Starting phenix.real_space_refine on Sun May 3 15:28:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pwc_71914/05_2026/9pwc_71914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pwc_71914/05_2026/9pwc_71914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pwc_71914/05_2026/9pwc_71914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pwc_71914/05_2026/9pwc_71914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pwc_71914/05_2026/9pwc_71914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pwc_71914/05_2026/9pwc_71914.map" } resolution = 3.0 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= 0.003 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8839 2.51 5 N 2344 2.21 5 O 2564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13819 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4836 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 22, 'TRANS': 590} Chain: "B" Number of atoms: 4413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4413 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 26, 'TRANS': 530} Chain: "C" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 122 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 3, 'TRANS': 11} Chain breaks: 1 Chain: "M" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3258 Classifications: {'peptide': 408} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 390} Chain breaks: 3 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "S" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1190 Classifications: {'peptide': 141} Link IDs: {'TRANS': 140} Time building chain proxies: 3.20, per 1000 atoms: 0.23 Number of scatterers: 13819 At special positions: 0 Unit cell: (105.996, 117.384, 125.268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2564 8.00 N 2344 7.00 C 8839 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: 0.97 Conformation dependent library (CDL) restraints added in 728.2 milliseconds 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 10 sheets defined 62.1% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 25 through 45 Processing helix chain 'A' and resid 51 through 69 removed outlier: 3.501A pdb=" N LYS A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 83 removed outlier: 3.645A pdb=" N VAL A 80 " --> pdb=" O HIS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 124 through 138 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 215 removed outlier: 3.764A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.920A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 273 through 292 removed outlier: 3.548A pdb=" N ARG A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.994A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.732A pdb=" N THR A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 361 removed outlier: 6.207A pdb=" N PHE A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 361' Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 382 through 396 Processing helix chain 'A' and resid 401 through 414 removed outlier: 3.753A pdb=" N GLU A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 435 Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.823A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 4.250A pdb=" N VAL A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRP A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 512 Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.817A pdb=" N LYS A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 533 removed outlier: 3.531A pdb=" N CYS A 533 " --> pdb=" O PHE A 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 530 through 533' Processing helix chain 'A' and resid 534 through 552 Processing helix chain 'A' and resid 555 through 564 Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 590 Processing helix chain 'A' and resid 593 through 599 removed outlier: 3.766A pdb=" N THR A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 620 removed outlier: 3.839A pdb=" N LYS A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 4.388A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 62 through 74 Processing helix chain 'B' and resid 86 through 95 removed outlier: 3.700A pdb=" N SER B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.502A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 131 removed outlier: 3.928A pdb=" N LYS B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 152 removed outlier: 3.551A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 170 removed outlier: 4.052A pdb=" N ASP B 163 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 165 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 252 through 266 Processing helix chain 'B' and resid 274 through 284 removed outlier: 4.236A pdb=" N ASN B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 291 removed outlier: 3.654A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.903A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.680A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 350 through 362 Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.566A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.803A pdb=" N ASP B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 435 removed outlier: 3.809A pdb=" N GLU B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 461 through 468 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.671A pdb=" N GLU B 476 " --> pdb=" O PHE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 499 through 512 Processing helix chain 'B' and resid 516 through 533 removed outlier: 3.505A pdb=" N ASP B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 542 Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.723A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.828A pdb=" N VAL C 155 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN C 156 " --> pdb=" O GLU C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 156' Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 74 through 94 Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 115 removed outlier: 3.958A pdb=" N ILE M 108 " --> pdb=" O ASN M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 157 removed outlier: 3.879A pdb=" N GLN M 148 " --> pdb=" O THR M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 418 Processing helix chain 'S' and resid 24 through 42 removed outlier: 4.048A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 95 removed outlier: 3.661A pdb=" N TYR S 80 " --> pdb=" O ASN S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 106 removed outlier: 3.712A pdb=" N LEU S 103 " --> pdb=" O CYS S 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 127 through 141 Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA2, first strand: chain 'C' and resid 69 through 70 removed outlier: 6.686A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER M 186 " --> pdb=" O VAL M 191 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL M 191 " --> pdb=" O SER M 186 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL M 196 " --> pdb=" O ARG M 278 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG M 278 " --> pdb=" O VAL M 196 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY M 198 " --> pdb=" O ARG M 276 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG M 276 " --> pdb=" O GLY M 198 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL M 200 " --> pdb=" O LEU M 274 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP M 245 " --> pdb=" O ARG M 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 70 removed outlier: 5.052A pdb=" N ARG M 427 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL M 392 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER M 387 " --> pdb=" O ARG M 323 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 16 through 18 Processing sheet with id=AA5, first strand: chain 'M' and resid 116 through 117 Processing sheet with id=AA6, first strand: chain 'M' and resid 263 through 265 removed outlier: 3.977A pdb=" N ILE M 263 " --> pdb=" O PHE M 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 287 through 296 removed outlier: 3.732A pdb=" N VAL M 296 " --> pdb=" O LYS M 300 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS M 300 " --> pdb=" O VAL M 296 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL M 303 " --> pdb=" O ALA M 368 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL M 305 " --> pdb=" O ILE M 366 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE M 366 " --> pdb=" O VAL M 305 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE M 307 " --> pdb=" O SER M 364 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER M 364 " --> pdb=" O ILE M 307 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.425A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP S 19 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ARG S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.425A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP S 19 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ARG S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 118 through 119 789 hydrogen bonds defined for protein. 2289 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: 2.43 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4513 1.34 - 1.46: 2331 1.46 - 1.58: 7109 1.58 - 1.69: 0 1.69 - 1.81: 111 Bond restraints: 14064 Sorted by residual: bond pdb=" N ASP A 181 " pdb=" CA ASP A 181 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 5.98e+00 bond pdb=" C SER A 179 " pdb=" N PRO A 180 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.19e-02 7.06e+03 4.48e+00 bond pdb=" CA ASP A 473 " pdb=" CB ASP A 473 " ideal model delta sigma weight residual 1.530 1.555 -0.025 1.69e-02 3.50e+03 2.12e+00 bond pdb=" N MET M 361 " pdb=" CA MET M 361 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.88e+00 bond pdb=" CA ASP A 473 " pdb=" C ASP A 473 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.34e-02 5.57e+03 1.76e+00 ... (remaining 14059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 18856 2.19 - 4.39: 161 4.39 - 6.58: 20 6.58 - 8.78: 4 8.78 - 10.97: 1 Bond angle restraints: 19042 Sorted by residual: angle pdb=" CA MET M 361 " pdb=" CB MET M 361 " pdb=" CG MET M 361 " ideal model delta sigma weight residual 114.10 122.11 -8.01 2.00e+00 2.50e-01 1.61e+01 angle pdb=" CA ASP A 473 " pdb=" CB ASP A 473 " pdb=" CG ASP A 473 " ideal model delta sigma weight residual 112.60 116.37 -3.77 1.00e+00 1.00e+00 1.42e+01 angle pdb=" CB MET M 361 " pdb=" CG MET M 361 " pdb=" SD MET M 361 " ideal model delta sigma weight residual 112.70 123.67 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA ARG A 11 " pdb=" CB ARG A 11 " pdb=" CG ARG A 11 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" C ARG A 472 " pdb=" N ASP A 473 " pdb=" CA ASP A 473 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 ... (remaining 19037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7299 17.93 - 35.86: 987 35.86 - 53.78: 272 53.78 - 71.71: 69 71.71 - 89.64: 25 Dihedral angle restraints: 8652 sinusoidal: 3512 harmonic: 5140 Sorted by residual: dihedral pdb=" CA HIS B 250 " pdb=" C HIS B 250 " pdb=" N ALA B 251 " pdb=" CA ALA B 251 " ideal model delta harmonic sigma weight residual 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA LEU B 199 " pdb=" C LEU B 199 " pdb=" N ASN B 200 " pdb=" CA ASN B 200 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA TRP A 462 " pdb=" C TRP A 462 " pdb=" N TYR A 463 " pdb=" CA TYR A 463 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 8649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1936 0.058 - 0.116: 262 0.116 - 0.173: 21 0.173 - 0.231: 0 0.231 - 0.289: 2 Chirality restraints: 2221 Sorted by residual: chirality pdb=" CB VAL A 475 " pdb=" CA VAL A 475 " pdb=" CG1 VAL A 475 " pdb=" CG2 VAL A 475 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE M 151 " pdb=" CA ILE M 151 " pdb=" CG1 ILE M 151 " pdb=" CG2 ILE M 151 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA MET M 361 " pdb=" N MET M 361 " pdb=" C MET M 361 " pdb=" CB MET M 361 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 2218 not shown) Planarity restraints: 2421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 473 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.93e+00 pdb=" C ASP A 473 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP A 473 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP A 474 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 179 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C SER A 179 " -0.034 2.00e-02 2.50e+03 pdb=" O SER A 179 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 180 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 295 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO B 296 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.025 5.00e-02 4.00e+02 ... (remaining 2418 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 284 2.70 - 3.25: 13167 3.25 - 3.80: 20914 3.80 - 4.35: 27467 4.35 - 4.90: 46788 Nonbonded interactions: 108620 Sorted by model distance: nonbonded pdb=" OD1 ASP A 417 " pdb=" OG SER A 419 " model vdw 2.149 3.040 nonbonded pdb=" OE1 GLU B 297 " pdb=" OH TYR M 83 " model vdw 2.195 3.040 nonbonded pdb=" O SER M 124 " pdb=" OG SER M 124 " model vdw 2.201 3.040 nonbonded pdb=" OE1 GLU B 186 " pdb=" OH TYR M 120 " model vdw 2.203 3.040 nonbonded pdb=" N GLU A 142 " pdb=" OE1 GLU A 142 " model vdw 2.217 3.120 ... (remaining 108615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.590 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 0.039 14064 Z= 0.129 Angle : 0.551 10.973 19042 Z= 0.306 Chirality : 0.040 0.289 2221 Planarity : 0.004 0.045 2421 Dihedral : 18.403 89.641 5300 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.39 % Allowed : 31.56 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.05 (0.20), residues: 1716 helix: 1.53 (0.17), residues: 980 sheet: 0.67 (0.40), residues: 170 loop : -0.74 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 235 TYR 0.014 0.001 TYR A 418 PHE 0.021 0.001 PHE A 97 TRP 0.024 0.001 TRP A 462 HIS 0.008 0.001 HIS M 195 Details of bonding type rmsd covalent geometry : bond 0.00267 (14064) covalent geometry : angle 0.55143 (19042) hydrogen bonds : bond 0.16741 ( 785) hydrogen bonds : angle 5.59415 ( 2289) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 345 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 SER cc_start: 0.8009 (m) cc_final: 0.7742 (p) REVERT: A 178 THR cc_start: 0.8213 (t) cc_final: 0.7975 (t) REVERT: A 216 GLN cc_start: 0.7635 (mt0) cc_final: 0.7357 (mt0) REVERT: A 286 THR cc_start: 0.8461 (m) cc_final: 0.8196 (t) REVERT: A 289 ASN cc_start: 0.7343 (m-40) cc_final: 0.6868 (m-40) REVERT: A 321 ASP cc_start: 0.8036 (t0) cc_final: 0.7749 (t0) REVERT: A 339 GLN cc_start: 0.8602 (mt0) cc_final: 0.8354 (mm-40) REVERT: A 375 ASN cc_start: 0.8169 (t0) cc_final: 0.7922 (t0) REVERT: A 408 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7241 (mm-30) REVERT: A 434 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7942 (ttmm) REVERT: B 152 ASN cc_start: 0.8409 (t160) cc_final: 0.7884 (t0) REVERT: B 155 MET cc_start: 0.3974 (mtp) cc_final: 0.3486 (mtt) REVERT: B 200 ASN cc_start: 0.6804 (p0) cc_final: 0.6332 (p0) REVERT: B 233 ASP cc_start: 0.7854 (t0) cc_final: 0.7515 (p0) REVERT: B 313 ARG cc_start: 0.8165 (mmt-90) cc_final: 0.7902 (tpt170) REVERT: B 360 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7575 (mm-30) REVERT: B 512 GLN cc_start: 0.8009 (mt0) cc_final: 0.7795 (mt0) REVERT: B 543 SER cc_start: 0.8657 (p) cc_final: 0.8344 (m) REVERT: M 102 LYS cc_start: 0.7766 (mmtt) cc_final: 0.7555 (mmtm) REVERT: M 103 ASN cc_start: 0.8080 (m-40) cc_final: 0.7755 (m-40) REVERT: M 125 GLU cc_start: 0.7685 (tp30) cc_final: 0.7469 (tp30) REVERT: M 203 LYS cc_start: 0.7318 (mtmt) cc_final: 0.7115 (mtmt) REVERT: M 209 MET cc_start: 0.7047 (mmm) cc_final: 0.6455 (mmt) REVERT: M 250 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7999 (mm-40) REVERT: M 391 GLU cc_start: 0.7059 (tt0) cc_final: 0.6741 (tt0) REVERT: M 408 GLU cc_start: 0.6430 (mm-30) cc_final: 0.5911 (mm-30) REVERT: S 21 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7358 (ptp) REVERT: S 40 THR cc_start: 0.8335 (t) cc_final: 0.8133 (t) REVERT: S 132 LEU cc_start: 0.8291 (mm) cc_final: 0.7990 (mm) REVERT: S 138 LEU cc_start: 0.8276 (mt) cc_final: 0.7967 (mp) outliers start: 6 outliers final: 3 residues processed: 347 average time/residue: 0.7936 time to fit residues: 295.6356 Evaluate side-chains 298 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 294 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain S residue 21 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 124 ASN A 166 GLN A 197 ASN A 216 GLN A 307 ASN A 332 ASN A 375 ASN A 448 ASN A 467 GLN A 524 ASN A 577 GLN A 578 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 173 ASN B 238 GLN B 329 ASN B 348 GLN B 435 ASN B 461 ASN B 505 GLN B 516 ASN B 579 ASN M 42 GLN M 123 ASN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN M 158 GLN M 250 GLN S 48 ASN S 86 ASN S 92 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.144229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116929 restraints weight = 19962.287| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.12 r_work: 0.3337 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14064 Z= 0.153 Angle : 0.549 9.074 19042 Z= 0.289 Chirality : 0.041 0.199 2221 Planarity : 0.004 0.047 2421 Dihedral : 4.365 51.096 1886 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.61 % Allowed : 27.60 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.22 (0.20), residues: 1716 helix: 1.61 (0.16), residues: 997 sheet: 1.03 (0.40), residues: 169 loop : -0.72 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 141 TYR 0.020 0.001 TYR A 347 PHE 0.018 0.002 PHE S 52 TRP 0.019 0.001 TRP A 462 HIS 0.010 0.001 HIS S 96 Details of bonding type rmsd covalent geometry : bond 0.00357 (14064) covalent geometry : angle 0.54944 (19042) hydrogen bonds : bond 0.04684 ( 785) hydrogen bonds : angle 4.34890 ( 2289) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 320 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6431 (mtt) cc_final: 0.6037 (mtt) REVERT: A 35 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7862 (ptmm) REVERT: A 191 ARG cc_start: 0.8301 (ttm110) cc_final: 0.7958 (ttm110) REVERT: A 238 THR cc_start: 0.8388 (t) cc_final: 0.8016 (p) REVERT: A 247 TYR cc_start: 0.8630 (m-80) cc_final: 0.8310 (m-80) REVERT: A 289 ASN cc_start: 0.7795 (m-40) cc_final: 0.7334 (m-40) REVERT: A 321 ASP cc_start: 0.8364 (t0) cc_final: 0.7991 (t0) REVERT: A 339 GLN cc_start: 0.8777 (mt0) cc_final: 0.8548 (mt0) REVERT: A 381 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7246 (ppt170) REVERT: A 386 ARG cc_start: 0.8532 (mtp180) cc_final: 0.8315 (ttp-170) REVERT: A 472 ARG cc_start: 0.7829 (mmm160) cc_final: 0.7587 (mmp-170) REVERT: A 567 SER cc_start: 0.8793 (m) cc_final: 0.8513 (p) REVERT: B 152 ASN cc_start: 0.8610 (t0) cc_final: 0.8303 (t0) REVERT: B 155 MET cc_start: 0.4453 (mtp) cc_final: 0.4182 (mtm) REVERT: B 200 ASN cc_start: 0.7307 (p0) cc_final: 0.6811 (p0) REVERT: B 236 GLU cc_start: 0.8046 (tt0) cc_final: 0.7694 (tt0) REVERT: B 313 ARG cc_start: 0.8394 (mmt-90) cc_final: 0.8170 (mmt180) REVERT: B 348 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7909 (tp40) REVERT: B 360 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7998 (mm-30) REVERT: B 386 GLN cc_start: 0.8401 (mp10) cc_final: 0.7966 (mp10) REVERT: B 512 GLN cc_start: 0.8215 (mt0) cc_final: 0.7951 (mt0) REVERT: B 543 SER cc_start: 0.8788 (p) cc_final: 0.8461 (m) REVERT: B 552 THR cc_start: 0.8500 (p) cc_final: 0.8203 (m) REVERT: M 80 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7861 (mm-30) REVERT: M 103 ASN cc_start: 0.8008 (m-40) cc_final: 0.7608 (m-40) REVERT: M 114 GLU cc_start: 0.6076 (tt0) cc_final: 0.5840 (tt0) REVERT: M 125 GLU cc_start: 0.8117 (tp30) cc_final: 0.7869 (tp30) REVERT: M 168 TYR cc_start: 0.8406 (m-80) cc_final: 0.8205 (m-80) REVERT: M 184 LEU cc_start: 0.7129 (tt) cc_final: 0.6886 (tp) REVERT: M 190 GLN cc_start: 0.7851 (tt0) cc_final: 0.7608 (tt0) REVERT: M 209 MET cc_start: 0.7295 (mmm) cc_final: 0.6856 (mmt) REVERT: M 218 ASP cc_start: 0.7498 (t0) cc_final: 0.7297 (t0) REVERT: M 280 THR cc_start: 0.8364 (p) cc_final: 0.8046 (m) REVERT: M 312 LYS cc_start: 0.7435 (tptp) cc_final: 0.6938 (tptt) REVERT: M 369 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.6006 (mm-30) REVERT: M 408 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6420 (mm-30) REVERT: S 21 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7796 (ptp) REVERT: S 40 THR cc_start: 0.8461 (t) cc_final: 0.8261 (t) REVERT: S 122 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7914 (mt-10) REVERT: S 132 LEU cc_start: 0.8377 (mm) cc_final: 0.8174 (mm) REVERT: S 138 LEU cc_start: 0.8424 (mt) cc_final: 0.8176 (mp) outliers start: 71 outliers final: 25 residues processed: 361 average time/residue: 0.7165 time to fit residues: 278.6512 Evaluate side-chains 330 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 150 GLN Chi-restraints excluded: chain M residue 185 MET Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain M residue 273 GLU Chi-restraints excluded: chain M residue 343 LYS Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain M residue 369 GLU Chi-restraints excluded: chain M residue 408 GLU Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain S residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 124 ASN A 197 ASN A 578 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN B 329 ASN B 348 GLN B 435 ASN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN M 195 HIS M 250 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.144012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116771 restraints weight = 19957.443| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.12 r_work: 0.3334 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14064 Z= 0.145 Angle : 0.532 8.360 19042 Z= 0.278 Chirality : 0.041 0.246 2221 Planarity : 0.004 0.050 2421 Dihedral : 4.296 51.723 1884 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.13 % Allowed : 26.10 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.18 (0.20), residues: 1716 helix: 1.59 (0.16), residues: 1007 sheet: 1.12 (0.40), residues: 169 loop : -0.85 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 60 TYR 0.017 0.001 TYR M 8 PHE 0.014 0.001 PHE M 93 TRP 0.018 0.001 TRP A 462 HIS 0.007 0.001 HIS S 96 Details of bonding type rmsd covalent geometry : bond 0.00338 (14064) covalent geometry : angle 0.53223 (19042) hydrogen bonds : bond 0.04433 ( 785) hydrogen bonds : angle 4.15395 ( 2289) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 304 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7841 (ptmm) REVERT: A 39 ASN cc_start: 0.7016 (t0) cc_final: 0.6734 (t0) REVERT: A 191 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8006 (ttm110) REVERT: A 247 TYR cc_start: 0.8621 (m-80) cc_final: 0.8413 (m-80) REVERT: A 289 ASN cc_start: 0.7813 (m-40) cc_final: 0.7354 (m-40) REVERT: A 321 ASP cc_start: 0.8368 (t0) cc_final: 0.7959 (t0) REVERT: A 339 GLN cc_start: 0.8771 (mt0) cc_final: 0.8538 (mt0) REVERT: A 371 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8171 (mm-30) REVERT: A 386 ARG cc_start: 0.8502 (mtp180) cc_final: 0.8189 (mtt90) REVERT: A 472 ARG cc_start: 0.7820 (mmm160) cc_final: 0.7583 (mmp-170) REVERT: A 554 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7794 (pt0) REVERT: A 567 SER cc_start: 0.8775 (m) cc_final: 0.8515 (p) REVERT: B 233 ASP cc_start: 0.7332 (t0) cc_final: 0.7122 (t0) REVERT: B 236 GLU cc_start: 0.8017 (tt0) cc_final: 0.7732 (tt0) REVERT: B 348 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8048 (tp40) REVERT: B 360 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 386 GLN cc_start: 0.8418 (mp10) cc_final: 0.8040 (mp10) REVERT: B 415 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8171 (ttp-170) REVERT: B 459 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6522 (mt) REVERT: B 512 GLN cc_start: 0.8204 (mt0) cc_final: 0.7906 (mt0) REVERT: B 543 SER cc_start: 0.8832 (p) cc_final: 0.8465 (m) REVERT: M 80 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7817 (mm-30) REVERT: M 103 ASN cc_start: 0.8005 (m-40) cc_final: 0.7628 (m-40) REVERT: M 125 GLU cc_start: 0.8111 (tp30) cc_final: 0.7873 (tp30) REVERT: M 168 TYR cc_start: 0.8418 (m-80) cc_final: 0.8199 (m-80) REVERT: M 178 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7194 (mp) REVERT: M 190 GLN cc_start: 0.7850 (tt0) cc_final: 0.7621 (tt0) REVERT: M 209 MET cc_start: 0.7307 (mmm) cc_final: 0.6844 (mmt) REVERT: M 218 ASP cc_start: 0.7473 (t0) cc_final: 0.7260 (t0) REVERT: M 280 THR cc_start: 0.8385 (p) cc_final: 0.8035 (m) REVERT: M 312 LYS cc_start: 0.7595 (tptp) cc_final: 0.7136 (tptt) REVERT: M 369 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5973 (mm-30) REVERT: M 408 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6396 (mm-30) REVERT: S 21 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7853 (ptp) REVERT: S 40 THR cc_start: 0.8471 (t) cc_final: 0.8251 (t) REVERT: S 122 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7927 (mt-10) REVERT: S 138 LEU cc_start: 0.8462 (mt) cc_final: 0.8216 (mp) outliers start: 79 outliers final: 27 residues processed: 351 average time/residue: 0.7315 time to fit residues: 276.3047 Evaluate side-chains 333 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 295 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 71 GLN Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 262 SER Chi-restraints excluded: chain M residue 343 LYS Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain M residue 369 GLU Chi-restraints excluded: chain M residue 408 GLU Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 93 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 136 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.0980 chunk 90 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 103 ASN A 124 ASN A 197 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN B 329 ASN B 348 GLN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN M 195 HIS M 250 GLN M 365 GLN S 77 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.143871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116764 restraints weight = 19721.217| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.11 r_work: 0.3337 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14064 Z= 0.137 Angle : 0.534 8.908 19042 Z= 0.276 Chirality : 0.040 0.159 2221 Planarity : 0.004 0.050 2421 Dihedral : 4.278 52.347 1882 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.81 % Allowed : 26.95 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.27 (0.20), residues: 1716 helix: 1.65 (0.16), residues: 1007 sheet: 1.32 (0.40), residues: 163 loop : -0.81 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 21 TYR 0.022 0.001 TYR A 347 PHE 0.013 0.001 PHE M 93 TRP 0.018 0.001 TRP A 462 HIS 0.010 0.001 HIS M 195 Details of bonding type rmsd covalent geometry : bond 0.00317 (14064) covalent geometry : angle 0.53359 (19042) hydrogen bonds : bond 0.04172 ( 785) hydrogen bonds : angle 4.04237 ( 2289) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 299 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7830 (ptmm) REVERT: A 39 ASN cc_start: 0.7008 (t0) cc_final: 0.6723 (t0) REVERT: A 191 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7897 (mtm180) REVERT: A 285 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 289 ASN cc_start: 0.7814 (m-40) cc_final: 0.7370 (m-40) REVERT: A 339 GLN cc_start: 0.8782 (mt0) cc_final: 0.8545 (mt0) REVERT: A 371 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8164 (mm-30) REVERT: A 386 ARG cc_start: 0.8514 (mtp180) cc_final: 0.8217 (mtt90) REVERT: A 554 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7755 (pt0) REVERT: A 567 SER cc_start: 0.8773 (m) cc_final: 0.8521 (p) REVERT: A 617 LYS cc_start: 0.6457 (OUTLIER) cc_final: 0.6015 (mppt) REVERT: B 86 MET cc_start: 0.6428 (ptp) cc_final: 0.6115 (ptp) REVERT: B 152 ASN cc_start: 0.8614 (t0) cc_final: 0.8306 (t0) REVERT: B 236 GLU cc_start: 0.8016 (tt0) cc_final: 0.7705 (tt0) REVERT: B 348 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8163 (tp-100) REVERT: B 360 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7957 (mm-30) REVERT: B 386 GLN cc_start: 0.8424 (mp10) cc_final: 0.8146 (mp10) REVERT: B 415 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8171 (ttp-170) REVERT: B 512 GLN cc_start: 0.8210 (mt0) cc_final: 0.7957 (mt0) REVERT: M 80 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7812 (mm-30) REVERT: M 103 ASN cc_start: 0.8028 (m-40) cc_final: 0.7716 (m-40) REVERT: M 114 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6404 (tp30) REVERT: M 125 GLU cc_start: 0.8092 (tp30) cc_final: 0.7873 (tp30) REVERT: M 178 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7208 (mt) REVERT: M 190 GLN cc_start: 0.7838 (tt0) cc_final: 0.7613 (tt0) REVERT: M 209 MET cc_start: 0.7280 (mmm) cc_final: 0.6828 (mmt) REVERT: M 218 ASP cc_start: 0.7510 (t0) cc_final: 0.7224 (t0) REVERT: M 241 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8368 (pp) REVERT: M 280 THR cc_start: 0.8398 (p) cc_final: 0.8014 (m) REVERT: M 312 LYS cc_start: 0.7606 (tptp) cc_final: 0.7182 (tptt) REVERT: M 369 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5923 (mm-30) REVERT: M 408 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6359 (mm-30) REVERT: S 21 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7816 (ptp) REVERT: S 40 THR cc_start: 0.8469 (t) cc_final: 0.8253 (t) REVERT: S 138 LEU cc_start: 0.8469 (mt) cc_final: 0.8219 (mp) outliers start: 74 outliers final: 30 residues processed: 338 average time/residue: 0.7304 time to fit residues: 266.0182 Evaluate side-chains 336 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 293 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 71 GLN Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 105 PHE Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 144 THR Chi-restraints excluded: chain M residue 150 GLN Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain M residue 262 SER Chi-restraints excluded: chain M residue 284 ILE Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain M residue 369 GLU Chi-restraints excluded: chain M residue 408 GLU Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain S residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 54 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 73 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 124 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN B 329 ASN B 348 GLN B 408 GLN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN M 195 HIS M 250 GLN M 365 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.144314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117238 restraints weight = 19900.807| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.11 r_work: 0.3342 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14064 Z= 0.122 Angle : 0.519 8.489 19042 Z= 0.269 Chirality : 0.040 0.135 2221 Planarity : 0.004 0.050 2421 Dihedral : 4.246 53.266 1882 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.55 % Allowed : 26.75 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.20), residues: 1716 helix: 1.73 (0.16), residues: 1007 sheet: 1.41 (0.40), residues: 164 loop : -0.77 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 166 TYR 0.017 0.001 TYR A 347 PHE 0.013 0.001 PHE S 52 TRP 0.018 0.001 TRP A 462 HIS 0.010 0.001 HIS M 195 Details of bonding type rmsd covalent geometry : bond 0.00277 (14064) covalent geometry : angle 0.51856 (19042) hydrogen bonds : bond 0.03906 ( 785) hydrogen bonds : angle 3.94523 ( 2289) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 304 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8210 (ptmm) cc_final: 0.7845 (ptmm) REVERT: A 39 ASN cc_start: 0.7004 (t0) cc_final: 0.6717 (t0) REVERT: A 87 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.7106 (mtt90) REVERT: A 103 ASN cc_start: 0.6611 (t0) cc_final: 0.6112 (p0) REVERT: A 191 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7979 (mtt90) REVERT: A 285 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7446 (mt-10) REVERT: A 289 ASN cc_start: 0.7836 (m-40) cc_final: 0.7389 (m-40) REVERT: A 339 GLN cc_start: 0.8803 (mt0) cc_final: 0.8564 (mt0) REVERT: A 554 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7726 (pt0) REVERT: A 567 SER cc_start: 0.8777 (m) cc_final: 0.8530 (p) REVERT: A 617 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.5996 (mppt) REVERT: B 86 MET cc_start: 0.6586 (ptp) cc_final: 0.6271 (ptp) REVERT: B 93 LYS cc_start: 0.7976 (tttt) cc_final: 0.7512 (tmtt) REVERT: B 152 ASN cc_start: 0.8496 (t0) cc_final: 0.8146 (t0) REVERT: B 233 ASP cc_start: 0.7308 (t0) cc_final: 0.7101 (t0) REVERT: B 236 GLU cc_start: 0.8042 (tt0) cc_final: 0.7745 (tt0) REVERT: B 348 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8177 (tp-100) REVERT: B 360 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7977 (mm-30) REVERT: B 386 GLN cc_start: 0.8459 (mp10) cc_final: 0.8166 (mp10) REVERT: B 400 GLN cc_start: 0.8278 (tp40) cc_final: 0.8069 (tp40) REVERT: B 415 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8163 (ttp-170) REVERT: B 512 GLN cc_start: 0.8222 (mt0) cc_final: 0.7904 (mt0) REVERT: M 80 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7746 (mm-30) REVERT: M 103 ASN cc_start: 0.8019 (m-40) cc_final: 0.7701 (m-40) REVERT: M 114 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6395 (tp30) REVERT: M 125 GLU cc_start: 0.8120 (tp30) cc_final: 0.7898 (tp30) REVERT: M 168 TYR cc_start: 0.8412 (m-80) cc_final: 0.8187 (m-80) REVERT: M 178 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7207 (mt) REVERT: M 184 LEU cc_start: 0.7070 (tt) cc_final: 0.6832 (tp) REVERT: M 204 SER cc_start: 0.8123 (OUTLIER) cc_final: 0.7903 (p) REVERT: M 209 MET cc_start: 0.7268 (mmm) cc_final: 0.6820 (mmt) REVERT: M 218 ASP cc_start: 0.7508 (t0) cc_final: 0.7199 (t0) REVERT: M 241 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8257 (pt) REVERT: M 280 THR cc_start: 0.8438 (p) cc_final: 0.8055 (m) REVERT: M 312 LYS cc_start: 0.7618 (tptp) cc_final: 0.7166 (tptt) REVERT: M 369 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5846 (mm-30) REVERT: M 408 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6382 (mm-30) REVERT: S 21 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7759 (ptp) REVERT: S 116 GLU cc_start: 0.8316 (tp30) cc_final: 0.8065 (tp30) REVERT: S 138 LEU cc_start: 0.8476 (mt) cc_final: 0.8224 (mp) outliers start: 70 outliers final: 32 residues processed: 347 average time/residue: 0.7210 time to fit residues: 269.9617 Evaluate side-chains 346 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 300 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 71 GLN Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 105 PHE Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 150 GLN Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain M residue 204 SER Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain M residue 262 SER Chi-restraints excluded: chain M residue 284 ILE Chi-restraints excluded: chain M residue 343 LYS Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain M residue 369 GLU Chi-restraints excluded: chain M residue 408 GLU Chi-restraints excluded: chain S residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 13 optimal weight: 0.0020 chunk 116 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.0040 chunk 68 optimal weight: 0.0060 chunk 1 optimal weight: 3.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN B 329 ASN B 348 GLN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN M 195 HIS M 250 GLN M 365 GLN S 96 HIS S 97 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120533 restraints weight = 19740.809| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.11 r_work: 0.3360 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14064 Z= 0.104 Angle : 0.518 14.384 19042 Z= 0.266 Chirality : 0.039 0.165 2221 Planarity : 0.004 0.048 2421 Dihedral : 4.179 54.111 1882 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.74 % Allowed : 26.95 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.20), residues: 1716 helix: 1.85 (0.16), residues: 1007 sheet: 1.44 (0.39), residues: 164 loop : -0.75 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 166 TYR 0.024 0.001 TYR M 344 PHE 0.021 0.001 PHE M 214 TRP 0.018 0.001 TRP A 462 HIS 0.008 0.001 HIS M 195 Details of bonding type rmsd covalent geometry : bond 0.00226 (14064) covalent geometry : angle 0.51805 (19042) hydrogen bonds : bond 0.03469 ( 785) hydrogen bonds : angle 3.79791 ( 2289) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 307 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7804 (ptmm) REVERT: A 39 ASN cc_start: 0.7014 (t0) cc_final: 0.6732 (t0) REVERT: A 77 MET cc_start: 0.6933 (tpp) cc_final: 0.6430 (tpp) REVERT: A 87 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.7033 (mtt90) REVERT: A 285 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7422 (mt-10) REVERT: A 289 ASN cc_start: 0.7813 (m-40) cc_final: 0.7337 (m-40) REVERT: A 339 GLN cc_start: 0.8750 (mt0) cc_final: 0.8510 (mt0) REVERT: A 370 ILE cc_start: 0.8483 (tp) cc_final: 0.8081 (tt) REVERT: A 386 ARG cc_start: 0.8495 (mtp180) cc_final: 0.8206 (mtt90) REVERT: A 472 ARG cc_start: 0.7784 (mmp-170) cc_final: 0.7528 (mmm160) REVERT: A 554 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7753 (pt0) REVERT: A 567 SER cc_start: 0.8771 (m) cc_final: 0.8505 (p) REVERT: A 617 LYS cc_start: 0.6445 (OUTLIER) cc_final: 0.6017 (mppt) REVERT: B 86 MET cc_start: 0.6544 (ptp) cc_final: 0.6250 (ptp) REVERT: B 93 LYS cc_start: 0.7985 (tttt) cc_final: 0.7515 (tmtt) REVERT: B 152 ASN cc_start: 0.8383 (t0) cc_final: 0.7997 (t0) REVERT: B 348 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8151 (tp40) REVERT: B 360 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7955 (mm-30) REVERT: B 365 VAL cc_start: 0.8427 (m) cc_final: 0.8201 (t) REVERT: B 386 GLN cc_start: 0.8418 (mp10) cc_final: 0.8186 (mp10) REVERT: B 415 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8148 (ttp-170) REVERT: B 436 LEU cc_start: 0.8266 (mt) cc_final: 0.8039 (mt) REVERT: B 512 GLN cc_start: 0.8220 (mt0) cc_final: 0.7896 (mt0) REVERT: B 543 SER cc_start: 0.8828 (p) cc_final: 0.8459 (m) REVERT: M 80 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7752 (mm-30) REVERT: M 103 ASN cc_start: 0.7999 (m-40) cc_final: 0.7686 (m-40) REVERT: M 114 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6403 (tp30) REVERT: M 125 GLU cc_start: 0.8084 (tp30) cc_final: 0.7863 (tp30) REVERT: M 168 TYR cc_start: 0.8402 (m-80) cc_final: 0.8130 (m-80) REVERT: M 178 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7189 (mt) REVERT: M 184 LEU cc_start: 0.7051 (tt) cc_final: 0.6823 (tp) REVERT: M 204 SER cc_start: 0.8139 (OUTLIER) cc_final: 0.7901 (p) REVERT: M 209 MET cc_start: 0.7255 (mmm) cc_final: 0.6827 (mmt) REVERT: M 218 ASP cc_start: 0.7456 (t0) cc_final: 0.7165 (t0) REVERT: M 241 ILE cc_start: 0.8719 (pp) cc_final: 0.8175 (pt) REVERT: M 280 THR cc_start: 0.8465 (p) cc_final: 0.8066 (m) REVERT: M 312 LYS cc_start: 0.7613 (tptp) cc_final: 0.7161 (tptt) REVERT: M 343 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7231 (ttpt) REVERT: M 408 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6249 (mm-30) REVERT: S 21 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7760 (ptp) REVERT: S 40 THR cc_start: 0.8547 (m) cc_final: 0.8180 (m) REVERT: S 116 GLU cc_start: 0.8353 (tp30) cc_final: 0.8082 (tp30) REVERT: S 138 LEU cc_start: 0.8478 (mt) cc_final: 0.8253 (mp) outliers start: 73 outliers final: 31 residues processed: 349 average time/residue: 0.7223 time to fit residues: 272.1542 Evaluate side-chains 336 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 293 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 105 PHE Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 150 GLN Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain M residue 204 SER Chi-restraints excluded: chain M residue 262 SER Chi-restraints excluded: chain M residue 284 ILE Chi-restraints excluded: chain M residue 343 LYS Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain M residue 408 GLU Chi-restraints excluded: chain S residue 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.0870 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 124 ASN A 369 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN B 329 ASN B 348 GLN B 461 ASN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN ** M 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 250 GLN M 365 GLN S 86 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.144518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117603 restraints weight = 19734.631| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.10 r_work: 0.3349 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14064 Z= 0.128 Angle : 0.535 8.795 19042 Z= 0.275 Chirality : 0.040 0.138 2221 Planarity : 0.004 0.049 2421 Dihedral : 4.216 54.493 1882 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.83 % Allowed : 28.51 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.20), residues: 1716 helix: 1.83 (0.16), residues: 1008 sheet: 1.44 (0.39), residues: 164 loop : -0.75 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 42 TYR 0.015 0.001 TYR A 347 PHE 0.013 0.001 PHE S 52 TRP 0.015 0.001 TRP A 462 HIS 0.007 0.001 HIS M 195 Details of bonding type rmsd covalent geometry : bond 0.00300 (14064) covalent geometry : angle 0.53451 (19042) hydrogen bonds : bond 0.03789 ( 785) hydrogen bonds : angle 3.79962 ( 2289) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 297 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7861 (ptmm) REVERT: A 39 ASN cc_start: 0.7029 (t0) cc_final: 0.6737 (t0) REVERT: A 87 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7091 (mtt90) REVERT: A 103 ASN cc_start: 0.6596 (t0) cc_final: 0.6167 (p0) REVERT: A 285 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7407 (mt-10) REVERT: A 289 ASN cc_start: 0.7861 (m-40) cc_final: 0.7405 (m-40) REVERT: A 339 GLN cc_start: 0.8779 (mt0) cc_final: 0.8541 (mt0) REVERT: A 370 ILE cc_start: 0.8478 (tp) cc_final: 0.8071 (tt) REVERT: A 554 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7773 (pt0) REVERT: A 567 SER cc_start: 0.8766 (m) cc_final: 0.8521 (p) REVERT: A 617 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.5999 (mppt) REVERT: B 86 MET cc_start: 0.6646 (ptp) cc_final: 0.6329 (ptp) REVERT: B 93 LYS cc_start: 0.8011 (tttt) cc_final: 0.7553 (tmtt) REVERT: B 152 ASN cc_start: 0.8422 (t0) cc_final: 0.8068 (t0) REVERT: B 233 ASP cc_start: 0.7213 (t0) cc_final: 0.6922 (t0) REVERT: B 337 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7656 (mm-30) REVERT: B 360 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7979 (mm-30) REVERT: B 365 VAL cc_start: 0.8462 (m) cc_final: 0.8241 (t) REVERT: B 459 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6594 (mt) REVERT: B 512 GLN cc_start: 0.8213 (mt0) cc_final: 0.7897 (mt0) REVERT: M 80 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7755 (mm-30) REVERT: M 103 ASN cc_start: 0.8019 (m-40) cc_final: 0.7712 (m-40) REVERT: M 114 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6370 (tp30) REVERT: M 125 GLU cc_start: 0.8136 (tp30) cc_final: 0.7924 (tp30) REVERT: M 163 ARG cc_start: 0.7545 (ttp-110) cc_final: 0.7330 (ttp-170) REVERT: M 168 TYR cc_start: 0.8409 (m-80) cc_final: 0.8112 (m-80) REVERT: M 184 LEU cc_start: 0.7069 (tt) cc_final: 0.6825 (tp) REVERT: M 209 MET cc_start: 0.7243 (mmm) cc_final: 0.6795 (mmt) REVERT: M 218 ASP cc_start: 0.7476 (t0) cc_final: 0.7218 (t0) REVERT: M 241 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8174 (pt) REVERT: M 280 THR cc_start: 0.8518 (p) cc_final: 0.8102 (m) REVERT: M 312 LYS cc_start: 0.7628 (tptp) cc_final: 0.7169 (tptt) REVERT: M 343 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7208 (ttpt) REVERT: M 408 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6302 (mm-30) REVERT: S 21 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7788 (ptp) REVERT: S 40 THR cc_start: 0.8577 (m) cc_final: 0.8203 (m) REVERT: S 116 GLU cc_start: 0.8344 (tp30) cc_final: 0.8090 (tp30) REVERT: S 138 LEU cc_start: 0.8493 (mt) cc_final: 0.8253 (mp) outliers start: 59 outliers final: 30 residues processed: 327 average time/residue: 0.7389 time to fit residues: 259.9766 Evaluate side-chains 331 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 291 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 105 PHE Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 150 GLN Chi-restraints excluded: chain M residue 201 VAL Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain M residue 262 SER Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 343 LYS Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain M residue 408 GLU Chi-restraints excluded: chain S residue 21 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 4 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 124 ASN A 568 GLN B 173 ASN B 329 ASN ** M 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 250 GLN M 365 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.114605 restraints weight = 19631.791| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.09 r_work: 0.3303 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14064 Z= 0.211 Angle : 0.612 9.634 19042 Z= 0.319 Chirality : 0.043 0.192 2221 Planarity : 0.004 0.049 2421 Dihedral : 4.518 53.867 1882 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.77 % Allowed : 28.77 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.14 (0.20), residues: 1716 helix: 1.56 (0.16), residues: 1010 sheet: 1.49 (0.39), residues: 158 loop : -0.98 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 42 TYR 0.021 0.002 TYR M 8 PHE 0.023 0.002 PHE M 214 TRP 0.010 0.002 TRP A 462 HIS 0.007 0.001 HIS M 195 Details of bonding type rmsd covalent geometry : bond 0.00510 (14064) covalent geometry : angle 0.61163 (19042) hydrogen bonds : bond 0.05049 ( 785) hydrogen bonds : angle 4.07088 ( 2289) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 296 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7912 (ptmm) REVERT: A 105 ASN cc_start: 0.7110 (m110) cc_final: 0.6868 (m-40) REVERT: A 285 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7367 (mt-10) REVERT: A 289 ASN cc_start: 0.7952 (m-40) cc_final: 0.7530 (m110) REVERT: A 339 GLN cc_start: 0.8836 (mt0) cc_final: 0.8598 (mt0) REVERT: A 370 ILE cc_start: 0.8443 (tp) cc_final: 0.8052 (tt) REVERT: A 554 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: A 567 SER cc_start: 0.8750 (m) cc_final: 0.8523 (p) REVERT: A 617 LYS cc_start: 0.6466 (OUTLIER) cc_final: 0.6029 (mppt) REVERT: B 86 MET cc_start: 0.6782 (ptp) cc_final: 0.6499 (ptp) REVERT: B 93 LYS cc_start: 0.8054 (tttt) cc_final: 0.7639 (tmtt) REVERT: B 152 ASN cc_start: 0.8615 (t0) cc_final: 0.8343 (t0) REVERT: B 337 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 360 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7904 (mm-30) REVERT: B 415 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8219 (ttp-170) REVERT: B 440 ASP cc_start: 0.7861 (m-30) cc_final: 0.7535 (p0) REVERT: B 512 GLN cc_start: 0.8211 (mt0) cc_final: 0.7968 (mt0) REVERT: M 44 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7854 (mpt180) REVERT: M 80 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: M 103 ASN cc_start: 0.8043 (m-40) cc_final: 0.7737 (m110) REVERT: M 114 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6358 (tp30) REVERT: M 125 GLU cc_start: 0.8114 (tp30) cc_final: 0.7885 (tp30) REVERT: M 133 ILE cc_start: 0.5776 (OUTLIER) cc_final: 0.5488 (mp) REVERT: M 163 ARG cc_start: 0.7669 (ttp-110) cc_final: 0.7429 (ttp-170) REVERT: M 168 TYR cc_start: 0.8522 (m-80) cc_final: 0.8150 (m-80) REVERT: M 184 LEU cc_start: 0.7056 (tt) cc_final: 0.6838 (tp) REVERT: M 190 GLN cc_start: 0.7891 (tt0) cc_final: 0.7676 (tt0) REVERT: M 209 MET cc_start: 0.7300 (mmm) cc_final: 0.6790 (mmt) REVERT: M 241 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8281 (pt) REVERT: M 312 LYS cc_start: 0.7702 (tptp) cc_final: 0.7241 (tptt) REVERT: M 343 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7315 (ttpt) REVERT: M 408 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6475 (mm-30) REVERT: S 21 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7914 (ptp) REVERT: S 116 GLU cc_start: 0.8352 (tp30) cc_final: 0.8097 (tp30) REVERT: S 138 LEU cc_start: 0.8527 (mt) cc_final: 0.8290 (mp) outliers start: 58 outliers final: 22 residues processed: 327 average time/residue: 0.7525 time to fit residues: 264.8902 Evaluate side-chains 323 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 289 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain M residue 262 SER Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 343 LYS Chi-restraints excluded: chain M residue 408 GLU Chi-restraints excluded: chain S residue 21 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 77 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 162 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 103 ASN A 124 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN B 329 ASN B 348 GLN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN ** M 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 250 GLN M 365 GLN S 48 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.145295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118473 restraints weight = 19880.957| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.14 r_work: 0.3335 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14064 Z= 0.128 Angle : 0.559 8.497 19042 Z= 0.290 Chirality : 0.041 0.189 2221 Planarity : 0.004 0.047 2421 Dihedral : 4.299 54.785 1882 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.99 % Allowed : 29.48 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.20), residues: 1716 helix: 1.77 (0.16), residues: 1000 sheet: 1.45 (0.39), residues: 158 loop : -0.83 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 42 TYR 0.030 0.001 TYR M 403 PHE 0.028 0.001 PHE M 214 TRP 0.017 0.001 TRP A 462 HIS 0.006 0.001 HIS M 195 Details of bonding type rmsd covalent geometry : bond 0.00296 (14064) covalent geometry : angle 0.55851 (19042) hydrogen bonds : bond 0.03935 ( 785) hydrogen bonds : angle 3.90717 ( 2289) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 298 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7813 (ptmm) REVERT: A 105 ASN cc_start: 0.7000 (m110) cc_final: 0.6727 (m-40) REVERT: A 285 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7319 (mt-10) REVERT: A 289 ASN cc_start: 0.7923 (m-40) cc_final: 0.7488 (m110) REVERT: A 339 GLN cc_start: 0.8799 (mt0) cc_final: 0.8551 (mt0) REVERT: A 370 ILE cc_start: 0.8406 (tp) cc_final: 0.7998 (tt) REVERT: A 554 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7773 (OUTLIER) REVERT: A 567 SER cc_start: 0.8732 (m) cc_final: 0.8507 (p) REVERT: A 617 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.5991 (mppt) REVERT: B 86 MET cc_start: 0.6792 (ptp) cc_final: 0.6508 (ptp) REVERT: B 93 LYS cc_start: 0.8052 (tttt) cc_final: 0.7621 (tmtt) REVERT: B 152 ASN cc_start: 0.8443 (t0) cc_final: 0.8023 (t0) REVERT: B 320 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7967 (mt-10) REVERT: B 360 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7947 (mm-30) REVERT: B 386 GLN cc_start: 0.8454 (mp10) cc_final: 0.8230 (mp10) REVERT: B 415 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8185 (ttp-170) REVERT: B 440 ASP cc_start: 0.7853 (m-30) cc_final: 0.7517 (p0) REVERT: B 512 GLN cc_start: 0.8200 (mt0) cc_final: 0.7879 (mt0) REVERT: M 80 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7854 (mm-30) REVERT: M 103 ASN cc_start: 0.8003 (m-40) cc_final: 0.7705 (m110) REVERT: M 114 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6348 (tp30) REVERT: M 125 GLU cc_start: 0.8084 (tp30) cc_final: 0.7856 (tp30) REVERT: M 163 ARG cc_start: 0.7581 (ttp-110) cc_final: 0.7350 (ttp-170) REVERT: M 168 TYR cc_start: 0.8514 (m-80) cc_final: 0.8206 (m-80) REVERT: M 178 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7242 (mp) REVERT: M 184 LEU cc_start: 0.7035 (tt) cc_final: 0.6800 (tp) REVERT: M 209 MET cc_start: 0.7315 (mmm) cc_final: 0.6823 (mmt) REVERT: M 241 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8284 (pt) REVERT: M 312 LYS cc_start: 0.7734 (tptp) cc_final: 0.7288 (tptt) REVERT: M 343 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7226 (ttpt) REVERT: M 408 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6443 (mm-30) REVERT: S 40 THR cc_start: 0.8598 (m) cc_final: 0.8207 (m) REVERT: S 116 GLU cc_start: 0.8336 (tp30) cc_final: 0.8070 (tp30) REVERT: S 138 LEU cc_start: 0.8523 (mt) cc_final: 0.8271 (mp) outliers start: 46 outliers final: 28 residues processed: 324 average time/residue: 0.7688 time to fit residues: 268.1810 Evaluate side-chains 328 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 150 GLN Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain M residue 262 SER Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 343 LYS Chi-restraints excluded: chain M residue 408 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 154 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 129 optimal weight: 0.0270 chunk 141 optimal weight: 0.2980 chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 173 ASN B 348 GLN M 150 GLN ** M 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 250 GLN M 365 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.145505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118695 restraints weight = 19690.868| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.13 r_work: 0.3340 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14064 Z= 0.131 Angle : 0.565 10.997 19042 Z= 0.292 Chirality : 0.040 0.145 2221 Planarity : 0.004 0.047 2421 Dihedral : 4.201 55.065 1879 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.86 % Allowed : 30.26 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 1716 helix: 1.81 (0.16), residues: 1000 sheet: 1.38 (0.39), residues: 157 loop : -0.82 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 3 TYR 0.029 0.001 TYR M 403 PHE 0.026 0.001 PHE M 214 TRP 0.016 0.001 TRP A 462 HIS 0.006 0.001 HIS M 195 Details of bonding type rmsd covalent geometry : bond 0.00306 (14064) covalent geometry : angle 0.56536 (19042) hydrogen bonds : bond 0.03924 ( 785) hydrogen bonds : angle 3.88552 ( 2289) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7807 (ptmm) REVERT: A 103 ASN cc_start: 0.6657 (t0) cc_final: 0.6124 (p0) REVERT: A 220 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7441 (mm-30) REVERT: A 285 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7306 (mt-10) REVERT: A 289 ASN cc_start: 0.7920 (m-40) cc_final: 0.7482 (m110) REVERT: A 339 GLN cc_start: 0.8793 (mt0) cc_final: 0.8549 (mt0) REVERT: A 370 ILE cc_start: 0.8410 (tp) cc_final: 0.8008 (tt) REVERT: A 554 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7759 (OUTLIER) REVERT: A 567 SER cc_start: 0.8737 (m) cc_final: 0.8511 (p) REVERT: A 617 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.5989 (mppt) REVERT: B 58 MET cc_start: 0.1017 (mpt) cc_final: 0.0339 (mpt) REVERT: B 86 MET cc_start: 0.6798 (ptp) cc_final: 0.6493 (ptp) REVERT: B 93 LYS cc_start: 0.8056 (tttt) cc_final: 0.7622 (tmtt) REVERT: B 152 ASN cc_start: 0.8433 (t0) cc_final: 0.8079 (t0) REVERT: B 320 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7965 (mt-10) REVERT: B 348 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8277 (tp40) REVERT: B 360 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7876 (mm-30) REVERT: B 415 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8178 (ttp-170) REVERT: B 512 GLN cc_start: 0.8181 (mt0) cc_final: 0.7859 (mt0) REVERT: M 80 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: M 103 ASN cc_start: 0.7996 (m-40) cc_final: 0.7696 (m110) REVERT: M 114 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6309 (tp30) REVERT: M 125 GLU cc_start: 0.8076 (tp30) cc_final: 0.7850 (tp30) REVERT: M 163 ARG cc_start: 0.7588 (ttp-110) cc_final: 0.7354 (ttp-170) REVERT: M 168 TYR cc_start: 0.8514 (m-80) cc_final: 0.8158 (m-80) REVERT: M 178 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7275 (mp) REVERT: M 184 LEU cc_start: 0.7037 (tt) cc_final: 0.6835 (tp) REVERT: M 204 SER cc_start: 0.8184 (OUTLIER) cc_final: 0.7922 (p) REVERT: M 209 MET cc_start: 0.7301 (mmm) cc_final: 0.6802 (mmt) REVERT: M 241 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8270 (pt) REVERT: M 312 LYS cc_start: 0.7708 (tptp) cc_final: 0.7259 (tptt) REVERT: M 343 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7256 (ttpt) REVERT: M 408 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6444 (mm-30) REVERT: S 40 THR cc_start: 0.8589 (m) cc_final: 0.8193 (m) REVERT: S 116 GLU cc_start: 0.8357 (tp30) cc_final: 0.8097 (tp30) REVERT: S 138 LEU cc_start: 0.8507 (mt) cc_final: 0.8251 (mp) outliers start: 44 outliers final: 28 residues processed: 317 average time/residue: 0.7842 time to fit residues: 267.2591 Evaluate side-chains 327 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 289 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 150 GLN Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 204 SER Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain M residue 262 SER Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 343 LYS Chi-restraints excluded: chain M residue 408 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 133 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 173 ASN B 348 GLN B 400 GLN M 150 GLN ** M 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 250 GLN M 365 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.145533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118849 restraints weight = 19832.808| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.12 r_work: 0.3331 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14064 Z= 0.135 Angle : 0.569 11.727 19042 Z= 0.294 Chirality : 0.041 0.213 2221 Planarity : 0.004 0.047 2421 Dihedral : 4.201 55.181 1879 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.18 % Allowed : 29.87 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 1716 helix: 1.82 (0.16), residues: 1000 sheet: 1.39 (0.39), residues: 157 loop : -0.83 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 3 TYR 0.028 0.002 TYR M 403 PHE 0.026 0.001 PHE M 214 TRP 0.015 0.001 TRP A 462 HIS 0.006 0.001 HIS M 195 Details of bonding type rmsd covalent geometry : bond 0.00318 (14064) covalent geometry : angle 0.56880 (19042) hydrogen bonds : bond 0.03946 ( 785) hydrogen bonds : angle 3.87754 ( 2289) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6476.49 seconds wall clock time: 110 minutes 51.78 seconds (6651.78 seconds total)