 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 GLN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 268 GLN Z 738 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.087019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.066316 restraints weight = 371041.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.065354 restraints weight = 215432.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.065967 restraints weight = 172498.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.065752 restraints weight = 142449.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.065820 restraints weight = 141327.252| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 42306 Z= 0.182 Angle : 0.647 13.950 57204 Z= 0.327 Chirality : 0.043 0.358 6559 Planarity : 0.004 0.057 7376 Dihedral : 7.088 87.304 5911 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.66 % Favored : 96.32 % Rotamer: Outliers : 1.99 % Allowed : 15.09 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.12), residues: 5242 helix: 1.13 (0.10), residues: 2791 sheet: -0.29 (0.21), residues: 592 loop : 0.59 (0.16), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 346 TYR 0.017 0.002 TYR Z 549 PHE 0.029 0.002 PHE J 353 TRP 0.022 0.002 TRP M 163 HIS 0.005 0.001 HIS Z 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (42306) covalent geometry : angle 0.64659 / 0.33 (57204) hydrogen bonds : bond 0.03929 / 2.60 ( 2182) hydrogen bonds : angle 4.75159 / 3.38 ( 6285) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 227 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7407 (ttm) cc_final: 0.6541 (ptm) REVERT: A 197 MET cc_start: 0.7087 (tmm) cc_final: 0.6806 (tmm) REVERT: A 289 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8729 (pmt-80) REVERT: A 290 MET cc_start: 0.9428 (mmm) cc_final: 0.8752 (mmm) REVERT: A 318 ARG cc_start: 0.4944 (OUTLIER) cc_final: 0.3858 (mmm160) REVERT: A 396 MET cc_start: 0.8354 (mmm) cc_final: 0.7983 (mmm) REVERT: B 259 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7278 (t0) REVERT: B 334 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8697 (mm) REVERT: B 369 MET cc_start: 0.1671 (mtm) cc_final: -0.1240 (tpt) REVERT: B 424 MET cc_start: 0.8987 (mmt) cc_final: 0.8455 (mmm) REVERT: C 82 MET cc_start: 0.0407 (mmt) cc_final: 0.0162 (mmt) REVERT: C 249 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.7816 (ppp) REVERT: C 406 TRP cc_start: 0.9166 (t-100) cc_final: 0.8762 (t-100) REVERT: C 525 MET cc_start: 0.9178 (mtm) cc_final: 0.8752 (ptp) REVERT: C 595 MET cc_start: 0.8242 (tpp) cc_final: 0.7707 (tpt) REVERT: C 813 PHE cc_start: 0.9220 (t80) cc_final: 0.8855 (t80) REVERT: C 864 MET cc_start: 0.8187 (mtt) cc_final: 0.7214 (mmt) REVERT: C 894 MET cc_start: 0.8940 (mmm) cc_final: 0.8562 (mmm) REVERT: C 903 MET cc_start: 0.8336 (tpp) cc_final: 0.8038 (tpp) REVERT: D 291 LEU cc_start: 0.9341 (tp) cc_final: 0.8946 (tt) REVERT: D 356 MET cc_start: 0.8788 (mmt) cc_final: 0.8574 (mmm) REVERT: I 121 MET cc_start: 0.8424 (tpp) cc_final: 0.7246 (tpp) REVERT: I 127 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: I 335 MET cc_start: 0.3821 (tpp) cc_final: 0.3415 (tpp) REVERT: I 350 MET cc_start: 0.8801 (ptm) cc_final: 0.7544 (ppp) REVERT: J 67 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7558 (p90) REVERT: J 221 MET cc_start: 0.8205 (ttp) cc_final: 0.7913 (ttp) REVERT: J 328 LEU cc_start: 0.9668 (tp) cc_final: 0.9140 (pp) REVERT: J 376 ASP cc_start: 0.8336 (m-30) cc_final: 0.8073 (t0) REVERT: L 3 MET cc_start: 0.3540 (mtt) cc_final: 0.0309 (tpp) REVERT: L 46 TRP cc_start: 0.2897 (m100) cc_final: 0.2646 (m100) REVERT: M 91 LEU cc_start: 0.4646 (OUTLIER) cc_final: 0.4326 (mm) REVERT: M 97 THR cc_start: 0.1012 (OUTLIER) cc_final: 0.0761 (p) REVERT: N 124 GLN cc_start: 0.9607 (OUTLIER) cc_final: 0.9195 (pt0) REVERT: N 125 PHE cc_start: 0.9440 (m-80) cc_final: 0.9117 (m-10) REVERT: N 180 HIS cc_start: 0.8355 (m-70) cc_final: 0.7877 (m170) REVERT: Z 217 MET cc_start: 0.8282 (tpp) cc_final: 0.7242 (tpp) REVERT: Z 268 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7586 (pp30) REVERT: Z 479 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: K 109 MET cc_start: 0.7305 (mmm) cc_final: 0.6992 (mmt) REVERT: K 187 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8662 (t) REVERT: K 188 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: K 280 MET cc_start: 0.8479 (pmm) cc_final: 0.8152 (ppp) REVERT: K 290 ARG cc_start: 0.5656 (OUTLIER) cc_final: 0.5301 (tmt170) REVERT: K 409 HIS cc_start: 0.9310 (m-70) cc_final: 0.8976 (m-70) REVERT: P 58 MET cc_start: 0.9426 (ttm) cc_final: 0.9214 (ttt) REVERT: P 86 MET cc_start: 0.8943 (pmm) cc_final: 0.8472 (pmm) REVERT: P 210 MET cc_start: 0.0771 (ptp) cc_final: 0.0140 (pmm) REVERT: P 254 MET cc_start: 0.5630 (tmm) cc_final: 0.4722 (tmm) REVERT: P 255 TYR cc_start: 0.5519 (m-80) cc_final: 0.4630 (m-80) REVERT: P 256 ILE cc_start: 0.2985 (OUTLIER) cc_final: 0.2713 (mt) REVERT: P 368 MET cc_start: 0.3104 (ptt) cc_final: 0.1569 (pmm) REVERT: P 400 MET cc_start: 0.6667 (mtp) cc_final: 0.6162 (ppp) outliers start: 91 outliers final: 65 residues processed: 309 average time/residue: 0.2238 time to fit residues: 116.5747 Evaluate side-chains 301 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 220 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 154 SER Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 220 THR Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 281 ARG Chi-restraints excluded: chain J residue 306 PHE Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 183 ASP Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 124 GLN Chi-restraints excluded: chain N residue 145 HIS Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 224 PHE Chi-restraints excluded: chain Z residue 268 GLN Chi-restraints excluded: chain Z residue 479 GLU Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 608 LEU Chi-restraints excluded: chain Z residue 625 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 660 LEU Chi-restraints excluded: chain Z residue 715 ILE Chi-restraints excluded: chain Z residue 813 ARG Chi-restraints excluded: chain Z residue 868 VAL Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 290 ARG Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 305 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: [514, 307, 57, 195, 502, 500, 16, 142, 457, 224, 45] chunk 514 optimal weight: 4.9990 chunk 307 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 502 optimal weight: 9.9990 chunk 500 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 457 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 204 HIS ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 GLN ** Z 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.085940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.065462 restraints weight = 372042.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.064645 restraints weight = 228094.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.064435 restraints weight = 202195.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.064268 restraints weight = 174291.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.064368 restraints weight = 150996.166| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 42306 Z= 0.266 Angle : 0.723 13.383 57204 Z= 0.370 Chirality : 0.044 0.330 6559 Planarity : 0.005 0.051 7376 Dihedral : 7.120 87.760 5911 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.33 % Favored : 95.65 % Rotamer: Outliers : 2.01 % Allowed : 15.19 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.12), residues: 5242 helix: 0.89 (0.10), residues: 2795 sheet: -0.41 (0.21), residues: 594 loop : 0.44 (0.16), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 295 TYR 0.025 0.002 TYR Z 549 PHE 0.032 0.002 PHE Z 651 TRP 0.026 0.002 TRP M 163 HIS 0.006 0.001 HIS Z 573 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.27 (42306) covalent geometry : angle 0.72289 / 0.37 (57204) hydrogen bonds : bond 0.04293 / 2.85 ( 2182) hydrogen bonds : angle 4.96068 / 3.52 ( 6285) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10484 Ramachandran restraints generated. 5242 Oldfield, 0 Emsley, 5242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 220 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7538 (ttm) cc_final: 0.6603 (ptm) REVERT: A 197 MET cc_start: 0.7443 (tmm) cc_final: 0.7219 (tmm) REVERT: A 289 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8669 (pmt-80) REVERT: A 290 MET cc_start: 0.9420 (mmm) cc_final: 0.8762 (mmm) REVERT: A 318 ARG cc_start: 0.5080 (OUTLIER) cc_final: 0.4005 (mmm160) REVERT: A 396 MET cc_start: 0.8298 (mmm) cc_final: 0.7813 (mmm) REVERT: B 334 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8651 (mm) REVERT: B 369 MET cc_start: 0.1717 (mtm) cc_final: -0.1282 (tpt) REVERT: B 395 MET cc_start: 0.2201 (ttt) cc_final: 0.1985 (ppp) REVERT: C 249 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.7901 (ppp) REVERT: C 406 TRP cc_start: 0.9166 (t-100) cc_final: 0.8724 (t-100) REVERT: C 525 MET cc_start: 0.9138 (mtm) cc_final: 0.8681 (ptp) REVERT: C 595 MET cc_start: 0.8235 (tpp) cc_final: 0.7737 (tpt) REVERT: C 813 PHE cc_start: 0.9221 (t80) cc_final: 0.8846 (t80) REVERT: C 864 MET cc_start: 0.8101 (mtt) cc_final: 0.7071 (mmt) REVERT: C 894 MET cc_start: 0.8951 (mmm) cc_final: 0.8589 (mmm) REVERT: C 903 MET cc_start: 0.8339 (tpp) cc_final: 0.7995 (tpp) REVERT: D 291 LEU cc_start: 0.9328 (tp) cc_final: 0.8960 (tt) REVERT: D 356 MET cc_start: 0.8757 (mmt) cc_final: 0.8531 (mmm) REVERT: I 121 MET cc_start: 0.8474 (tpp) cc_final: 0.7315 (tpp) REVERT: I 335 MET cc_start: 0.3866 (tpp) cc_final: 0.3433 (tpp) REVERT: J 221 MET cc_start: 0.8206 (ttp) cc_final: 0.7869 (ttp) REVERT: J 376 ASP cc_start: 0.8354 (m-30) cc_final: 0.8072 (t0) REVERT: L 3 MET cc_start: 0.3601 (mtt) cc_final: 0.0189 (tpp) REVERT: L 46 TRP cc_start: 0.3090 (m100) cc_final: 0.2870 (m100) REVERT: M 91 LEU cc_start: 0.4845 (OUTLIER) cc_final: 0.4544 (mm) REVERT: M 97 THR cc_start: 0.1081 (OUTLIER) cc_final: 0.0837 (p) REVERT: N 124 GLN cc_start: 0.9557 (OUTLIER) cc_final: 0.9088 (pt0) REVERT: N 125 PHE cc_start: 0.9472 (m-80) cc_final: 0.9175 (m-10) REVERT: N 180 HIS cc_start: 0.8350 (m-70) cc_final: 0.7874 (m170) REVERT: Z 129 ILE cc_start: 0.1355 (OUTLIER) cc_final: 0.0964 (mt) REVERT: Z 217 MET cc_start: 0.8334 (tpp) cc_final: 0.7306 (tpp) REVERT: Z 657 MET cc_start: 0.8125 (ptt) cc_final: 0.7836 (ptt) REVERT: K 109 MET cc_start: 0.7359 (mmm) cc_final: 0.7031 (mmt) REVERT: K 187 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8709 (t) REVERT: K 188 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: K 409 HIS cc_start: 0.9269 (m-70) cc_final: 0.8959 (m-70) REVERT: P 58 MET cc_start: 0.9448 (ttm) cc_final: 0.9247 (ttt) REVERT: P 86 MET cc_start: 0.8883 (pmm) cc_final: 0.8543 (pmm) REVERT: P 210 MET cc_start: 0.1265 (ptp) cc_final: -0.0278 (pmm) REVERT: P 254 MET cc_start: 0.5659 (tmm) cc_final: 0.5104 (tmm) REVERT: P 255 TYR cc_start: 0.5401 (m-80) cc_final: 0.4757 (m-80) REVERT: P 256 ILE cc_start: 0.3087 (OUTLIER) cc_final: 0.2833 (mt) REVERT: P 368 MET cc_start: 0.3606 (ptt) cc_final: 0.3161 (ptp) REVERT: P 400 MET cc_start: 0.6645 (mtp) cc_final: 0.6170 (ppp) outliers start: 92 outliers final: 74 residues processed: 304 average time/residue: 0.2264 time to fit residues: 114.9906 Evaluate side-chains 300 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 215 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 154 SER Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 220 THR Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 281 ARG Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 183 ASP Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain N residue 8 GLN Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 124 GLN Chi-restraints excluded: chain N residue 145 HIS Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 224 PHE Chi-restraints excluded: chain Z residue 129 ILE Chi-restraints excluded: chain Z residue 427 ILE Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 608 LEU Chi-restraints excluded: chain Z residue 625 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 660 LEU Chi-restraints excluded: chain Z residue 715 ILE Chi-restraints excluded: chain Z residue 813 ARG Chi-restraints excluded: chain Z residue 868 VAL Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 ILE Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 305 MET Chi-restraints excluded: chain P residue 394 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: [99, 457, 342, 78, 449, 63, 420, 480, 521, 334, 184] chunk 99 optimal weight: 0.9990 chunk 457 optimal weight: 5.9990 chunk 342 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 449 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 420 optimal weight: 0.9980 chunk 480 optimal weight: 9.9990 chunk 521 optimal weight: 20.0000 chunk 334 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN ** D 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 716 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.087822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.067534 restraints weight = 369498.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.066667 restraints weight = 217281.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.067097 restraints weight = 159053.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.066915 restraints weight = 146013.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.066996 restraints weight = 133444.546| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 42306 Z= 0.130 Angle : 0.638 14.660 57204 Z= 0.317 Chirality : 0.043 0.373 6559 Planarity : 0.004 0.050 7376 Dihedral : 6.918 87.142 5911 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.59 % Favored : 96.39 % Rotamer: Outliers : 1.66 % Allowed : 15.61 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.12), residues: 5242 helix: 1.28 (0.10), residues: 2786 sheet: -0.39 (0.21), residues: 587 loop : 0.64 (0.16), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 346 TYR 0.014 0.001 TYR Z 549 PHE 0.042 0.002 PHE J 353 TRP 0.026 0.002 TRP M 163 HIS 0.011 0.001 HIS N 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (42306) covalent geometry : angle 0.63802 / 0.32 (57204) hydrogen bonds : bond 0.03630 / 2.38 ( 2182) hydrogen bonds : angle 4.63819 / 3.30 ( 6285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9564.97 seconds wall clock time: 165 minutes 17.77 seconds (9917.77 seconds total)