Starting phenix.real_space_refine on Sat Oct 31 10:01:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36bl_77358/10_2026/36bl_77358.cif Found real_map, /net/cci-nas-00/data/ceres_data/36bl_77358/10_2026/36bl_77358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/36bl_77358/10_2026/36bl_77358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36bl_77358/10_2026/36bl_77358.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/36bl_77358/10_2026/36bl_77358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36bl_77358/10_2026/36bl_77358.map" } resolution = 3.91 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 180 5.16 5 C 26215 2.51 5 N 7065 2.21 5 O 8044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.04s 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: 41522 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2962 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 20, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3011 Classifications: {'peptide': 384} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 364} Chain: "C" Number of atoms: 6573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 847, 6573 Classifications: {'peptide': 847} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 817} Chain breaks: 2 Chain: "D" Number of atoms: 3804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3804 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 451} Chain: "I" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2994 Classifications: {'peptide': 381} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 364} 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: "K" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3037 Classifications: {'peptide': 383} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 364} 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: "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: "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: "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: 8.72, per 1000 atoms: 0.21 Number of scatterers: 41522 At special positions: 0 Unit cell: (215.888, 219.032, 199.12, 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 180 16.00 P 18 15.00 O 8044 8.00 N 7065 7.00 C 26215 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: 3.97 Conformation dependent library (CDL) restraints added in 2.1 seconds 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9870 Finding SS restraints... Secondary structure from input PDB file: 262 helices and 23 sheets defined 59.2% alpha, 8.7% 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 45 through 66 removed outlier: 4.192A pdb=" N LYS A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.014A pdb=" N MET A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.761A 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: 4.400A 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 281 removed outlier: 3.624A pdb=" N VAL A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 4.039A pdb=" N MET A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 3.878A 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 393 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 415 through 433 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'B' and resid 55 through 83 removed outlier: 3.558A pdb=" N LEU B 59 " --> pdb=" O CYS B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 101 removed outlier: 4.277A pdb=" N GLU B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.657A 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 211 removed outlier: 4.057A 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 removed outlier: 3.755A pdb=" N LYS B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 290 Processing helix chain 'B' and resid 298 through 316 removed outlier: 4.371A pdb=" N ILE B 302 " --> pdb=" O GLY B 298 " (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 429 Processing helix chain 'C' and resid 41 through 58 removed outlier: 3.738A pdb=" N THR C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) 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 removed outlier: 3.545A pdb=" N LYS C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) 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 126 removed outlier: 3.933A pdb=" N VAL C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 removed outlier: 3.542A pdb=" N LEU C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 149 removed outlier: 3.540A pdb=" N TRP C 149 " --> pdb=" O PHE C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 150 through 178 removed outlier: 3.527A pdb=" N ILE C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 214 removed outlier: 3.609A pdb=" N THR C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) 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 removed outlier: 3.514A pdb=" N TYR C 248 " --> pdb=" O ARG C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 275 Processing helix chain 'C' and resid 277 through 289 Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 303 through 318 removed outlier: 3.573A pdb=" N ILE C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 334 through 346 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 365 through 372 Processing helix chain 'C' and resid 375 through 391 Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 411 through 412 No H-bonds generated for 'chain 'C' and resid 411 through 412' Processing helix chain 'C' and resid 413 through 426 removed outlier: 4.145A pdb=" N ILE C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY C 423 " --> pdb=" O VAL C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 438 removed outlier: 4.283A pdb=" N GLN C 434 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS C 438 " --> pdb=" O GLN C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 442 removed outlier: 3.607A pdb=" N VAL C 442 " --> pdb=" O TYR C 439 " (cutoff:3.500A) No H-bonds generated for '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: 5.108A pdb=" N ASP C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TYR C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 4.369A 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 removed outlier: 3.529A pdb=" N MET C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 553 Processing helix chain 'C' and resid 556 through 561 removed outlier: 5.820A pdb=" N ASP C 561 " --> pdb=" O LEU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 574 removed outlier: 3.787A pdb=" N TYR C 574 " --> pdb=" O LEU C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 580 removed outlier: 3.704A pdb=" N GLN C 580 " --> pdb=" O GLN C 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 577 through 580' Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 608 Processing helix chain 'C' and resid 613 through 625 removed outlier: 3.685A pdb=" N ILE C 617 " --> pdb=" O ASP C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 747 removed outlier: 3.683A pdb=" N ALA C 744 " --> pdb=" O VAL C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 768 removed outlier: 3.611A pdb=" N MET C 756 " --> pdb=" O ILE C 752 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG C 759 " --> pdb=" O GLU C 755 " (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: 3.512A pdb=" N PHE C 793 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 795 " --> pdb=" O LYS C 791 " (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 removed outlier: 3.678A pdb=" N THR C 884 " --> pdb=" O SER C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 897 removed outlier: 3.937A pdb=" N MET C 894 " --> pdb=" O SER C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 907 removed outlier: 3.567A pdb=" N LEU C 904 " --> pdb=" O PHE C 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.637A pdb=" N THR D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 7 " --> pdb=" O GLU D 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2 through 7' Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 28 through 43 removed outlier: 4.083A pdb=" N THR D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.989A 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 removed outlier: 3.548A pdb=" N VAL D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 106 Processing helix chain 'D' and resid 109 through 122 Processing helix chain 'D' and resid 127 through 132 removed outlier: 4.255A pdb=" N THR D 131 " --> pdb=" O LEU D 128 " (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 removed outlier: 3.718A pdb=" N ARG D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 188 removed outlier: 3.585A pdb=" N MET D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 207 removed outlier: 3.702A pdb=" N GLN D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.967A 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 251 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 261 removed outlier: 4.075A pdb=" N VAL D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 273 removed outlier: 3.776A pdb=" N PHE D 267 " --> pdb=" O ILE D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 removed outlier: 4.085A pdb=" N ARG D 281 " --> pdb=" O TYR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 297 removed outlier: 3.765A pdb=" N ARG D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 313 Processing helix chain 'D' and resid 322 through 330 Processing helix chain 'D' and resid 331 through 338 Processing helix chain 'D' and resid 339 through 347 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 370 Processing helix chain 'D' and resid 375 through 381 Processing helix chain 'D' and resid 383 through 395 Processing helix chain 'D' and resid 397 through 408 removed outlier: 3.564A pdb=" N MET D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 417 Processing helix chain 'D' and resid 426 through 442 Processing helix chain 'D' and resid 444 through 449 removed outlier: 3.507A pdb=" N LEU D 448 " --> pdb=" O GLY D 444 " (cutoff:3.500A) 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 Processing helix chain 'I' and resid 131 through 138 removed outlier: 3.807A pdb=" N MET I 137 " --> pdb=" O LEU I 133 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET I 138 " --> pdb=" O VAL I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 150 removed outlier: 3.628A pdb=" N MET I 149 " --> pdb=" O THR I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 164 removed outlier: 3.556A pdb=" N GLU I 162 " --> pdb=" O LYS I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 170 removed outlier: 3.506A pdb=" N VAL I 168 " --> pdb=" O ILE I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 178 Processing helix chain 'I' and resid 194 through 206 removed outlier: 3.518A pdb=" N THR I 206 " --> pdb=" O VAL I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 219 Processing helix chain 'I' and resid 224 through 240 removed outlier: 3.707A pdb=" N MET I 229 " --> pdb=" O GLU I 225 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL I 230 " --> pdb=" O GLY I 226 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG I 238 " --> pdb=" O PHE I 234 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU I 239 " --> pdb=" O VAL I 235 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS I 240 " --> pdb=" O MET I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 282 removed outlier: 4.290A pdb=" N GLN I 269 " --> pdb=" O ASP I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 306 Processing helix chain 'I' and resid 320 through 332 Processing helix chain 'I' and resid 342 through 350 removed outlier: 3.896A pdb=" N VAL I 346 " --> pdb=" O ASN I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 372 Processing helix chain 'I' and resid 378 through 396 removed outlier: 3.525A pdb=" N MET I 390 " --> pdb=" O VAL I 386 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN I 391 " --> pdb=" O GLY I 387 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS I 392 " --> pdb=" O LYS I 388 " (cutoff:3.500A) 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: 4.270A pdb=" N SER J 154 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP J 155 " --> pdb=" O PRO J 152 " (cutoff:3.500A) 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: 3.612A pdb=" N TYR J 198 " --> pdb=" O GLN J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 230 Processing helix chain 'J' and resid 240 through 243 Processing helix chain 'J' and resid 248 through 264 Processing helix chain 'J' and resid 273 through 277 Processing helix chain 'J' and resid 286 through 305 Processing helix chain 'J' and resid 320 through 324 removed outlier: 3.870A pdb=" N LEU J 324 " --> pdb=" O ALA J 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 330 removed outlier: 3.772A pdb=" N LEU J 329 " --> pdb=" O ASP J 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 345 through 359 removed outlier: 4.125A pdb=" N LYS J 359 " --> pdb=" O THR J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 367 through 373 removed outlier: 4.228A pdb=" N LEU J 371 " --> pdb=" O ASP J 367 " (cutoff:3.500A) removed outlier: 3.643A 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: 3.503A pdb=" N LYS J 416 " --> pdb=" O ALA J 412 " (cutoff:3.500A) 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 172 removed outlier: 3.974A pdb=" N THR K 171 " --> pdb=" O VAL K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 183 Processing helix chain 'K' and resid 186 through 203 removed outlier: 3.513A pdb=" N VAL K 196 " --> pdb=" O GLU K 192 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE K 197 " --> pdb=" O LEU K 193 " (cutoff:3.500A) removed outlier: 4.449A 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 Processing helix chain 'K' and resid 248 through 252 removed outlier: 3.591A pdb=" N VAL K 252 " --> pdb=" O ALA K 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 248 through 252' Processing helix chain 'K' and resid 257 through 273 Processing helix chain 'K' and resid 283 through 286 Processing helix chain 'K' and resid 295 through 314 Processing helix chain 'K' and resid 329 through 333 Processing helix chain 'K' and resid 353 through 367 removed outlier: 4.106A 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 Processing helix chain 'L' and resid 40 through 44 removed outlier: 3.551A pdb=" N LEU L 43 " --> pdb=" O GLU L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 130 removed outlier: 3.777A pdb=" N MET L 125 " --> pdb=" O ILE L 121 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY L 127 " --> pdb=" O ASN L 123 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU L 129 " --> pdb=" O MET L 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 20 removed outlier: 3.645A 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 91 Processing helix chain 'N' and resid 4 through 12 removed outlier: 3.513A pdb=" N MET N 11 " --> pdb=" O HIS N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 25 Processing helix chain 'N' and resid 26 through 31 Processing helix chain 'N' and resid 38 through 46 removed outlier: 3.798A pdb=" N TRP N 42 " --> pdb=" O ILE N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 59 removed outlier: 3.763A pdb=" N LYS N 58 " --> pdb=" O PHE N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 74 through 83 Processing helix chain 'N' and resid 84 through 93 Processing helix chain 'N' and resid 109 through 117 removed outlier: 3.531A pdb=" N LEU N 113 " --> pdb=" O THR N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 129 Processing helix chain 'N' and resid 142 through 151 removed outlier: 3.750A pdb=" N ARG N 146 " --> pdb=" O ILE N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 162 Processing helix chain 'N' and resid 176 through 184 Processing helix chain 'N' and resid 186 through 198 Processing helix chain 'N' and resid 217 through 227 Processing helix chain 'P' and resid 20 through 24 Processing helix chain 'P' and resid 26 through 73 Processing helix chain 'P' and resid 167 through 169 No H-bonds generated for 'chain 'P' and resid 167 through 169' 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 Processing helix chain 'P' and resid 203 through 211 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: 3.555A 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 366 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 helix chain 'Z' and resid 6 through 11 Processing helix chain 'Z' and resid 12 through 15 removed outlier: 3.626A pdb=" N GLU Z 15 " --> pdb=" O LEU Z 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 12 through 15' Processing helix chain 'Z' and resid 17 through 30 removed outlier: 4.016A pdb=" N ASN Z 30 " --> pdb=" O GLU Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 40 removed outlier: 7.549A pdb=" N SER Z 37 " --> pdb=" O ASP Z 33 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU Z 38 " --> pdb=" O GLN Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 52 removed outlier: 3.575A pdb=" N ILE Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 57 through 73 Processing helix chain 'Z' and resid 74 through 83 removed outlier: 4.082A pdb=" N VAL Z 79 " --> pdb=" O TYR Z 75 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS Z 80 " --> pdb=" O GLU Z 76 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR Z 81 " --> pdb=" O SER Z 77 " (cutoff:3.500A) Processing helix chain 'Z' and resid 84 through 89 removed outlier: 6.454A pdb=" N ASP Z 87 " --> pdb=" O ALA Z 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 117 removed outlier: 3.703A pdb=" N ILE Z 106 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU Z 107 " --> pdb=" O SER Z 103 " (cutoff:3.500A) Processing helix chain 'Z' and resid 122 through 127 removed outlier: 3.505A pdb=" N ASP Z 127 " --> pdb=" O TYR Z 124 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 148 Processing helix chain 'Z' and resid 149 through 158 removed outlier: 3.860A pdb=" N ALA Z 157 " --> pdb=" O ALA Z 153 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU Z 158 " --> pdb=" O LEU Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 177 Processing helix chain 'Z' and resid 178 through 197 removed outlier: 3.536A pdb=" N THR Z 195 " --> pdb=" O THR Z 191 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL Z 197 " --> pdb=" O ALA Z 193 " (cutoff:3.500A) Processing helix chain 'Z' and resid 199 through 217 removed outlier: 3.510A pdb=" N ASP Z 212 " --> pdb=" O ARG Z 208 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET Z 217 " --> pdb=" O PHE Z 213 " (cutoff:3.500A) Processing helix chain 'Z' and resid 221 through 233 Processing helix chain 'Z' and resid 234 through 249 removed outlier: 3.817A pdb=" N ALA Z 238 " --> pdb=" O ASP Z 234 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS Z 244 " --> pdb=" O GLN Z 240 " (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 removed outlier: 3.806A pdb=" N LEU Z 290 " --> pdb=" O LEU Z 286 " (cutoff:3.500A) Processing helix chain 'Z' and resid 292 through 306 Processing helix chain 'Z' and resid 310 through 321 removed outlier: 4.056A pdb=" N LEU Z 314 " --> pdb=" O ASP Z 310 " (cutoff:3.500A) Processing helix chain 'Z' and resid 325 through 340 removed outlier: 3.589A pdb=" N MET Z 339 " --> pdb=" O ALA Z 335 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS Z 340 " --> pdb=" O ASN Z 336 " (cutoff:3.500A) Processing helix chain 'Z' and resid 346 through 352 Processing helix chain 'Z' and resid 352 through 357 Processing helix chain 'Z' and resid 358 through 360 No H-bonds generated for 'chain 'Z' and resid 358 through 360' Processing helix chain 'Z' and resid 361 through 375 removed outlier: 3.717A pdb=" N LEU Z 371 " --> pdb=" O ALA Z 367 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY Z 372 " --> pdb=" O THR Z 368 " (cutoff:3.500A) Processing helix chain 'Z' and resid 381 through 386 Processing helix chain 'Z' and resid 387 through 390 Processing helix chain 'Z' and resid 397 through 412 removed outlier: 3.538A pdb=" N LEU Z 410 " --> pdb=" O TYR Z 406 " (cutoff:3.500A) Processing helix chain 'Z' and resid 418 through 433 removed outlier: 3.721A pdb=" N TYR Z 422 " --> pdb=" O ASP Z 418 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY Z 432 " --> pdb=" O VAL Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 436 through 454 removed outlier: 3.642A pdb=" N LEU Z 448 " --> pdb=" O HIS Z 444 " (cutoff:3.500A) Processing helix chain 'Z' and resid 459 through 471 Processing helix chain 'Z' and resid 474 through 489 removed outlier: 4.644A pdb=" N GLU Z 479 " --> pdb=" O ALA Z 475 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA Z 480 " --> pdb=" O THR Z 476 " (cutoff:3.500A) Processing helix chain 'Z' and resid 494 through 508 removed outlier: 3.723A pdb=" N GLN Z 506 " --> pdb=" O PHE Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 510 through 525 removed outlier: 3.602A pdb=" N ALA Z 522 " --> pdb=" O ALA Z 518 " (cutoff:3.500A) Processing helix chain 'Z' and resid 528 through 531 Processing helix chain 'Z' and resid 532 through 542 Processing helix chain 'Z' and resid 544 through 559 removed outlier: 3.580A pdb=" N PHE Z 553 " --> pdb=" O TYR Z 549 " (cutoff:3.500A) Processing helix chain 'Z' and resid 564 through 578 Processing helix chain 'Z' and resid 580 through 595 removed outlier: 3.991A pdb=" N GLY Z 592 " --> pdb=" O VAL Z 588 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE Z 593 " --> pdb=" O ILE Z 589 " (cutoff:3.500A) Processing helix chain 'Z' and resid 596 through 600 removed outlier: 3.637A pdb=" N TYR Z 599 " --> pdb=" O LEU Z 596 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR Z 600 " --> pdb=" O ARG Z 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 596 through 600' Processing helix chain 'Z' and resid 601 through 612 removed outlier: 3.863A pdb=" N ILE Z 605 " --> pdb=" O THR Z 601 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU Z 608 " --> pdb=" O ARG Z 604 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU Z 609 " --> pdb=" O ILE Z 605 " (cutoff:3.500A) Processing helix chain 'Z' and resid 614 through 629 Processing helix chain 'Z' and resid 634 through 645 removed outlier: 3.608A pdb=" N ILE Z 638 " --> pdb=" O LEU Z 634 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL Z 640 " --> pdb=" O SER Z 636 " (cutoff:3.500A) Proline residue: Z 643 - end of helix Processing helix chain 'Z' and resid 649 through 664 Processing helix chain 'Z' and resid 672 through 688 removed outlier: 4.329A pdb=" N ALA Z 676 " --> pdb=" O ASN Z 672 " (cutoff:3.500A) Processing helix chain 'Z' and resid 692 through 707 removed outlier: 3.581A pdb=" N GLY Z 704 " --> pdb=" O CYS Z 700 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN Z 707 " --> pdb=" O GLN Z 703 " (cutoff:3.500A) Processing helix chain 'Z' and resid 726 through 738 removed outlier: 3.748A 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: 3.650A pdb=" N HIS Z 747 " --> pdb=" O PRO Z 744 " (cutoff:3.500A) Processing helix chain 'Z' and resid 804 through 821 removed outlier: 4.275A pdb=" N ALA Z 808 " --> pdb=" O LEU Z 804 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG Z 809 " --> pdb=" O SER Z 805 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA Z 812 " --> pdb=" O ALA Z 808 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG Z 813 " --> pdb=" O ARG Z 809 " (cutoff:3.500A) Processing helix chain 'Z' and resid 875 through 879 Processing helix chain 'Z' and resid 919 through 925 Processing helix chain 'Z' and resid 937 through 942 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 107 removed outlier: 5.550A pdb=" N CYS A 102 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 5.845A 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 117 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 157 Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 201 removed outlier: 6.422A pdb=" N CYS A 304 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N MET A 352 " --> pdb=" O CYS A 304 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ILE A 306 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA A 354 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE A 308 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE A 246 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N THR A 355 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 248 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY A 245 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N VAL A 375 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 6.279A 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: 6.509A pdb=" N THR B 243 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE B 280 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 245 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP B 282 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 247 " --> pdb=" O ASP B 282 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N SER B 277 " --> pdb=" O LYS B 323 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE B 325 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL B 279 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ALA B 327 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE B 281 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLY B 218 " --> pdb=" O ARG B 346 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ILE B 348 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE B 220 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE B 350 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.394A 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 955 through 956 removed outlier: 6.017A pdb=" N PHE C 912 " --> pdb=" O GLY C 979 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL C 981 " --> pdb=" O PHE C 912 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU C 914 " --> pdb=" O VAL C 981 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C 983 " --> pdb=" O LEU C 914 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 916 " --> pdb=" O LEU C 983 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS C 985 " --> pdb=" O LEU C 916 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 945 through 952 removed outlier: 5.823A pdb=" N GLY C 947 " --> pdb=" O GLN C 931 " (cutoff:3.500A) removed outlier: 4.960A 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: 6.652A pdb=" N SER I 243 " --> pdb=" O LYS I 289 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE I 291 " --> pdb=" O SER I 243 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE I 245 " --> pdb=" O ILE I 291 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL I 185 " --> pdb=" O MET I 292 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG I 312 " --> pdb=" O GLY I 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 233 through 238 removed outlier: 6.598A pdb=" N SER J 267 " --> pdb=" O LYS J 313 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE J 315 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE J 269 " --> pdb=" O ILE J 315 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA J 317 " --> pdb=" O ILE J 269 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE J 271 " --> pdb=" O ALA J 317 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY J 208 " --> pdb=" O ARG J 336 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE J 338 " --> pdb=" O GLY J 208 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU J 210 " --> pdb=" O ILE J 338 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 242 through 247 removed outlier: 6.356A pdb=" N CYS K 276 " --> pdb=" O LYS K 322 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE K 324 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE K 278 " --> pdb=" O ILE K 324 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA K 326 " --> pdb=" O ILE K 278 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET K 280 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL K 218 " --> pdb=" O MET K 325 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR K 327 " --> pdb=" O VAL K 218 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU K 220 " --> pdb=" O THR K 327 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY K 217 " --> pdb=" O ARG K 345 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL K 347 " --> pdb=" O GLY K 217 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU K 219 " --> pdb=" O VAL K 347 " (cutoff:3.500A) Processing sheet with id=AB1, 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 52 removed outlier: 3.946A pdb=" N TRP L 46 " --> pdb=" O LEU L 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 65 through 68 current: chain 'L' and resid 86 through 90 Processing sheet with id=AB2, first strand: chain 'M' and resid 2 through 5 removed outlier: 6.624A pdb=" N LYS M 3 " --> pdb=" O LEU M 328 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY M 325 " --> pdb=" O GLN M 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 8 through 10 Processing sheet with id=AB4, 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=AB5, first strand: chain 'M' and resid 85 through 86 removed outlier: 3.824A pdb=" N ARG M 85 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE M 408 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL M 403 " --> pdb=" O GLN M 387 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN M 387 " --> pdb=" O VAL M 403 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 96 through 102 removed outlier: 3.709A pdb=" N ALA M 98 " --> pdb=" O GLY M 112 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG M 129 " --> pdb=" O VAL M 120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 139 through 144 removed outlier: 4.114A pdb=" N GLN M 159 " --> pdb=" O SER M 155 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG M 172 " --> pdb=" O ILE M 162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 181 through 187 removed outlier: 3.995A pdb=" N ASP M 183 " --> pdb=" O ALA M 196 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN M 192 " --> pdb=" O ILE M 187 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE M 202 " --> pdb=" O THR M 215 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR M 215 " --> pdb=" O ILE M 202 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU M 204 " --> pdb=" O ILE M 213 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR M 211 " --> pdb=" O GLU M 206 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 226 through 233 removed outlier: 3.904A pdb=" N SER M 228 " --> pdb=" O GLY M 262 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN M 272 " --> pdb=" O GLN M 278 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN M 278 " --> pdb=" O ASN M 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 171 through 172 removed outlier: 4.484A pdb=" N PHE P 243 " --> pdb=" O VAL P 172 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR P 276 " --> pdb=" O LYS P 322 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU P 324 " --> pdb=" O THR P 276 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE P 278 " --> pdb=" O LEU P 324 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ALA P 326 " --> pdb=" O ILE P 278 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE P 280 " --> pdb=" O ALA P 326 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG P 345 " --> pdb=" O GLY P 217 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Z' and resid 713 through 715 Processing sheet with id=AC3, first strand: chain 'Z' and resid 718 through 719 removed outlier: 3.701A pdb=" N THR Z 724 " --> pdb=" O ASN Z 719 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Z' and resid 758 through 762 Processing sheet with id=AC5, first strand: chain 'Z' and resid 768 through 769 2150 hydrogen bonds defined for protein. 6165 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: 12.09 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13854 1.34 - 1.46: 8733 1.46 - 1.58: 19286 1.58 - 1.70: 21 1.70 - 1.82: 310 Bond restraints: 42204 Sorted by residual: bond pdb=" CB LYS A 50 " pdb=" CG LYS A 50 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 2.95e+00 bond pdb=" SD MET N 11 " pdb=" CE MET N 11 " ideal model delta sigma weight residual 1.791 1.754 0.037 2.50e-02 1.60e+03 2.19e+00 bond pdb=" CB LYS I 108 " pdb=" CG LYS I 108 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CA GLN K 282 " pdb=" CB GLN K 282 " ideal model delta sigma weight residual 1.532 1.512 0.020 1.48e-02 4.57e+03 1.86e+00 bond pdb=" SD MET I 121 " pdb=" CE MET I 121 " ideal model delta sigma weight residual 1.791 1.757 0.034 2.50e-02 1.60e+03 1.85e+00 ... (remaining 42199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 56623 2.93 - 5.85: 357 5.85 - 8.78: 69 8.78 - 11.71: 11 11.71 - 14.64: 3 Bond angle restraints: 57063 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 117.23 110.42 6.81 1.36e+00 5.41e-01 2.51e+01 angle pdb=" CA MET N 59 " pdb=" CB MET N 59 " pdb=" CG MET N 59 " ideal model delta sigma weight residual 114.10 122.46 -8.36 2.00e+00 2.50e-01 1.75e+01 angle pdb=" CA LEU C 51 " pdb=" CB LEU C 51 " pdb=" CG LEU C 51 " ideal model delta sigma weight residual 116.30 130.94 -14.64 3.50e+00 8.16e-02 1.75e+01 angle pdb=" C TRP Z 742 " pdb=" N PHE Z 743 " pdb=" CA PHE Z 743 " ideal model delta sigma weight residual 120.58 125.89 -5.31 1.32e+00 5.74e-01 1.62e+01 angle pdb=" N ILE P 286 " pdb=" CA ILE P 286 " pdb=" C ILE P 286 " ideal model delta sigma weight residual 113.53 109.63 3.90 9.80e-01 1.04e+00 1.58e+01 ... (remaining 57058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 23173 17.94 - 35.88: 2258 35.88 - 53.82: 462 53.82 - 71.76: 79 71.76 - 89.70: 36 Dihedral angle restraints: 26008 sinusoidal: 10743 harmonic: 15265 Sorted by residual: dihedral pdb=" CA ASN D 7 " pdb=" C ASN D 7 " pdb=" N TYR D 8 " pdb=" CA TYR D 8 " ideal model delta harmonic sigma weight residual 180.00 145.06 34.94 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA TYR B 292 " pdb=" C TYR B 292 " pdb=" N ASP B 293 " pdb=" CA ASP B 293 " ideal model delta harmonic sigma weight residual 180.00 148.79 31.21 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA ASP B 293 " pdb=" C ASP B 293 " pdb=" N SER B 294 " pdb=" CA SER B 294 " ideal model delta harmonic sigma weight residual 180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 26005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 4740 0.040 - 0.080: 1311 0.080 - 0.120: 433 0.120 - 0.161: 54 0.161 - 0.201: 5 Chirality restraints: 6543 Sorted by residual: chirality pdb=" CG LEU C 834 " pdb=" CB LEU C 834 " pdb=" CD1 LEU C 834 " pdb=" CD2 LEU C 834 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL Z 914 " pdb=" N VAL Z 914 " pdb=" C VAL Z 914 " pdb=" CB VAL Z 914 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA VAL J 92 " pdb=" N VAL J 92 " pdb=" C VAL J 92 " pdb=" CB VAL J 92 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 6540 not shown) Planarity restraints: 7356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 428 " -0.016 2.00e-02 2.50e+03 1.89e-02 8.96e+00 pdb=" CG TRP C 428 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP C 428 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP C 428 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 428 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 428 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 428 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 428 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 428 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 428 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 46 " -0.019 2.00e-02 2.50e+03 1.44e-02 5.16e+00 pdb=" CG TRP L 46 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP L 46 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP L 46 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 46 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 46 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 46 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 46 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 46 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP L 46 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 833 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" CD GLN C 833 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN C 833 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN C 833 " 0.012 2.00e-02 2.50e+03 ... (remaining 7353 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 15436 2.89 - 3.39: 44091 3.39 - 3.89: 72806 3.89 - 4.40: 83708 4.40 - 4.90: 133714 Nonbonded interactions: 349755 Sorted by model distance: nonbonded pdb=" O ASP C 988 " pdb=" OD1 ASP C 988 " model vdw 2.382 3.040 nonbonded pdb=" O ASN M 381 " pdb=" OD1 ASP M 382 " model vdw 2.507 3.040 nonbonded pdb=" O GLN C 275 " pdb=" OD1 ASN C 276 " model vdw 2.515 3.040 nonbonded pdb=" O VAL I 235 " pdb=" OE1 GLU I 239 " model vdw 2.529 3.040 nonbonded pdb=" N ASP C 865 " pdb=" OD1 ASP C 865 " model vdw 2.530 3.120 ... (remaining 349750 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: 12.690 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: 0.030 Extract box with map and model: 0.850 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 42.300 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 42204 Z= 0.128 Angle : 0.660 14.636 57063 Z= 0.353 Chirality : 0.041 0.201 6543 Planarity : 0.004 0.065 7356 Dihedral : 14.710 89.702 16138 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.30 % Favored : 97.65 % Rotamer: Outliers : 0.94 % Allowed : 13.69 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.83 (0.12), residues: 5228 helix: 0.77 (0.10), residues: 2724 sheet: 0.14 (0.20), residues: 619 loop : 0.66 (0.15), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 832 TYR 0.034 0.001 TYR B 292 PHE 0.027 0.001 PHE Z 338 TRP 0.051 0.002 TRP C 428 HIS 0.016 0.001 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (42204) covalent geometry : angle 0.66032 / 0.35 (57063) hydrogen bonds : bond 0.21356 / 14.15 ( 2150) hydrogen bonds : angle 7.32648 / 5.22 ( 6165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 1.722 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.1544 (ttm) cc_final: -0.0870 (mtt) REVERT: A 290 MET cc_start: 0.3344 (mtt) cc_final: 0.1023 (ppp) REVERT: A 297 MET cc_start: 0.2878 (ptm) cc_final: 0.2438 (ppp) REVERT: B 171 MET cc_start: 0.2860 (mtt) cc_final: 0.2552 (mtt) REVERT: B 173 MET cc_start: 0.5353 (mtt) cc_final: 0.4576 (mmp) REVERT: C 124 MET cc_start: 0.7864 (ttp) cc_final: 0.7079 (tmm) REVERT: C 379 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7973 (pp30) REVERT: C 415 MET cc_start: 0.7978 (mmm) cc_final: 0.7570 (mmm) REVERT: C 503 ASP cc_start: 0.9088 (t0) cc_final: 0.8734 (p0) REVERT: C 583 ASP cc_start: 0.9399 (m-30) cc_final: 0.9101 (p0) REVERT: C 595 MET cc_start: 0.5395 (ttp) cc_final: 0.5168 (ptm) REVERT: C 815 MET cc_start: 0.8127 (mtp) cc_final: 0.7248 (mtt) REVERT: C 818 CYS cc_start: 0.8975 (m) cc_final: 0.8306 (m) REVERT: I 174 PHE cc_start: 0.9255 (m-10) cc_final: 0.9050 (m-10) REVERT: I 209 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.6799 (tptp) REVERT: I 272 MET cc_start: 0.9667 (ptm) cc_final: 0.9294 (ppp) REVERT: J 238 ASN cc_start: 0.8032 (t0) cc_final: 0.7605 (t0) REVERT: J 273 GLU cc_start: 0.8802 (pt0) cc_final: 0.8444 (pp20) REVERT: J 296 LEU cc_start: 0.9164 (tt) cc_final: 0.8952 (pp) REVERT: J 347 ARG cc_start: 0.9193 (ttt180) cc_final: 0.8857 (tmm-80) REVERT: K 109 MET cc_start: 0.8131 (mmp) cc_final: 0.7852 (mmp) REVERT: K 312 MET cc_start: 0.7496 (ttm) cc_final: 0.6776 (ptm) REVERT: K 416 MET cc_start: 0.3085 (ppp) cc_final: 0.2607 (ppp) REVERT: M 14 PHE cc_start: 0.8391 (p90) cc_final: 0.8102 (p90) REVERT: M 156 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8575 (pt0) REVERT: M 311 MET cc_start: 0.3879 (tpp) cc_final: 0.3603 (tpt) REVERT: N 1 MET cc_start: 0.8923 (mtt) cc_final: 0.8395 (ptm) REVERT: P 58 MET cc_start: 0.3262 (ttm) cc_final: 0.2850 (ttt) REVERT: P 210 MET cc_start: 0.1939 (mtp) cc_final: 0.1428 (mtp) REVERT: P 368 MET cc_start: 0.1201 (mtp) cc_final: 0.0776 (ptm) REVERT: Z 217 MET cc_start: 0.4481 (ptt) cc_final: 0.4277 (ppp) REVERT: Z 241 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8114 (mt) REVERT: Z 290 LEU cc_start: 0.9387 (mt) cc_final: 0.9107 (mp) REVERT: Z 429 GLU cc_start: 0.8528 (mp0) cc_final: 0.7184 (tm-30) REVERT: Z 455 MET cc_start: 0.8233 (ppp) cc_final: 0.7905 (ppp) REVERT: Z 489 MET cc_start: 0.8228 (mmt) cc_final: 0.7682 (mmp) REVERT: Z 657 MET cc_start: 0.9050 (pmm) cc_final: 0.8306 (pmm) REVERT: Z 773 MET cc_start: 0.7924 (mpp) cc_final: 0.7430 (mpp) outliers start: 43 outliers final: 36 residues processed: 322 average time/residue: 0.2426 time to fit residues: 132.2468 Evaluate side-chains 315 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 276 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 324 ILE Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain N residue 23 HIS Chi-restraints excluded: chain N residue 37 ARG Chi-restraints excluded: chain N residue 49 HIS Chi-restraints excluded: chain P residue 77 TYR Chi-restraints excluded: chain P residue 150 LYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain Z residue 241 LEU Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 606 VAL Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 743 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: [394, 430, 41, 265, 497, 414, 310, 488, 366, 223, 516] chunk 394 optimal weight: 7.9990 chunk 430 optimal weight: 50.0000 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 30.0000 chunk 310 optimal weight: 0.1980 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 516 optimal weight: 10.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 311 GLN ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 231 ASN ** Z 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.088003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.064881 restraints weight = 373884.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.064823 restraints weight = 267875.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.065033 restraints weight = 192553.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.064695 restraints weight = 166065.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.064885 restraints weight = 160131.658| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 42204 Z= 0.152 Angle : 0.602 11.438 57063 Z= 0.314 Chirality : 0.042 0.223 6543 Planarity : 0.004 0.047 7356 Dihedral : 8.090 84.000 5949 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.40 % Rotamer: Outliers : 1.82 % Allowed : 12.97 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.12 (0.12), residues: 5228 helix: 1.12 (0.10), residues: 2786 sheet: 0.12 (0.20), residues: 624 loop : 0.63 (0.16), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 928 TYR 0.016 0.001 TYR Z 549 PHE 0.023 0.002 PHE Z 365 TRP 0.035 0.002 TRP L 46 HIS 0.005 0.001 HIS N 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (42204) covalent geometry : angle 0.60216 / 0.31 (57063) hydrogen bonds : bond 0.04891 / 3.19 ( 2150) hydrogen bonds : angle 5.07118 / 3.62 ( 6165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 291 time to evaluate : 1.613 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: 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 197 MET cc_start: 0.1991 (ttm) cc_final: -0.0260 (mtt) REVERT: A 290 MET cc_start: 0.4009 (mtt) cc_final: 0.1770 (ppp) REVERT: A 297 MET cc_start: 0.3663 (ptm) cc_final: 0.3109 (ppp) REVERT: B 171 MET cc_start: 0.4198 (mtt) cc_final: 0.3933 (mtt) REVERT: B 173 MET cc_start: 0.5913 (mtt) cc_final: 0.5282 (mmp) REVERT: C 124 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7137 (tmm) REVERT: C 415 MET cc_start: 0.8183 (mmm) cc_final: 0.7630 (mmt) REVERT: C 503 ASP cc_start: 0.8867 (t0) cc_final: 0.8610 (p0) REVERT: C 583 ASP cc_start: 0.9442 (m-30) cc_final: 0.9084 (p0) REVERT: C 775 MET cc_start: 0.8556 (mmm) cc_final: 0.8210 (mmm) REVERT: C 815 MET cc_start: 0.8082 (mtp) cc_final: 0.7793 (mtt) REVERT: I 138 MET cc_start: 0.9381 (tmm) cc_final: 0.9088 (tmm) REVERT: I 236 MET cc_start: 0.9654 (tpp) cc_final: 0.9247 (tmm) REVERT: I 272 MET cc_start: 0.9715 (ptm) cc_final: 0.9417 (ptt) REVERT: J 238 ASN cc_start: 0.8016 (t0) cc_final: 0.7669 (t0) REVERT: J 252 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8526 (ttp80) REVERT: J 272 ASP cc_start: 0.8404 (t0) cc_final: 0.7391 (p0) REVERT: J 273 GLU cc_start: 0.8716 (pt0) cc_final: 0.8326 (pp20) REVERT: K 109 MET cc_start: 0.8245 (mmp) cc_final: 0.7971 (mmp) REVERT: K 312 MET cc_start: 0.7799 (ttm) cc_final: 0.7552 (ttp) REVERT: K 416 MET cc_start: 0.2299 (ppp) cc_final: 0.1761 (ppp) REVERT: L 86 ILE cc_start: 0.2337 (OUTLIER) cc_final: 0.1445 (tp) REVERT: N 136 LYS cc_start: 0.5889 (OUTLIER) cc_final: 0.5463 (pptt) REVERT: P 58 MET cc_start: 0.2788 (ttm) cc_final: 0.2443 (ttt) REVERT: P 210 MET cc_start: 0.3696 (mtp) cc_final: 0.3168 (mtp) REVERT: P 315 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.5454 (m-80) REVERT: P 368 MET cc_start: 0.1783 (mtp) cc_final: 0.1320 (ptm) REVERT: Z 217 MET cc_start: 0.4867 (ptt) cc_final: 0.4344 (ptt) REVERT: Z 429 GLU cc_start: 0.8834 (mp0) cc_final: 0.7694 (tm-30) REVERT: Z 489 MET cc_start: 0.8159 (mmt) cc_final: 0.7642 (mmp) outliers start: 83 outliers final: 38 residues processed: 358 average time/residue: 0.2363 time to fit residues: 142.9115 Evaluate side-chains 309 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 266 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 375 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 283 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 324 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 402 GLU Chi-restraints excluded: chain N residue 136 LYS Chi-restraints excluded: chain P residue 77 TYR Chi-restraints excluded: chain P residue 150 LYS Chi-restraints excluded: chain P residue 315 PHE Chi-restraints excluded: chain Z residue 381 GLU Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 606 VAL Chi-restraints excluded: chain Z residue 609 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 737 SER Chi-restraints excluded: chain Z residue 743 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: [324, 507, 205, 269, 39, 54, 219, 58, 166, 438, 263] chunk 324 optimal weight: 40.0000 chunk 507 optimal weight: 0.6980 chunk 205 optimal weight: 9.9990 chunk 269 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 219 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 438 optimal weight: 50.0000 chunk 263 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 833 GLN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 HIS ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 375 ASN K 311 GLN ** M 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 900 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.088170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.063206 restraints weight = 372069.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.063381 restraints weight = 240131.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.063660 restraints weight = 171230.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.064022 restraints weight = 140357.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.064022 restraints weight = 124752.567| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42204 Z= 0.129 Angle : 0.561 10.138 57063 Z= 0.291 Chirality : 0.042 0.233 6543 Planarity : 0.004 0.046 7356 Dihedral : 7.717 82.165 5907 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 1.84 % Allowed : 13.43 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.44 % 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: 1.19 (0.12), residues: 5228 helix: 1.24 (0.10), residues: 2776 sheet: 0.04 (0.20), residues: 613 loop : 0.59 (0.16), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 60 TYR 0.020 0.001 TYR K 70 PHE 0.026 0.001 PHE Z 338 TRP 0.023 0.001 TRP L 46 HIS 0.006 0.001 HIS K 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (42204) covalent geometry : angle 0.56123 / 0.29 (57063) hydrogen bonds : bond 0.04353 / 2.83 ( 2150) hydrogen bonds : angle 4.75580 / 3.39 ( 6165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 287 time to evaluate : 2.099 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7570 (tm-30) REVERT: A 197 MET cc_start: 0.4186 (ttm) cc_final: -0.0957 (mtt) REVERT: A 290 MET cc_start: 0.5054 (mtt) cc_final: 0.1546 (ppp) REVERT: A 297 MET cc_start: 0.4531 (ptm) cc_final: 0.3901 (ppp) REVERT: B 128 TYR cc_start: 0.9356 (m-80) cc_final: 0.8753 (m-80) REVERT: B 171 MET cc_start: 0.5015 (mtt) cc_final: 0.4060 (mtt) REVERT: B 173 MET cc_start: 0.6566 (mtt) cc_final: 0.5938 (mmp) REVERT: C 124 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7242 (tmm) REVERT: C 415 MET cc_start: 0.8286 (mmm) cc_final: 0.7795 (mmt) REVERT: C 503 ASP cc_start: 0.8905 (t0) cc_final: 0.8650 (p0) REVERT: C 583 ASP cc_start: 0.9322 (m-30) cc_final: 0.8960 (p0) REVERT: C 775 MET cc_start: 0.8600 (mmm) cc_final: 0.8201 (mmm) REVERT: C 790 MET cc_start: 0.9090 (mmp) cc_final: 0.8742 (mmm) REVERT: C 815 MET cc_start: 0.7999 (mtp) cc_final: 0.7634 (mtt) REVERT: D 412 MET cc_start: 0.2288 (mmm) cc_final: 0.1816 (mmm) REVERT: I 236 MET cc_start: 0.9559 (OUTLIER) cc_final: 0.9234 (tmm) REVERT: I 272 MET cc_start: 0.9698 (ptm) cc_final: 0.9375 (ptt) REVERT: J 238 ASN cc_start: 0.7932 (t0) cc_final: 0.7670 (t0) REVERT: J 252 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8408 (ttp80) REVERT: J 272 ASP cc_start: 0.8144 (t70) cc_final: 0.7265 (p0) REVERT: J 273 GLU cc_start: 0.8600 (pt0) cc_final: 0.8353 (pp20) REVERT: J 347 ARG cc_start: 0.9333 (ttt180) cc_final: 0.9032 (tpp-160) REVERT: K 109 MET cc_start: 0.8291 (mmp) cc_final: 0.8022 (mmp) REVERT: K 416 MET cc_start: 0.2894 (ppp) cc_final: 0.2264 (ppp) REVERT: L 86 ILE cc_start: 0.4500 (OUTLIER) cc_final: 0.3219 (tp) REVERT: M 117 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8212 (t70) REVERT: M 315 TRP cc_start: 0.5607 (m100) cc_final: 0.5049 (m100) REVERT: N 136 LYS cc_start: 0.5736 (OUTLIER) cc_final: 0.5223 (pptt) REVERT: P 201 MET cc_start: 0.7633 (mmt) cc_final: 0.7351 (mmp) REVERT: P 210 MET cc_start: 0.1687 (mtp) cc_final: 0.1367 (mtp) REVERT: P 254 MET cc_start: 0.0451 (ttp) cc_final: -0.0525 (ttp) REVERT: P 315 PHE cc_start: 0.5773 (OUTLIER) cc_final: 0.5039 (m-80) REVERT: P 368 MET cc_start: 0.2953 (mtp) cc_final: 0.2285 (ptp) REVERT: Z 217 MET cc_start: 0.4760 (ptt) cc_final: 0.4177 (ptt) REVERT: Z 241 LEU cc_start: 0.8492 (tp) cc_final: 0.8058 (mt) REVERT: Z 429 GLU cc_start: 0.8750 (mp0) cc_final: 0.7810 (tm-30) REVERT: Z 489 MET cc_start: 0.8098 (mmt) cc_final: 0.7556 (mmp) outliers start: 84 outliers final: 46 residues processed: 359 average time/residue: 0.2340 time to fit residues: 143.8141 Evaluate side-chains 328 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 275 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 236 MET Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 375 ASN Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 324 ILE Chi-restraints excluded: chain K residue 349 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 402 GLU Chi-restraints excluded: chain N residue 23 HIS Chi-restraints excluded: chain N residue 49 HIS Chi-restraints excluded: chain N residue 136 LYS Chi-restraints excluded: chain P residue 77 TYR Chi-restraints excluded: chain P residue 150 LYS Chi-restraints excluded: chain P residue 288 THR Chi-restraints excluded: chain P residue 315 PHE Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 381 GLU Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 608 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 657 MET Chi-restraints excluded: chain Z residue 737 SER Chi-restraints excluded: chain Z residue 743 PHE Chi-restraints excluded: chain Z residue 752 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: [96, 345, 496, 137, 394, 80, 242, 8, 68, 306, 100] chunk 96 optimal weight: 0.9990 chunk 345 optimal weight: 9.9990 chunk 496 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 394 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 242 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 306 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN C 132 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.088414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.065978 restraints weight = 371781.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.065445 restraints weight = 270111.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.066278 restraints weight = 208929.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.066023 restraints weight = 155913.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.065879 restraints weight = 156227.222| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 42204 Z= 0.117 Angle : 0.560 11.339 57063 Z= 0.285 Chirality : 0.041 0.192 6543 Planarity : 0.003 0.046 7356 Dihedral : 7.532 82.344 5902 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 1.84 % Allowed : 13.36 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.44 % 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: 1.29 (0.12), residues: 5228 helix: 1.36 (0.10), residues: 2780 sheet: 0.08 (0.21), residues: 596 loop : 0.57 (0.16), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 60 TYR 0.016 0.001 TYR B 292 PHE 0.026 0.001 PHE Z 365 TRP 0.020 0.001 TRP L 46 HIS 0.007 0.001 HIS C 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (42204) covalent geometry : angle 0.56032 / 0.29 (57063) hydrogen bonds : bond 0.03878 / 2.52 ( 2150) hydrogen bonds : angle 4.54213 / 3.24 ( 6165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 292 time to evaluate : 1.709 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.9047 (pp30) REVERT: A 197 MET cc_start: -0.1889 (ttm) cc_final: -0.2706 (mmm) REVERT: A 290 MET cc_start: 0.2050 (mtt) cc_final: 0.0424 (ppp) REVERT: A 297 MET cc_start: 0.2480 (ptm) cc_final: 0.1937 (ppp) REVERT: A 428 MET cc_start: 0.3999 (tpp) cc_final: 0.3691 (tpp) REVERT: B 128 TYR cc_start: 0.9303 (m-80) cc_final: 0.8737 (m-80) REVERT: B 171 MET cc_start: 0.2015 (mtt) cc_final: 0.0785 (mtm) REVERT: B 173 MET cc_start: 0.5032 (mtt) cc_final: 0.3742 (mmp) REVERT: C 124 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7253 (tmm) REVERT: C 415 MET cc_start: 0.8396 (mmm) cc_final: 0.8159 (mmm) REVERT: C 503 ASP cc_start: 0.8920 (t0) cc_final: 0.8656 (p0) REVERT: C 583 ASP cc_start: 0.9418 (m-30) cc_final: 0.9049 (p0) REVERT: C 775 MET cc_start: 0.8637 (mmm) cc_final: 0.8150 (mmm) REVERT: C 790 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8858 (mmp) REVERT: C 815 MET cc_start: 0.8008 (mtp) cc_final: 0.7632 (mtt) REVERT: I 236 MET cc_start: 0.9640 (OUTLIER) cc_final: 0.9330 (tmm) REVERT: I 272 MET cc_start: 0.9713 (ptm) cc_final: 0.9449 (ptt) REVERT: J 238 ASN cc_start: 0.7895 (t0) cc_final: 0.7665 (t0) REVERT: J 252 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8424 (ttp80) REVERT: J 253 MET cc_start: 0.8276 (ptm) cc_final: 0.7447 (ptm) REVERT: J 272 ASP cc_start: 0.8122 (t70) cc_final: 0.7241 (p0) REVERT: J 273 GLU cc_start: 0.8565 (pt0) cc_final: 0.8197 (pp20) REVERT: J 347 ARG cc_start: 0.9325 (ttt180) cc_final: 0.8999 (tpp-160) REVERT: K 93 ASN cc_start: 0.9433 (m-40) cc_final: 0.9174 (p0) REVERT: K 109 MET cc_start: 0.8267 (mmp) cc_final: 0.7996 (mmp) REVERT: K 416 MET cc_start: 0.2391 (ppp) cc_final: 0.1908 (ppp) REVERT: L 86 ILE cc_start: 0.1642 (OUTLIER) cc_final: 0.0994 (tp) REVERT: N 136 LYS cc_start: 0.5736 (OUTLIER) cc_final: 0.5227 (pptt) REVERT: P 58 MET cc_start: 0.3239 (ttm) cc_final: 0.2968 (ttm) REVERT: P 201 MET cc_start: 0.7524 (mmt) cc_final: 0.7115 (mmp) REVERT: P 210 MET cc_start: 0.2465 (mtp) cc_final: 0.2011 (mtp) REVERT: P 254 MET cc_start: 0.0524 (ttp) cc_final: -0.0554 (ttp) REVERT: P 315 PHE cc_start: 0.5584 (OUTLIER) cc_final: 0.3767 (t80) REVERT: P 368 MET cc_start: 0.0513 (mtp) cc_final: 0.0236 (ptm) REVERT: Z 217 MET cc_start: 0.4847 (ptt) cc_final: 0.4145 (ptt) REVERT: Z 241 LEU cc_start: 0.8467 (tp) cc_final: 0.8137 (mt) REVERT: Z 338 PHE cc_start: 0.7730 (m-80) cc_final: 0.7444 (m-80) REVERT: Z 429 GLU cc_start: 0.8825 (mp0) cc_final: 0.8035 (tm-30) REVERT: Z 489 MET cc_start: 0.8230 (mmt) cc_final: 0.8011 (mmt) REVERT: Z 641 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8832 (mm) outliers start: 84 outliers final: 44 residues processed: 363 average time/residue: 0.2396 time to fit residues: 147.2061 Evaluate side-chains 320 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 790 MET Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 236 MET Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 283 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 324 ILE Chi-restraints excluded: chain K residue 349 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 402 GLU Chi-restraints excluded: chain N residue 23 HIS Chi-restraints excluded: chain N residue 49 HIS Chi-restraints excluded: chain N residue 136 LYS Chi-restraints excluded: chain P residue 77 TYR Chi-restraints excluded: chain P residue 86 MET Chi-restraints excluded: chain P residue 150 LYS Chi-restraints excluded: chain P residue 288 THR Chi-restraints excluded: chain P residue 315 PHE Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 381 GLU Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 608 LEU Chi-restraints excluded: chain Z residue 641 LEU Chi-restraints excluded: chain Z residue 657 MET Chi-restraints excluded: chain Z residue 737 SER Chi-restraints excluded: chain Z residue 743 PHE Chi-restraints excluded: chain Z residue 752 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: [148, 91, 334, 94, 331, 397, 19, 182, 268, 181, 155] chunk 148 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 334 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 331 optimal weight: 0.0020 chunk 397 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 GLN ** C 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 ASN C 829 GLN ** C 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 871 HIS ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 GLN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 264 ASN ** J 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN M 336 ASN N 226 ASN ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 226 ASN ** Z 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 635 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.085580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.060443 restraints weight = 376222.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.060657 restraints weight = 238995.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.060930 restraints weight = 175895.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.060930 restraints weight = 147503.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.060930 restraints weight = 147503.406| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 42204 Z= 0.217 Angle : 0.646 13.270 57063 Z= 0.336 Chirality : 0.043 0.177 6543 Planarity : 0.004 0.055 7356 Dihedral : 7.705 84.264 5900 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 2.26 % Allowed : 13.80 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.44 % 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: 0.98 (0.12), residues: 5228 helix: 1.12 (0.10), residues: 2778 sheet: -0.14 (0.21), residues: 609 loop : 0.41 (0.16), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 22 TYR 0.018 0.002 TYR Z 549 PHE 0.025 0.002 PHE C 793 TRP 0.019 0.002 TRP N 175 HIS 0.008 0.001 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.22 (42204) covalent geometry : angle 0.64609 / 0.34 (57063) hydrogen bonds : bond 0.04195 / 2.73 ( 2150) hydrogen bonds : angle 4.76519 / 3.38 ( 6165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 271 time to evaluate : 1.474 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.9088 (pp30) REVERT: A 172 MET cc_start: 0.7247 (pmm) cc_final: 0.7038 (pmm) REVERT: A 197 MET cc_start: 0.1554 (ttm) cc_final: -0.1172 (mmm) REVERT: A 290 MET cc_start: 0.3769 (mtt) cc_final: 0.1309 (ppp) REVERT: A 297 MET cc_start: 0.4491 (ptm) cc_final: 0.4117 (ppp) REVERT: B 128 TYR cc_start: 0.9340 (m-80) cc_final: 0.8717 (m-80) REVERT: B 173 MET cc_start: 0.6080 (mtt) cc_final: 0.5585 (mmp) REVERT: C 124 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7356 (tmm) REVERT: C 415 MET cc_start: 0.8471 (mmm) cc_final: 0.8129 (mmm) REVERT: C 503 ASP cc_start: 0.8980 (t0) cc_final: 0.8683 (p0) REVERT: C 583 ASP cc_start: 0.9354 (m-30) cc_final: 0.9003 (p0) REVERT: C 775 MET cc_start: 0.8595 (mmm) cc_final: 0.8113 (mmm) REVERT: C 790 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8857 (mmp) REVERT: C 815 MET cc_start: 0.8342 (mtp) cc_final: 0.7961 (mtt) REVERT: D 412 MET cc_start: 0.2091 (mmm) cc_final: 0.1662 (mmm) REVERT: I 107 LEU cc_start: 0.8380 (pp) cc_final: 0.8168 (pp) REVERT: I 236 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.9211 (tmm) REVERT: I 272 MET cc_start: 0.9716 (ptm) cc_final: 0.9493 (ptt) REVERT: I 292 MET cc_start: 0.7081 (tpp) cc_final: 0.6749 (tpp) REVERT: J 238 ASN cc_start: 0.7803 (t0) cc_final: 0.7578 (t0) REVERT: J 252 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8466 (ttp80) REVERT: J 253 MET cc_start: 0.8293 (ptm) cc_final: 0.7338 (ptm) REVERT: J 347 ARG cc_start: 0.9349 (ttt180) cc_final: 0.9043 (tpp-160) REVERT: J 367 ASP cc_start: 0.8424 (t0) cc_final: 0.7111 (t0) REVERT: K 98 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8586 (mt) REVERT: K 109 MET cc_start: 0.8413 (mmp) cc_final: 0.8179 (mmp) REVERT: K 312 MET cc_start: 0.7608 (ptm) cc_final: 0.7215 (ptm) REVERT: K 416 MET cc_start: 0.2465 (ppp) cc_final: 0.1984 (ppp) REVERT: M 117 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8392 (t70) REVERT: N 1 MET cc_start: 0.8706 (mtt) cc_final: 0.8315 (ptm) REVERT: N 117 LYS cc_start: 0.8247 (mmtt) cc_final: 0.8011 (mtmm) REVERT: N 136 LYS cc_start: 0.6248 (OUTLIER) cc_final: 0.5814 (pptt) REVERT: P 201 MET cc_start: 0.7965 (mmt) cc_final: 0.7643 (mmp) REVERT: P 210 MET cc_start: 0.4694 (mtp) cc_final: 0.4197 (mtp) REVERT: P 254 MET cc_start: 0.1810 (ttp) cc_final: 0.1359 (ttp) REVERT: P 315 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.3902 (t80) REVERT: P 368 MET cc_start: 0.3728 (mtp) cc_final: 0.3220 (ptm) REVERT: Z 217 MET cc_start: 0.4963 (ptt) cc_final: 0.4149 (ptt) REVERT: Z 429 GLU cc_start: 0.8803 (mp0) cc_final: 0.7921 (tm-30) REVERT: Z 489 MET cc_start: 0.8135 (mmt) cc_final: 0.7531 (mmm) outliers start: 103 outliers final: 64 residues processed: 357 average time/residue: 0.2296 time to fit residues: 139.3066 Evaluate side-chains 330 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 257 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 790 MET Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain I residue 236 MET Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 142 HIS Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 330 ARG Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 324 ILE Chi-restraints excluded: chain K residue 349 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 402 GLU Chi-restraints excluded: chain N residue 23 HIS Chi-restraints excluded: chain N residue 37 ARG Chi-restraints excluded: chain N residue 49 HIS Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 136 LYS Chi-restraints excluded: chain P residue 77 TYR Chi-restraints excluded: chain P residue 86 MET Chi-restraints excluded: chain P residue 150 LYS Chi-restraints excluded: chain P residue 238 GLN Chi-restraints excluded: chain P residue 288 THR Chi-restraints excluded: chain P residue 315 PHE Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 381 GLU Chi-restraints excluded: chain Z residue 452 LEU Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 595 LEU Chi-restraints excluded: chain Z residue 606 VAL Chi-restraints excluded: chain Z residue 608 LEU Chi-restraints excluded: chain Z residue 609 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 657 MET Chi-restraints excluded: chain Z residue 737 SER Chi-restraints excluded: chain Z residue 743 PHE Chi-restraints excluded: chain Z residue 752 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: [494, 109, 153, 17, 56, 240, 33, 100, 225, 203, 131] chunk 494 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 153 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 240 optimal weight: 0.7980 chunk 33 optimal weight: 40.0000 chunk 100 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 203 optimal weight: 30.0000 chunk 131 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN I 351 ASN J 302 GLN Z 226 ASN ** Z 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.086915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.061483 restraints weight = 375795.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.061619 restraints weight = 235451.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.062147 restraints weight = 168514.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.062532 restraints weight = 137219.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.062532 restraints weight = 124269.076| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 42204 Z= 0.128 Angle : 0.584 13.192 57063 Z= 0.295 Chirality : 0.042 0.197 6543 Planarity : 0.004 0.045 7356 Dihedral : 7.569 86.848 5900 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.91 % Favored : 97.05 % Rotamer: Outliers : 2.15 % Allowed : 14.61 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.44 % 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: 1.20 (0.12), residues: 5228 helix: 1.33 (0.10), residues: 2774 sheet: -0.13 (0.21), residues: 602 loop : 0.51 (0.16), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 96 TYR 0.016 0.001 TYR I 120 PHE 0.024 0.001 PHE C 264 TRP 0.032 0.002 TRP M 315 HIS 0.008 0.001 HIS C 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (42204) covalent geometry : angle 0.58380 / 0.30 (57063) hydrogen bonds : bond 0.03746 / 2.43 ( 2150) hydrogen bonds : angle 4.54688 / 3.24 ( 6165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 277 time to evaluate : 1.535 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.9063 (pp30) REVERT: A 172 MET cc_start: 0.7159 (pmm) cc_final: 0.6948 (pmm) REVERT: A 197 MET cc_start: 0.2372 (ttm) cc_final: -0.1178 (mmt) REVERT: A 290 MET cc_start: 0.4727 (mtt) cc_final: 0.1898 (ppp) REVERT: A 297 MET cc_start: 0.4547 (ptm) cc_final: 0.4198 (ppp) REVERT: B 119 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9010 (pt) REVERT: B 128 TYR cc_start: 0.9390 (m-80) cc_final: 0.8762 (m-80) REVERT: B 173 MET cc_start: 0.6427 (mtt) cc_final: 0.5979 (mmp) REVERT: C 124 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7367 (tmm) REVERT: C 415 MET cc_start: 0.8494 (mmm) cc_final: 0.8236 (mmm) REVERT: C 503 ASP cc_start: 0.8917 (t0) cc_final: 0.8635 (p0) REVERT: C 583 ASP cc_start: 0.9321 (m-30) cc_final: 0.8974 (p0) REVERT: C 790 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8881 (mmp) REVERT: C 815 MET cc_start: 0.8235 (mtp) cc_final: 0.7689 (mtp) REVERT: D 412 MET cc_start: 0.3317 (mmm) cc_final: 0.2568 (mmm) REVERT: I 236 MET cc_start: 0.9499 (OUTLIER) cc_final: 0.9267 (tmm) REVERT: I 269 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8736 (pm20) REVERT: I 272 MET cc_start: 0.9694 (ptm) cc_final: 0.9424 (ptt) REVERT: I 292 MET cc_start: 0.6878 (tpp) cc_final: 0.6547 (tpp) REVERT: J 221 MET cc_start: 0.9122 (mtm) cc_final: 0.8890 (ptp) REVERT: J 253 MET cc_start: 0.8299 (ptm) cc_final: 0.7475 (ptm) REVERT: J 347 ARG cc_start: 0.9330 (ttt180) cc_final: 0.9071 (tpp-160) REVERT: J 367 ASP cc_start: 0.8413 (t0) cc_final: 0.7764 (t0) REVERT: K 93 ASN cc_start: 0.9532 (m110) cc_final: 0.9281 (p0) REVERT: K 98 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8513 (mt) REVERT: K 109 MET cc_start: 0.8351 (mmp) cc_final: 0.8104 (mmp) REVERT: K 312 MET cc_start: 0.7687 (ptm) cc_final: 0.7312 (ptm) REVERT: K 325 MET cc_start: 0.8246 (mpp) cc_final: 0.7564 (mpp) REVERT: K 416 MET cc_start: 0.2824 (ppp) cc_final: 0.2242 (ppp) REVERT: M 117 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8275 (t0) REVERT: M 144 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6520 (m-10) REVERT: N 1 MET cc_start: 0.8629 (mtt) cc_final: 0.8209 (ptm) REVERT: N 8 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: N 136 LYS cc_start: 0.6097 (OUTLIER) cc_final: 0.5673 (pptt) REVERT: P 201 MET cc_start: 0.7842 (mmt) cc_final: 0.7488 (mmp) REVERT: P 210 MET cc_start: 0.3448 (mtp) cc_final: 0.2970 (mtp) REVERT: P 254 MET cc_start: 0.1033 (ttp) cc_final: -0.0249 (ttp) REVERT: P 315 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.3513 (t80) REVERT: P 368 MET cc_start: 0.4338 (mtp) cc_final: 0.3840 (ptm) REVERT: Z 217 MET cc_start: 0.4623 (ptt) cc_final: 0.3770 (ptt) REVERT: Z 241 LEU cc_start: 0.8626 (mt) cc_final: 0.8322 (mt) REVERT: Z 429 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: Z 489 MET cc_start: 0.8063 (mmt) cc_final: 0.7547 (mmp) REVERT: Z 641 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8680 (mm) outliers start: 98 outliers final: 61 residues processed: 359 average time/residue: 0.2345 time to fit residues: 143.3007 Evaluate side-chains 339 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 264 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 790 MET Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 236 MET Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 330 ARG Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 290 ARG Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 324 ILE Chi-restraints excluded: chain K residue 349 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 277 GLU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 402 GLU Chi-restraints excluded: chain N residue 8 GLN Chi-restraints excluded: chain N residue 23 HIS Chi-restraints excluded: chain N residue 37 ARG Chi-restraints excluded: chain N residue 49 HIS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 136 LYS Chi-restraints excluded: chain P residue 77 TYR Chi-restraints excluded: chain P residue 86 MET Chi-restraints excluded: chain P residue 150 LYS Chi-restraints excluded: chain P residue 288 THR Chi-restraints excluded: chain P residue 315 PHE Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 381 GLU Chi-restraints excluded: chain Z residue 429 GLU Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 608 LEU Chi-restraints excluded: chain Z residue 641 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 657 MET Chi-restraints excluded: chain Z residue 737 SER Chi-restraints excluded: chain Z residue 743 PHE Chi-restraints excluded: chain Z residue 752 SER Chi-restraints excluded: chain Z residue 866 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: [30, 254, 16, 384, 400, 101, 273, 343, 29, 310, 93] chunk 30 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 16 optimal weight: 40.0000 chunk 384 optimal weight: 5.9990 chunk 400 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 273 optimal weight: 0.2980 chunk 343 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 310 optimal weight: 0.0370 chunk 93 optimal weight: 0.9980 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.087215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.063553 restraints weight = 373160.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.064046 restraints weight = 268719.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.064390 restraints weight = 204034.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.063806 restraints weight = 169789.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.063660 restraints weight = 145652.532| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 42204 Z= 0.120 Angle : 0.585 12.108 57063 Z= 0.294 Chirality : 0.042 0.186 6543 Planarity : 0.003 0.048 7356 Dihedral : 7.421 89.854 5900 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 1.99 % Allowed : 14.81 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 5228 helix: 1.42 (0.10), residues: 2775 sheet: -0.17 (0.20), residues: 603 loop : 0.54 (0.16), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 96 TYR 0.014 0.001 TYR I 120 PHE 0.024 0.001 PHE Z 365 TRP 0.033 0.001 TRP M 315 HIS 0.009 0.001 HIS C 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (42204) covalent geometry : angle 0.58541 / 0.29 (57063) hydrogen bonds : bond 0.03600 / 2.33 ( 2150) hydrogen bonds : angle 4.47039 / 3.18 ( 6165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 278 time to evaluate : 1.696 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 57 LYS cc_start: 0.8957 (mtmm) cc_final: 0.8715 (mtmm) REVERT: A 89 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.9044 (pp30) REVERT: A 172 MET cc_start: 0.7305 (pmm) cc_final: 0.7037 (pmm) REVERT: A 197 MET cc_start: -0.0621 (ttm) cc_final: -0.0829 (mmt) REVERT: A 297 MET cc_start: 0.4020 (ptm) cc_final: 0.3667 (ppp) REVERT: B 119 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8831 (tp) REVERT: B 128 TYR cc_start: 0.9367 (m-80) cc_final: 0.8861 (m-80) REVERT: B 171 MET cc_start: 0.4114 (mtt) cc_final: 0.3068 (mtm) REVERT: B 173 MET cc_start: 0.5173 (mtt) cc_final: 0.4379 (mmp) REVERT: B 259 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.8014 (t70) REVERT: B 369 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7468 (ttt) REVERT: C 124 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7393 (tmm) REVERT: C 415 MET cc_start: 0.8515 (mmm) cc_final: 0.8268 (mmm) REVERT: C 503 ASP cc_start: 0.9015 (t0) cc_final: 0.8698 (p0) REVERT: C 583 ASP cc_start: 0.9368 (m-30) cc_final: 0.9023 (p0) REVERT: C 815 MET cc_start: 0.8219 (mtp) cc_final: 0.7803 (mtt) REVERT: C 862 MET cc_start: 0.8604 (tpp) cc_final: 0.8403 (tpp) REVERT: D 412 MET cc_start: 0.0901 (mmm) cc_final: -0.0522 (mmm) REVERT: I 247 MET cc_start: 0.8843 (mmm) cc_final: 0.8591 (mmm) REVERT: I 269 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8871 (pm20) REVERT: I 272 MET cc_start: 0.9721 (ptm) cc_final: 0.9475 (ptt) REVERT: I 292 MET cc_start: 0.6830 (tpp) cc_final: 0.6540 (tpp) REVERT: I 350 MET cc_start: 0.9027 (mtm) cc_final: 0.8708 (ptm) REVERT: J 252 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8493 (ttp80) REVERT: J 253 MET cc_start: 0.8414 (ptm) cc_final: 0.7709 (ptm) REVERT: J 272 ASP cc_start: 0.8461 (t70) cc_final: 0.7386 (p0) REVERT: J 316 MET cc_start: 0.8138 (mmm) cc_final: 0.7821 (mmm) REVERT: J 347 ARG cc_start: 0.9351 (ttt180) cc_final: 0.9000 (tpp80) REVERT: J 367 ASP cc_start: 0.8043 (t0) cc_final: 0.6571 (t0) REVERT: K 93 ASN cc_start: 0.9542 (m110) cc_final: 0.9310 (p0) REVERT: K 98 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8531 (mt) REVERT: K 109 MET cc_start: 0.8295 (mmp) cc_final: 0.8052 (mmp) REVERT: K 312 MET cc_start: 0.7592 (ptm) cc_final: 0.7208 (ptm) REVERT: K 416 MET cc_start: 0.2514 (ppp) cc_final: 0.1987 (ppp) REVERT: M 117 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8347 (t0) REVERT: M 144 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6673 (m-10) REVERT: N 136 LYS cc_start: 0.6106 (OUTLIER) cc_final: 0.5656 (pptt) REVERT: P 201 MET cc_start: 0.7987 (mmt) cc_final: 0.7621 (mmp) REVERT: P 210 MET cc_start: 0.4080 (mtp) cc_final: 0.3609 (mtp) REVERT: P 254 MET cc_start: 0.1012 (ttp) cc_final: -0.0172 (ttp) REVERT: P 315 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.3464 (t80) REVERT: P 368 MET cc_start: 0.2967 (mtp) cc_final: 0.2360 (ptp) REVERT: Z 217 MET cc_start: 0.4444 (ptt) cc_final: 0.3530 (ptt) REVERT: Z 241 LEU cc_start: 0.8621 (mt) cc_final: 0.8325 (mt) REVERT: Z 429 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: Z 489 MET cc_start: 0.8526 (mmt) cc_final: 0.7938 (mmp) REVERT: Z 641 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8786 (mm) outliers start: 91 outliers final: 60 residues processed: 355 average time/residue: 0.2322 time to fit residues: 140.0194 Evaluate side-chains 336 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 262 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 330 ARG Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 283 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 324 ILE Chi-restraints excluded: chain K residue 349 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 402 GLU Chi-restraints excluded: chain N residue 23 HIS Chi-restraints excluded: chain N residue 37 ARG Chi-restraints excluded: chain N residue 49 HIS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 136 LYS Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 77 TYR Chi-restraints excluded: chain P residue 86 MET Chi-restraints excluded: chain P residue 150 LYS Chi-restraints excluded: chain P residue 238 GLN Chi-restraints excluded: chain P residue 288 THR Chi-restraints excluded: chain P residue 315 PHE Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 311 ILE Chi-restraints excluded: chain Z residue 381 GLU Chi-restraints excluded: chain Z residue 429 GLU Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 499 HIS Chi-restraints excluded: chain Z residue 641 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 645 THR Chi-restraints excluded: chain Z residue 657 MET Chi-restraints excluded: chain Z residue 737 SER Chi-restraints excluded: chain Z residue 743 PHE Chi-restraints excluded: chain Z residue 752 SER Chi-restraints excluded: chain Z residue 866 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: [481, 253, 142, 517, 520, 174, 404, 360, 149, 287, 439] chunk 481 optimal weight: 0.8980 chunk 253 optimal weight: 0.0570 chunk 142 optimal weight: 6.9990 chunk 517 optimal weight: 6.9990 chunk 520 optimal weight: 0.0980 chunk 174 optimal weight: 20.0000 chunk 404 optimal weight: 7.9990 chunk 360 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 287 optimal weight: 0.0370 chunk 439 optimal weight: 9.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.088004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.065065 restraints weight = 370858.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.065608 restraints weight = 258877.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.065363 restraints weight = 189127.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.065472 restraints weight = 175066.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.065257 restraints weight = 138875.319| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 42204 Z= 0.108 Angle : 0.592 13.949 57063 Z= 0.293 Chirality : 0.042 0.187 6543 Planarity : 0.003 0.048 7356 Dihedral : 7.247 88.598 5900 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.07 % Rotamer: Outliers : 1.82 % Allowed : 14.98 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.44 % 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: 1.37 (0.12), residues: 5228 helix: 1.51 (0.10), residues: 2769 sheet: -0.13 (0.20), residues: 600 loop : 0.54 (0.16), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 96 TYR 0.012 0.001 TYR B 292 PHE 0.023 0.001 PHE C 211 TRP 0.030 0.001 TRP M 315 HIS 0.005 0.001 HIS N 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (42204) covalent geometry : angle 0.59243 / 0.29 (57063) hydrogen bonds : bond 0.03433 / 2.23 ( 2150) hydrogen bonds : angle 4.37651 / 3.11 ( 6165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 283 time to evaluate : 1.500 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8998 (pp30) REVERT: A 172 MET cc_start: 0.7379 (pmm) cc_final: 0.7104 (pmm) REVERT: A 197 MET cc_start: -0.2268 (ttm) cc_final: -0.3070 (mmt) REVERT: A 290 MET cc_start: 0.2987 (mtt) cc_final: 0.0940 (ppp) REVERT: A 297 MET cc_start: 0.3045 (ptm) cc_final: 0.2798 (ppp) REVERT: B 119 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8618 (tp) REVERT: B 128 TYR cc_start: 0.9283 (m-80) cc_final: 0.8839 (m-80) REVERT: B 171 MET cc_start: 0.2234 (mtt) cc_final: 0.2014 (mtm) REVERT: B 173 MET cc_start: 0.4357 (mtt) cc_final: 0.4102 (mmp) REVERT: B 259 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7943 (t70) REVERT: B 369 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6290 (ttt) REVERT: C 124 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7272 (tmm) REVERT: C 415 MET cc_start: 0.8507 (mmm) cc_final: 0.8297 (mmm) REVERT: C 503 ASP cc_start: 0.8968 (t0) cc_final: 0.8677 (p0) REVERT: C 583 ASP cc_start: 0.9387 (m-30) cc_final: 0.9024 (p0) REVERT: C 790 MET cc_start: 0.9051 (mmp) cc_final: 0.8680 (tpp) REVERT: C 815 MET cc_start: 0.8146 (mtp) cc_final: 0.7709 (mtt) REVERT: C 864 MET cc_start: 0.8548 (tpp) cc_final: 0.8097 (tpp) REVERT: I 247 MET cc_start: 0.8761 (mmm) cc_final: 0.8526 (mmm) REVERT: I 269 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8894 (pm20) REVERT: I 272 MET cc_start: 0.9712 (ptm) cc_final: 0.9470 (ptt) REVERT: I 292 MET cc_start: 0.6590 (tpp) cc_final: 0.6346 (tpp) REVERT: J 252 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8439 (ttp80) REVERT: J 253 MET cc_start: 0.8371 (ptm) cc_final: 0.7409 (ptm) REVERT: J 272 ASP cc_start: 0.8254 (t70) cc_final: 0.7285 (p0) REVERT: J 347 ARG cc_start: 0.9331 (ttt180) cc_final: 0.9022 (tpp-160) REVERT: J 367 ASP cc_start: 0.7404 (t0) cc_final: 0.6641 (t0) REVERT: K 93 ASN cc_start: 0.9508 (m110) cc_final: 0.9278 (p0) REVERT: K 109 MET cc_start: 0.8276 (mmp) cc_final: 0.8025 (mmp) REVERT: K 312 MET cc_start: 0.7600 (ptm) cc_final: 0.7234 (ptm) REVERT: K 416 MET cc_start: 0.2448 (ppp) cc_final: 0.2144 (ppp) REVERT: M 144 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6784 (m-10) REVERT: N 136 LYS cc_start: 0.5978 (OUTLIER) cc_final: 0.5476 (pptt) REVERT: P 201 MET cc_start: 0.7734 (mmt) cc_final: 0.7236 (mmp) REVERT: P 210 MET cc_start: 0.3187 (mtp) cc_final: 0.2754 (mtp) REVERT: P 254 MET cc_start: 0.0720 (ttp) cc_final: -0.0369 (ttp) REVERT: P 315 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.3046 (t80) REVERT: P 368 MET cc_start: 0.1529 (mtp) cc_final: 0.1083 (ptp) REVERT: Z 217 MET cc_start: 0.4681 (ptt) cc_final: 0.3730 (ptt) REVERT: Z 241 LEU cc_start: 0.8589 (mt) cc_final: 0.8321 (mt) REVERT: Z 429 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: Z 489 MET cc_start: 0.8508 (mmt) cc_final: 0.7946 (mmp) REVERT: Z 641 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8709 (mm) outliers start: 83 outliers final: 54 residues processed: 355 average time/residue: 0.2334 time to fit residues: 140.6684 Evaluate side-chains 334 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 268 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 330 ARG Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 283 VAL Chi-restraints excluded: chain K residue 290 ARG Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 324 ILE Chi-restraints excluded: chain K residue 349 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 277 GLU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 402 GLU Chi-restraints excluded: chain N residue 23 HIS Chi-restraints excluded: chain N residue 49 HIS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 136 LYS Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 77 TYR Chi-restraints excluded: chain P residue 86 MET Chi-restraints excluded: chain P residue 150 LYS Chi-restraints excluded: chain P residue 238 GLN Chi-restraints excluded: chain P residue 288 THR Chi-restraints excluded: chain P residue 315 PHE Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 311 ILE Chi-restraints excluded: chain Z residue 381 GLU Chi-restraints excluded: chain Z residue 429 GLU Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 641 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 657 MET Chi-restraints excluded: chain Z residue 737 SER Chi-restraints excluded: chain Z residue 743 PHE Chi-restraints excluded: chain Z residue 752 SER Chi-restraints excluded: chain Z residue 866 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: [447, 396, 13, 419, 392, 125, 209, 469, 359, 255, 501] chunk 447 optimal weight: 5.9990 chunk 396 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 419 optimal weight: 0.0670 chunk 392 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 469 optimal weight: 0.3980 chunk 359 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 501 optimal weight: 0.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 HIS ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 635 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.087903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.063620 restraints weight = 371526.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.064412 restraints weight = 244628.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.063937 restraints weight = 181054.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.064333 restraints weight = 165029.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.064187 restraints weight = 132750.469| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 42204 Z= 0.109 Angle : 0.599 16.216 57063 Z= 0.296 Chirality : 0.042 0.217 6543 Planarity : 0.003 0.048 7356 Dihedral : 7.094 85.172 5898 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.87 % Favored : 97.09 % Rotamer: Outliers : 1.60 % Allowed : 15.66 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.44 % 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: 1.37 (0.12), residues: 5228 helix: 1.53 (0.10), residues: 2770 sheet: -0.12 (0.20), residues: 602 loop : 0.51 (0.16), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 357 TYR 0.029 0.001 TYR I 94 PHE 0.024 0.001 PHE Z 365 TRP 0.028 0.001 TRP M 315 HIS 0.005 0.001 HIS N 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (42204) covalent geometry : angle 0.59866 / 0.30 (57063) hydrogen bonds : bond 0.03404 / 2.22 ( 2150) hydrogen bonds : angle 4.33948 / 3.09 ( 6165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 269 time to evaluate : 1.706 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7238 (pmm) cc_final: 0.7016 (pmm) REVERT: A 197 MET cc_start: -0.0553 (ttm) cc_final: -0.2243 (tpp) REVERT: A 290 MET cc_start: 0.4531 (mtt) cc_final: 0.1757 (ppp) REVERT: A 297 MET cc_start: 0.4559 (ptm) cc_final: 0.4234 (ppp) REVERT: B 119 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8592 (tp) REVERT: B 128 TYR cc_start: 0.9208 (m-80) cc_final: 0.8786 (m-80) REVERT: B 171 MET cc_start: 0.4666 (mtt) cc_final: 0.3902 (mtm) REVERT: B 173 MET cc_start: 0.6100 (mtt) cc_final: 0.5468 (mmt) REVERT: B 259 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8218 (t70) REVERT: B 369 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7624 (ttt) REVERT: C 124 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7430 (tmm) REVERT: C 503 ASP cc_start: 0.8895 (t0) cc_final: 0.8617 (p0) REVERT: C 583 ASP cc_start: 0.9314 (m-30) cc_final: 0.8937 (p0) REVERT: C 756 MET cc_start: 0.5401 (ppp) cc_final: 0.4970 (ppp) REVERT: C 790 MET cc_start: 0.9008 (mmp) cc_final: 0.8632 (tpp) REVERT: C 815 MET cc_start: 0.8089 (mtp) cc_final: 0.7647 (mtt) REVERT: C 862 MET cc_start: 0.7918 (tpp) cc_final: 0.7523 (tpp) REVERT: C 864 MET cc_start: 0.8405 (tpp) cc_final: 0.8000 (tpp) REVERT: I 229 MET cc_start: 0.9169 (ptp) cc_final: 0.8451 (pmm) REVERT: I 247 MET cc_start: 0.8746 (mmm) cc_final: 0.8376 (mmm) REVERT: I 269 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8820 (pm20) REVERT: I 272 MET cc_start: 0.9668 (ptm) cc_final: 0.9413 (ptt) REVERT: I 292 MET cc_start: 0.6918 (tpp) cc_final: 0.6660 (tpp) REVERT: J 221 MET cc_start: 0.8816 (ptp) cc_final: 0.8386 (ptp) REVERT: J 252 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8425 (ttp80) REVERT: J 253 MET cc_start: 0.8364 (ptm) cc_final: 0.7428 (ptm) REVERT: J 272 ASP cc_start: 0.8071 (t70) cc_final: 0.7296 (p0) REVERT: J 347 ARG cc_start: 0.9313 (ttt180) cc_final: 0.9039 (tpp-160) REVERT: J 367 ASP cc_start: 0.7535 (t0) cc_final: 0.6770 (t0) REVERT: K 93 ASN cc_start: 0.9494 (m110) cc_final: 0.9257 (p0) REVERT: K 109 MET cc_start: 0.8245 (mmp) cc_final: 0.7998 (mmp) REVERT: K 312 MET cc_start: 0.7649 (ptm) cc_final: 0.7281 (ptm) REVERT: K 382 MET cc_start: 0.8721 (mmt) cc_final: 0.8293 (mpp) REVERT: K 416 MET cc_start: 0.3048 (ppp) cc_final: 0.2303 (ppp) REVERT: N 1 MET cc_start: 0.8653 (mtt) cc_final: 0.8245 (ptm) REVERT: N 8 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7880 (pp30) REVERT: N 136 LYS cc_start: 0.5884 (OUTLIER) cc_final: 0.5342 (pptt) REVERT: P 201 MET cc_start: 0.7802 (mmt) cc_final: 0.7547 (mmp) REVERT: P 210 MET cc_start: 0.3592 (mtp) cc_final: 0.3121 (mtp) REVERT: P 254 MET cc_start: 0.0663 (ttp) cc_final: -0.0473 (ttp) REVERT: P 315 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.3353 (t80) REVERT: P 368 MET cc_start: 0.3857 (mtp) cc_final: 0.3310 (ptp) REVERT: Z 217 MET cc_start: 0.4233 (ptt) cc_final: 0.3389 (ptt) REVERT: Z 241 LEU cc_start: 0.8508 (mt) cc_final: 0.8245 (mt) REVERT: Z 429 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: Z 489 MET cc_start: 0.7983 (mmt) cc_final: 0.7472 (mmp) REVERT: Z 641 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8587 (mm) outliers start: 73 outliers final: 56 residues processed: 329 average time/residue: 0.2350 time to fit residues: 131.7264 Evaluate side-chains 330 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 263 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 894 MET Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 316 MET Chi-restraints excluded: chain J residue 330 ARG Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 283 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 324 ILE Chi-restraints excluded: chain K residue 349 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 277 GLU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 402 GLU Chi-restraints excluded: chain N residue 8 GLN Chi-restraints excluded: chain N residue 23 HIS Chi-restraints excluded: chain N residue 49 HIS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 136 LYS Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 77 TYR Chi-restraints excluded: chain P residue 86 MET Chi-restraints excluded: chain P residue 150 LYS Chi-restraints excluded: chain P residue 238 GLN Chi-restraints excluded: chain P residue 288 THR Chi-restraints excluded: chain P residue 315 PHE Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 311 ILE Chi-restraints excluded: chain Z residue 381 GLU Chi-restraints excluded: chain Z residue 429 GLU Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 499 HIS Chi-restraints excluded: chain Z residue 641 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 657 MET Chi-restraints excluded: chain Z residue 737 SER Chi-restraints excluded: chain Z residue 743 PHE Chi-restraints excluded: chain Z residue 752 SER Chi-restraints excluded: chain Z residue 866 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: [99, 53, 320, 448, 88, 245, 456, 240, 497, 109, 207] chunk 99 optimal weight: 6.9990 chunk 53 optimal weight: 30.0000 chunk 320 optimal weight: 7.9990 chunk 448 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 chunk 456 optimal weight: 5.9990 chunk 240 optimal weight: 0.9980 chunk 497 optimal weight: 0.1980 chunk 109 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 125 GLN Z 510 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.087110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.063398 restraints weight = 372861.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.063440 restraints weight = 252857.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.063270 restraints weight = 175611.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.063394 restraints weight = 137668.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.063394 restraints weight = 123392.472| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 42204 Z= 0.130 Angle : 0.610 14.342 57063 Z= 0.304 Chirality : 0.042 0.266 6543 Planarity : 0.003 0.048 7356 Dihedral : 7.081 87.783 5898 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 1.60 % Allowed : 15.71 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.44 % 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: 1.34 (0.12), residues: 5228 helix: 1.51 (0.10), residues: 2782 sheet: -0.18 (0.20), residues: 614 loop : 0.50 (0.16), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 78 TYR 0.027 0.001 TYR K 70 PHE 0.031 0.001 PHE C 264 TRP 0.030 0.002 TRP M 315 HIS 0.005 0.001 HIS N 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (42204) covalent geometry : angle 0.61037 / 0.30 (57063) hydrogen bonds : bond 0.03453 / 2.25 ( 2150) hydrogen bonds : angle 4.37542 / 3.12 ( 6165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 265 time to evaluate : 1.294 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8947 (mtmm) cc_final: 0.8656 (mtmm) REVERT: A 65 GLU cc_start: 0.8610 (pp20) cc_final: 0.8372 (pp20) REVERT: A 66 LYS cc_start: 0.8640 (mttt) cc_final: 0.8247 (mttm) REVERT: A 172 MET cc_start: 0.7192 (pmm) cc_final: 0.6963 (pmm) REVERT: A 297 MET cc_start: 0.4117 (ptm) cc_final: 0.3776 (ppp) REVERT: A 428 MET cc_start: 0.2103 (tpt) cc_final: 0.1671 (ttt) REVERT: B 119 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8816 (tp) REVERT: B 128 TYR cc_start: 0.9179 (m-80) cc_final: 0.8720 (m-80) REVERT: B 171 MET cc_start: 0.3350 (mtt) cc_final: 0.2542 (mtm) REVERT: B 173 MET cc_start: 0.5562 (mtt) cc_final: 0.4840 (mmt) REVERT: B 259 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.8019 (t70) REVERT: B 369 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7426 (ttt) REVERT: C 124 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7489 (tmm) REVERT: C 503 ASP cc_start: 0.8930 (t0) cc_final: 0.8653 (p0) REVERT: C 583 ASP cc_start: 0.9326 (m-30) cc_final: 0.8984 (p0) REVERT: C 790 MET cc_start: 0.9059 (mmp) cc_final: 0.8677 (tpp) REVERT: C 815 MET cc_start: 0.8173 (mtp) cc_final: 0.7738 (mtt) REVERT: C 862 MET cc_start: 0.8340 (tpp) cc_final: 0.8007 (tpp) REVERT: I 247 MET cc_start: 0.8692 (mmm) cc_final: 0.8291 (mmm) REVERT: I 269 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8830 (pm20) REVERT: I 272 MET cc_start: 0.9670 (ptm) cc_final: 0.9432 (ptt) REVERT: I 292 MET cc_start: 0.7024 (tpp) cc_final: 0.6733 (tpp) REVERT: J 221 MET cc_start: 0.8987 (ptp) cc_final: 0.8582 (ptp) REVERT: J 252 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8491 (ttp80) REVERT: J 253 MET cc_start: 0.8347 (ptm) cc_final: 0.7623 (ptm) REVERT: J 272 ASP cc_start: 0.8233 (t70) cc_final: 0.7358 (p0) REVERT: J 347 ARG cc_start: 0.9335 (ttt180) cc_final: 0.9089 (tpp-160) REVERT: J 367 ASP cc_start: 0.7682 (t0) cc_final: 0.7234 (t0) REVERT: K 93 ASN cc_start: 0.9459 (m110) cc_final: 0.9223 (p0) REVERT: K 109 MET cc_start: 0.8307 (mmp) cc_final: 0.8066 (mmp) REVERT: K 312 MET cc_start: 0.7673 (ptm) cc_final: 0.7303 (ptm) REVERT: K 382 MET cc_start: 0.8729 (mmt) cc_final: 0.8298 (mpp) REVERT: K 416 MET cc_start: 0.3207 (ppp) cc_final: 0.2431 (ppp) REVERT: N 1 MET cc_start: 0.8570 (mtt) cc_final: 0.8173 (ptm) REVERT: N 11 MET cc_start: 0.8229 (mpp) cc_final: 0.7962 (mpp) REVERT: N 136 LYS cc_start: 0.6077 (OUTLIER) cc_final: 0.5546 (pptt) REVERT: N 146 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7456 (mpt90) REVERT: P 201 MET cc_start: 0.7732 (mmt) cc_final: 0.7422 (mmp) REVERT: P 210 MET cc_start: 0.2776 (mtp) cc_final: 0.2316 (mtp) REVERT: P 254 MET cc_start: 0.0642 (ttp) cc_final: -0.0576 (ttp) REVERT: P 315 PHE cc_start: 0.5955 (OUTLIER) cc_final: 0.3045 (t80) REVERT: P 368 MET cc_start: 0.2882 (mtp) cc_final: 0.2354 (ptp) REVERT: Z 217 MET cc_start: 0.4341 (ptt) cc_final: 0.3499 (ptt) REVERT: Z 241 LEU cc_start: 0.8491 (mt) cc_final: 0.8287 (mt) REVERT: Z 429 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: Z 489 MET cc_start: 0.8133 (mmt) cc_final: 0.7606 (mmp) REVERT: Z 641 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8579 (mm) outliers start: 73 outliers final: 58 residues processed: 327 average time/residue: 0.2264 time to fit residues: 125.9557 Evaluate side-chains 330 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 262 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 894 MET Chi-restraints excluded: chain C residue 898 HIS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 67 TYR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 330 ARG Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 283 VAL Chi-restraints excluded: chain K residue 290 ARG Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 324 ILE Chi-restraints excluded: chain K residue 349 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 277 GLU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 402 GLU Chi-restraints excluded: chain N residue 23 HIS Chi-restraints excluded: chain N residue 49 HIS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 136 LYS Chi-restraints excluded: chain P residue 53 HIS Chi-restraints excluded: chain P residue 77 TYR Chi-restraints excluded: chain P residue 86 MET Chi-restraints excluded: chain P residue 150 LYS Chi-restraints excluded: chain P residue 238 GLN Chi-restraints excluded: chain P residue 288 THR Chi-restraints excluded: chain P residue 315 PHE Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 381 GLU Chi-restraints excluded: chain Z residue 429 GLU Chi-restraints excluded: chain Z residue 483 LEU Chi-restraints excluded: chain Z residue 499 HIS Chi-restraints excluded: chain Z residue 641 LEU Chi-restraints excluded: chain Z residue 644 LEU Chi-restraints excluded: chain Z residue 645 THR Chi-restraints excluded: chain Z residue 657 MET Chi-restraints excluded: chain Z residue 737 SER Chi-restraints excluded: chain Z residue 743 PHE Chi-restraints excluded: chain Z residue 752 SER Chi-restraints excluded: chain Z residue 866 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: [205, 193, 55, 32, 320, 470, 446, 342, 116, 14, 453] chunk 205 optimal weight: 7.9990 chunk 193 optimal weight: 30.0000 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 320 optimal weight: 4.9990 chunk 470 optimal weight: 0.9980 chunk 446 optimal weight: 0.1980 chunk 342 optimal weight: 4.9990 chunk 116 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 453 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 HIS ** C 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 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 = 0.4297 r_free = 0.4297 target = 0.087451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.063527 restraints weight = 375429.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.063628 restraints weight = 257212.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.063678 restraints weight = 180768.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.063864 restraints weight = 134372.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.063821 restraints weight = 123830.531| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42204 Z= 0.117 Angle : 0.599 13.889 57063 Z= 0.297 Chirality : 0.042 0.198 6543 Planarity : 0.003 0.049 7356 Dihedral : 7.021 89.625 5898 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.08 % Favored : 96.88 % Rotamer: Outliers : 1.60 % Allowed : 15.77 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.44 % 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: 1.37 (0.12), residues: 5228 helix: 1.53 (0.10), residues: 2789 sheet: -0.20 (0.20), residues: 617 loop : 0.53 (0.16), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 90 TYR 0.033 0.001 TYR I 94 PHE 0.033 0.001 PHE C 264 TRP 0.027 0.001 TRP M 315 HIS 0.005 0.001 HIS N 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (42204) covalent geometry : angle 0.59929 / 0.30 (57063) hydrogen bonds : bond 0.03346 / 2.18 ( 2150) hydrogen bonds : angle 4.32798 / 3.08 ( 6165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13139.63 seconds wall clock time: 224 minutes 52.98 seconds (13492.98 seconds total)