Starting phenix.real_space_refine on Sat Mar 7 05:28:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xps_67102/03_2026/9xps_67102.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xps_67102/03_2026/9xps_67102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xps_67102/03_2026/9xps_67102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xps_67102/03_2026/9xps_67102.map" model { file = "/net/cci-nas-00/data/ceres_data/9xps_67102/03_2026/9xps_67102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xps_67102/03_2026/9xps_67102.cif" } resolution = 3.52 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= -0.002 sd= 0.063 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 178 5.16 5 C 24118 2.51 5 N 6381 2.21 5 O 7125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37802 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3697 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 26, 'TRANS': 422} Chain: "B" Number of atoms: 3603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3603 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 24, 'TRANS': 412} Chain: "x" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5099 Classifications: {'peptide': 649} Link IDs: {'PTRANS': 32, 'TRANS': 616} Chain breaks: 2 Chain: "y" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1995 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 13, 'TRANS': 236} Chain: "z" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2216 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 13, 'TRANS': 268} Chain: "w" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4431 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain: "1" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1915 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 8, 'TRANS': 222} Chain breaks: 1 Chain: "3" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2019 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 10, 'TRANS': 234} Chain breaks: 2 Chain: "5" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1944 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 3 Chain: "6" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1866 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 1 Chain: "4" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2019 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 10, 'TRANS': 234} Chain breaks: 2 Chain: "7" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1858 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 2 Chain: "8" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1741 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 9, 'TRANS': 201} Chain breaks: 5 Chain: "2" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1915 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 8, 'TRANS': 222} Chain breaks: 1 Chain: "S" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1484 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 12, 'TRANS': 176} Chain breaks: 5 Time building chain proxies: 7.97, per 1000 atoms: 0.21 Number of scatterers: 37802 At special positions: 0 Unit cell: (159.12, 223.04, 212.16, 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 178 16.00 O 7125 8.00 N 6381 7.00 C 24118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS w 58 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 46 " - pdb=" SG CYS 8 23 " distance=2.02 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: 2.85 Conformation dependent library (CDL) restraints added in 1.3 seconds 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8772 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 44 sheets defined 34.7% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.588A pdb=" N ASP A 172 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 222 removed outlier: 3.795A pdb=" N GLU A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.604A pdb=" N VAL A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.982A pdb=" N LYS A 262 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 263 " --> pdb=" O MET A 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 263' Processing helix chain 'A' and resid 278 through 285 removed outlier: 4.061A pdb=" N ALA A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.535A pdb=" N THR A 318 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.950A pdb=" N ASN A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 406 through 412 removed outlier: 3.794A pdb=" N TYR A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 430 Processing helix chain 'A' and resid 434 through 445 removed outlier: 3.646A pdb=" N LEU A 438 " --> pdb=" O ASN A 434 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.938A pdb=" N TYR A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 457 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 459 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 197 through 222 Processing helix chain 'B' and resid 241 through 250 removed outlier: 3.548A pdb=" N VAL B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 278 through 286 removed outlier: 3.827A pdb=" N ALA B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 removed outlier: 3.535A pdb=" N ARG B 290 " --> pdb=" O ASP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 314 through 319 removed outlier: 4.202A pdb=" N GLY B 319 " --> pdb=" O GLY B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 378 through 382 removed outlier: 4.147A pdb=" N GLU B 382 " --> pdb=" O PRO B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.633A pdb=" N ARG B 399 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 400 " --> pdb=" O ILE B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 400' Processing helix chain 'B' and resid 406 through 412 removed outlier: 3.626A pdb=" N TYR B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 430 Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.536A pdb=" N LYS B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.847A pdb=" N TRP B 448 " --> pdb=" O SER B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 468 removed outlier: 4.779A pdb=" N ILE B 458 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL B 459 " --> pdb=" O TYR B 455 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) Processing helix chain 'x' and resid 54 through 60 removed outlier: 3.569A pdb=" N PHE x 58 " --> pdb=" O SER x 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 64 through 68 removed outlier: 3.663A pdb=" N LEU x 67 " --> pdb=" O GLN x 64 " (cutoff:3.500A) Processing helix chain 'x' and resid 75 through 88 Processing helix chain 'x' and resid 198 through 203 Processing helix chain 'x' and resid 221 through 228 removed outlier: 4.024A pdb=" N PHE x 227 " --> pdb=" O ALA x 223 " (cutoff:3.500A) Processing helix chain 'x' and resid 276 through 285 removed outlier: 4.948A pdb=" N VAL x 282 " --> pdb=" O GLY x 278 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP x 283 " --> pdb=" O ASP x 279 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR x 285 " --> pdb=" O LEU x 281 " (cutoff:3.500A) Processing helix chain 'x' and resid 307 through 326 Processing helix chain 'x' and resid 335 through 339 Processing helix chain 'x' and resid 384 through 398 removed outlier: 3.797A pdb=" N ASN x 398 " --> pdb=" O ILE x 394 " (cutoff:3.500A) Processing helix chain 'x' and resid 423 through 430 Processing helix chain 'x' and resid 431 through 436 Processing helix chain 'x' and resid 456 through 472 removed outlier: 3.808A pdb=" N GLU x 460 " --> pdb=" O ASP x 456 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU x 461 " --> pdb=" O GLU x 457 " (cutoff:3.500A) Processing helix chain 'x' and resid 507 through 520 removed outlier: 3.735A pdb=" N VAL x 511 " --> pdb=" O GLN x 507 " (cutoff:3.500A) Processing helix chain 'x' and resid 534 through 538 removed outlier: 3.555A pdb=" N ASN x 538 " --> pdb=" O SER x 535 " (cutoff:3.500A) Processing helix chain 'x' and resid 552 through 563 Processing helix chain 'x' and resid 593 through 614 removed outlier: 3.819A pdb=" N VAL x 597 " --> pdb=" O SER x 593 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS x 608 " --> pdb=" O ILE x 604 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS x 609 " --> pdb=" O ARG x 605 " (cutoff:3.500A) Processing helix chain 'x' and resid 621 through 638 removed outlier: 3.730A pdb=" N GLU x 627 " --> pdb=" O GLU x 623 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG x 638 " --> pdb=" O LEU x 634 " (cutoff:3.500A) Processing helix chain 'y' and resid 59 through 63 Processing helix chain 'y' and resid 67 through 81 removed outlier: 3.891A pdb=" N LEU y 71 " --> pdb=" O ASN y 67 " (cutoff:3.500A) Processing helix chain 'y' and resid 129 through 131 No H-bonds generated for 'chain 'y' and resid 129 through 131' Processing helix chain 'y' and resid 132 through 146 Processing helix chain 'y' and resid 154 through 160 removed outlier: 3.556A pdb=" N VAL y 157 " --> pdb=" O PRO y 154 " (cutoff:3.500A) Processing helix chain 'y' and resid 183 through 186 removed outlier: 4.126A pdb=" N GLN y 186 " --> pdb=" O PRO y 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 183 through 186' Processing helix chain 'y' and resid 231 through 247 removed outlier: 3.612A pdb=" N GLN y 235 " --> pdb=" O SER y 231 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU y 236 " --> pdb=" O GLU y 232 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR y 237 " --> pdb=" O GLY y 233 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE y 247 " --> pdb=" O ARG y 243 " (cutoff:3.500A) Processing helix chain 'y' and resid 257 through 265 removed outlier: 6.128A pdb=" N LEU y 262 " --> pdb=" O TRP y 259 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER y 263 " --> pdb=" O GLY y 260 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA y 264 " --> pdb=" O GLY y 261 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP y 265 " --> pdb=" O LEU y 262 " (cutoff:3.500A) Processing helix chain 'y' and resid 272 through 281 removed outlier: 3.547A pdb=" N VAL y 281 " --> pdb=" O ILE y 277 " (cutoff:3.500A) Processing helix chain 'z' and resid 59 through 63 removed outlier: 3.666A pdb=" N LYS z 63 " --> pdb=" O ARG z 60 " (cutoff:3.500A) Processing helix chain 'z' and resid 67 through 80 removed outlier: 3.920A pdb=" N LEU z 71 " --> pdb=" O ASN z 67 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL z 72 " --> pdb=" O THR z 68 " (cutoff:3.500A) Processing helix chain 'z' and resid 129 through 131 No H-bonds generated for 'chain 'z' and resid 129 through 131' Processing helix chain 'z' and resid 132 through 146 Processing helix chain 'z' and resid 163 through 167 removed outlier: 4.329A pdb=" N TYR z 167 " --> pdb=" O VAL z 164 " (cutoff:3.500A) Processing helix chain 'z' and resid 183 through 186 removed outlier: 4.113A pdb=" N GLN z 186 " --> pdb=" O PRO z 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 183 through 186' Processing helix chain 'z' and resid 231 through 243 removed outlier: 3.901A pdb=" N GLN z 235 " --> pdb=" O SER z 231 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU z 236 " --> pdb=" O GLU z 232 " (cutoff:3.500A) Processing helix chain 'z' and resid 244 through 245 No H-bonds generated for 'chain 'z' and resid 244 through 245' Processing helix chain 'z' and resid 246 through 250 Processing helix chain 'z' and resid 263 through 270 removed outlier: 3.695A pdb=" N LEU z 267 " --> pdb=" O SER z 263 " (cutoff:3.500A) Processing helix chain 'w' and resid 10 through 32 removed outlier: 4.027A pdb=" N ARG w 17 " --> pdb=" O GLU w 13 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ARG w 18 " --> pdb=" O SER w 14 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA w 20 " --> pdb=" O THR w 16 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA w 21 " --> pdb=" O ARG w 17 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP w 22 " --> pdb=" O ARG w 18 " (cutoff:3.500A) Processing helix chain 'w' and resid 49 through 53 removed outlier: 3.543A pdb=" N GLY w 52 " --> pdb=" O PRO w 49 " (cutoff:3.500A) Processing helix chain 'w' and resid 85 through 89 removed outlier: 3.769A pdb=" N SER w 88 " --> pdb=" O TYR w 85 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR w 89 " --> pdb=" O THR w 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 85 through 89' Processing helix chain 'w' and resid 128 through 143 removed outlier: 4.057A pdb=" N PHE w 143 " --> pdb=" O GLN w 139 " (cutoff:3.500A) Processing helix chain 'w' and resid 161 through 177 Processing helix chain 'w' and resid 185 through 193 removed outlier: 3.726A pdb=" N TYR w 193 " --> pdb=" O TYR w 189 " (cutoff:3.500A) Processing helix chain 'w' and resid 284 through 288 removed outlier: 3.739A pdb=" N VAL w 288 " --> pdb=" O TYR w 285 " (cutoff:3.500A) Processing helix chain 'w' and resid 293 through 303 Processing helix chain 'w' and resid 342 through 349 Processing helix chain 'w' and resid 363 through 374 Processing helix chain 'w' and resid 375 through 378 Processing helix chain 'w' and resid 427 through 431 Processing helix chain 'w' and resid 432 through 437 Processing helix chain 'w' and resid 442 through 454 removed outlier: 3.612A pdb=" N PHE w 453 " --> pdb=" O ILE w 449 " (cutoff:3.500A) Processing helix chain 'w' and resid 455 through 460 removed outlier: 3.835A pdb=" N ARG w 459 " --> pdb=" O GLY w 456 " (cutoff:3.500A) Processing helix chain 'w' and resid 461 through 465 Processing helix chain 'w' and resid 501 through 514 removed outlier: 3.569A pdb=" N ILE w 505 " --> pdb=" O ASN w 501 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU w 510 " --> pdb=" O VAL w 506 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR w 514 " --> pdb=" O GLU w 510 " (cutoff:3.500A) Processing helix chain '1' and resid 21 through 32 removed outlier: 3.571A pdb=" N HIS 1 28 " --> pdb=" O GLN 1 24 " (cutoff:3.500A) Processing helix chain '1' and resid 37 through 42 Processing helix chain '1' and resid 90 through 103 removed outlier: 3.767A pdb=" N ILE 1 103 " --> pdb=" O GLU 1 99 " (cutoff:3.500A) Processing helix chain '1' and resid 105 through 122 removed outlier: 3.731A pdb=" N ALA 1 122 " --> pdb=" O GLY 1 118 " (cutoff:3.500A) Processing helix chain '1' and resid 182 through 200 Processing helix chain '1' and resid 250 through 254 Processing helix chain '3' and resid 21 through 32 Processing helix chain '3' and resid 33 through 41 removed outlier: 3.641A pdb=" N LYS 3 37 " --> pdb=" O PHE 3 33 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU 3 39 " --> pdb=" O TYR 3 35 " (cutoff:3.500A) Processing helix chain '3' and resid 47 through 49 No H-bonds generated for 'chain '3' and resid 47 through 49' Processing helix chain '3' and resid 88 through 102 removed outlier: 3.849A pdb=" N LEU 3 102 " --> pdb=" O ILE 3 98 " (cutoff:3.500A) Processing helix chain '3' and resid 105 through 122 removed outlier: 3.750A pdb=" N ALA 3 122 " --> pdb=" O GLY 3 118 " (cutoff:3.500A) Processing helix chain '3' and resid 182 through 199 Processing helix chain '3' and resid 243 through 251 removed outlier: 3.698A pdb=" N HIS 3 251 " --> pdb=" O LEU 3 247 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 42 removed outlier: 3.828A pdb=" N PHE 5 33 " --> pdb=" O LEU 5 29 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE 5 34 " --> pdb=" O GLN 5 30 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 51 removed outlier: 3.940A pdb=" N ARG 5 50 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR 5 51 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 47 through 51' Processing helix chain '5' and resid 88 through 102 removed outlier: 3.898A pdb=" N LEU 5 102 " --> pdb=" O ILE 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 105 through 121 Processing helix chain '5' and resid 182 through 200 Processing helix chain '5' and resid 243 through 253 removed outlier: 3.669A pdb=" N VAL 5 248 " --> pdb=" O ASP 5 244 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR 5 249 " --> pdb=" O PRO 5 245 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR 5 253 " --> pdb=" O THR 5 249 " (cutoff:3.500A) Processing helix chain '6' and resid 21 through 32 removed outlier: 3.501A pdb=" N MET 6 32 " --> pdb=" O HIS 6 28 " (cutoff:3.500A) Processing helix chain '6' and resid 34 through 41 removed outlier: 3.511A pdb=" N GLU 6 38 " --> pdb=" O PHE 6 34 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG 6 40 " --> pdb=" O LEU 6 36 " (cutoff:3.500A) Processing helix chain '6' and resid 88 through 102 removed outlier: 3.987A pdb=" N LEU 6 102 " --> pdb=" O ILE 6 98 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 122 removed outlier: 3.521A pdb=" N ALA 6 122 " --> pdb=" O GLY 6 118 " (cutoff:3.500A) Processing helix chain '6' and resid 182 through 200 Processing helix chain '6' and resid 243 through 251 Processing helix chain '4' and resid 21 through 39 removed outlier: 3.799A pdb=" N PHE 4 33 " --> pdb=" O LEU 4 29 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE 4 34 " --> pdb=" O GLN 4 30 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU 4 36 " --> pdb=" O MET 4 32 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS 4 37 " --> pdb=" O PHE 4 33 " (cutoff:3.500A) Processing helix chain '4' and resid 88 through 105 removed outlier: 3.672A pdb=" N LEU 4 102 " --> pdb=" O ILE 4 98 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE 4 103 " --> pdb=" O GLU 4 99 " (cutoff:3.500A) Processing helix chain '4' and resid 105 through 122 removed outlier: 3.791A pdb=" N ALA 4 122 " --> pdb=" O GLY 4 118 " (cutoff:3.500A) Processing helix chain '4' and resid 182 through 199 Processing helix chain '4' and resid 243 through 251 Processing helix chain '7' and resid 21 through 41 removed outlier: 3.984A pdb=" N PHE 7 34 " --> pdb=" O GLN 7 30 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU 7 36 " --> pdb=" O MET 7 32 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS 7 37 " --> pdb=" O PHE 7 33 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG 7 40 " --> pdb=" O LEU 7 36 " (cutoff:3.500A) Processing helix chain '7' and resid 88 through 102 removed outlier: 4.072A pdb=" N LEU 7 102 " --> pdb=" O ILE 7 98 " (cutoff:3.500A) Processing helix chain '7' and resid 105 through 122 removed outlier: 3.858A pdb=" N ALA 7 122 " --> pdb=" O GLY 7 118 " (cutoff:3.500A) Processing helix chain '7' and resid 182 through 200 Processing helix chain '7' and resid 243 through 252 removed outlier: 3.629A pdb=" N THR 7 249 " --> pdb=" O PRO 7 245 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS 7 252 " --> pdb=" O VAL 7 248 " (cutoff:3.500A) Processing helix chain '8' and resid 24 through 42 removed outlier: 4.195A pdb=" N PHE 8 33 " --> pdb=" O LEU 8 29 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE 8 34 " --> pdb=" O GLN 8 30 " (cutoff:3.500A) Processing helix chain '8' and resid 47 through 49 No H-bonds generated for 'chain '8' and resid 47 through 49' Processing helix chain '8' and resid 88 through 102 removed outlier: 3.953A pdb=" N LEU 8 102 " --> pdb=" O ILE 8 98 " (cutoff:3.500A) Processing helix chain '8' and resid 105 through 120 removed outlier: 3.809A pdb=" N LEU 8 116 " --> pdb=" O LEU 8 112 " (cutoff:3.500A) Processing helix chain '8' and resid 182 through 200 Processing helix chain '2' and resid 25 through 30 removed outlier: 3.755A pdb=" N GLN 2 30 " --> pdb=" O TYR 2 26 " (cutoff:3.500A) Processing helix chain '2' and resid 31 through 33 No H-bonds generated for 'chain '2' and resid 31 through 33' Processing helix chain '2' and resid 34 through 42 removed outlier: 4.015A pdb=" N ARG 2 40 " --> pdb=" O LEU 2 36 " (cutoff:3.500A) Processing helix chain '2' and resid 88 through 103 removed outlier: 3.900A pdb=" N LEU 2 102 " --> pdb=" O ILE 2 98 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE 2 103 " --> pdb=" O GLU 2 99 " (cutoff:3.500A) Processing helix chain '2' and resid 105 through 122 removed outlier: 3.813A pdb=" N ALA 2 122 " --> pdb=" O GLY 2 118 " (cutoff:3.500A) Processing helix chain '2' and resid 182 through 200 Processing helix chain '2' and resid 243 through 251 removed outlier: 3.650A pdb=" N HIS 2 251 " --> pdb=" O LEU 2 247 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 24 removed outlier: 3.579A pdb=" N GLY S 24 " --> pdb=" O LEU S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 49 Processing helix chain 'S' and resid 58 through 69 Processing helix chain 'S' and resid 73 through 77 Processing helix chain 'S' and resid 89 through 101 removed outlier: 4.352A pdb=" N VAL S 93 " --> pdb=" O ALA S 89 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA S 96 " --> pdb=" O PRO S 92 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL S 97 " --> pdb=" O VAL S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 116 Processing helix chain 'S' and resid 138 through 148 removed outlier: 3.759A pdb=" N THR S 142 " --> pdb=" O GLY S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 163 Processing helix chain 'S' and resid 164 through 184 removed outlier: 3.813A pdb=" N LEU S 170 " --> pdb=" O ARG S 166 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 187 No H-bonds generated for 'chain 'S' and resid 185 through 187' Processing helix chain 'S' and resid 192 through 203 Processing helix chain 'S' and resid 205 through 211 Processing helix chain 'S' and resid 245 through 257 removed outlier: 3.559A pdb=" N ALA S 257 " --> pdb=" O GLY S 253 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 removed outlier: 3.526A pdb=" N VAL A 109 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 69 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASP A 72 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP A 130 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER A 136 " --> pdb=" O TYR A 164 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR A 164 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 138 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.929A pdb=" N TYR A 155 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 182 through 184 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.773A pdb=" N THR A 229 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 240 removed outlier: 7.275A pdb=" N TYR A 240 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 195 through 196 removed outlier: 8.036A pdb=" N TYR B 82 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N SER B 180 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA B 84 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR B 182 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS B 86 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ARG B 54 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASP B 130 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET B 126 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 127 " --> pdb=" O PHE B 139 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N SER B 136 " --> pdb=" O TYR B 164 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR B 164 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU B 138 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR B 158 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL B 144 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA B 156 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR B 155 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL B 109 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N HIS B 163 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 11.731A pdb=" N PHE B 107 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS B 108 " --> pdb=" O GLN B 97 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLN B 97 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP B 110 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA B 95 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR B 112 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 91 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.763A pdb=" N THR B 229 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 239 through 240 removed outlier: 7.641A pdb=" N TYR B 240 " --> pdb=" O VAL B 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'x' and resid 49 through 50 removed outlier: 8.126A pdb=" N LYS x 94 " --> pdb=" O PRO x 35 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU x 37 " --> pdb=" O LYS x 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'x' and resid 108 through 115 removed outlier: 4.071A pdb=" N ILE x 108 " --> pdb=" O ILE x 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'x' and resid 151 through 158 current: chain 'x' and resid 183 through 191 Processing sheet with id=AB2, first strand: chain 'x' and resid 258 through 260 removed outlier: 3.665A pdb=" N MET x 206 " --> pdb=" O ILE x 373 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE x 373 " --> pdb=" O MET x 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'x' and resid 237 through 238 Processing sheet with id=AB4, first strand: chain 'x' and resid 443 through 445 Processing sheet with id=AB5, first strand: chain 'x' and resid 505 through 506 removed outlier: 6.834A pdb=" N SER x 493 " --> pdb=" O LEU x 546 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU x 546 " --> pdb=" O SER x 493 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS x 495 " --> pdb=" O LYS x 544 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'x' and resid 568 through 569 Processing sheet with id=AB7, first strand: chain 'x' and resid 646 through 655 removed outlier: 3.625A pdb=" N GLU x 671 " --> pdb=" O ASN x 646 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR x 669 " --> pdb=" O ILE x 648 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR x 654 " --> pdb=" O SER x 663 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'y' and resid 52 through 57 removed outlier: 6.543A pdb=" N THR y 175 " --> pdb=" O LEU y 56 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N MET y 174 " --> pdb=" O ASN y 196 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN y 190 " --> pdb=" O GLU y 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'y' and resid 86 through 87 removed outlier: 3.653A pdb=" N CYS y 126 " --> pdb=" O LEU y 220 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'y' and resid 93 through 101 removed outlier: 6.903A pdb=" N THR y 94 " --> pdb=" O VAL y 115 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL y 115 " --> pdb=" O THR y 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP y 96 " --> pdb=" O THR y 113 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'z' and resid 52 through 57 removed outlier: 6.577A pdb=" N THR z 175 " --> pdb=" O LEU z 56 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET z 174 " --> pdb=" O ASN z 196 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN z 190 " --> pdb=" O GLU z 180 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR z 195 " --> pdb=" O LEU z 227 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'z' and resid 85 through 87 removed outlier: 3.977A pdb=" N ASP z 87 " --> pdb=" O ASN z 123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'z' and resid 93 through 95 Processing sheet with id=AC5, first strand: chain 'z' and resid 100 through 101 Processing sheet with id=AC6, first strand: chain 'w' and resid 3 through 7 WARNING: can't find start of bonding for strands! previous: chain 'w' and resid 3 through 7 current: chain 'w' and resid 72 through 76 WARNING: can't find start of bonding for strands! previous: chain 'w' and resid 72 through 76 current: chain 'w' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'w' and resid 107 through 126 current: chain 'w' and resid 209 through 224 WARNING: can't find start of bonding for strands! previous: chain 'w' and resid 209 through 224 current: chain 'w' and resid 243 through 262 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'w' and resid 331 through 338 removed outlier: 5.667A pdb=" N THR w 333 " --> pdb=" O ILE w 424 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE w 424 " --> pdb=" O THR w 333 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE w 335 " --> pdb=" O ILE w 422 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE w 422 " --> pdb=" O PHE w 335 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'w' and resid 350 through 353 removed outlier: 6.759A pdb=" N LEU w 406 " --> pdb=" O LEU w 351 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'w' and resid 467 through 468 Processing sheet with id=AD1, first strand: chain '1' and resid 73 through 81 removed outlier: 4.635A pdb=" N GLU 1 74 " --> pdb=" O ASP 1 69 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER 1 52 " --> pdb=" O THR 1 68 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE 1 53 " --> pdb=" O ILE 3 14 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '1' and resid 129 through 132 removed outlier: 3.502A pdb=" N TYR 1 137 " --> pdb=" O LEU 1 154 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE 1 152 " --> pdb=" O ILE 1 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 152 through 160 current: chain '1' and resid 214 through 225 removed outlier: 3.797A pdb=" N GLY 1 221 " --> pdb=" O LEU 1 233 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '3' and resid 51 through 59 removed outlier: 3.958A pdb=" N VAL 3 58 " --> pdb=" O THR 3 62 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR 3 62 " --> pdb=" O VAL 3 58 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '3' and resid 128 through 133 removed outlier: 6.869A pdb=" N TYR 3 137 " --> pdb=" O LYS 3 153 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS 3 153 " --> pdb=" O TYR 3 137 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE 3 139 " --> pdb=" O ILE 3 151 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU 3 147 " --> pdb=" O ILE 3 143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '3' and resid 147 through 160 current: chain '3' and resid 214 through 224 Processing sheet with id=AD5, first strand: chain '5' and resid 52 through 59 removed outlier: 4.324A pdb=" N VAL 5 58 " --> pdb=" O THR 5 62 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N THR 5 62 " --> pdb=" O VAL 5 58 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '5' and resid 129 through 132 removed outlier: 7.017A pdb=" N TYR 5 137 " --> pdb=" O LYS 5 153 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS 5 153 " --> pdb=" O TYR 5 137 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE 5 139 " --> pdb=" O ILE 5 151 " (cutoff:3.500A) removed outlier: 11.189A pdb=" N ALA 5 149 " --> pdb=" O ILE 5 240 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N ILE 5 240 " --> pdb=" O ALA 5 149 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ILE 5 151 " --> pdb=" O GLN 5 238 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '6' and resid 51 through 55 removed outlier: 3.703A pdb=" N ASP 6 69 " --> pdb=" O GLU 6 74 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU 6 74 " --> pdb=" O ASP 6 69 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '6' and resid 127 through 132 removed outlier: 4.565A pdb=" N VAL 6 127 " --> pdb=" O ARG 6 142 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS 6 129 " --> pdb=" O LEU 6 140 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR 6 223 " --> pdb=" O VAL 6 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU 6 233 " --> pdb=" O GLY 6 221 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY 6 221 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET 6 235 " --> pdb=" O LEU 6 219 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU 6 219 " --> pdb=" O MET 6 235 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS 6 216 " --> pdb=" O ASP 6 209 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP 6 209 " --> pdb=" O LYS 6 216 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL 6 207 " --> pdb=" O GLU 6 218 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '4' and resid 51 through 56 removed outlier: 3.525A pdb=" N ILE 4 76 " --> pdb=" O LEU 4 67 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '4' and resid 128 through 133 removed outlier: 3.735A pdb=" N LYS 4 129 " --> pdb=" O LEU 4 140 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE 4 152 " --> pdb=" O ILE 4 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '4' and resid 152 through 160 current: chain '4' and resid 214 through 224 removed outlier: 3.633A pdb=" N ILE 4 237 " --> pdb=" O MET 4 217 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY 4 221 " --> pdb=" O LEU 4 233 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '7' and resid 51 through 55 Processing sheet with id=AE3, first strand: chain '7' and resid 129 through 132 removed outlier: 4.580A pdb=" N GLY 7 148 " --> pdb=" O ARG 7 141 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE 7 143 " --> pdb=" O GLU 7 146 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '7' and resid 146 through 148 current: chain '7' and resid 229 through 234 Processing sheet with id=AE4, first strand: chain '7' and resid 209 through 211 Processing sheet with id=AE5, first strand: chain '8' and resid 51 through 59 removed outlier: 4.243A pdb=" N VAL 8 58 " --> pdb=" O THR 8 62 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR 8 62 " --> pdb=" O VAL 8 58 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '8' and resid 129 through 133 removed outlier: 3.810A pdb=" N LYS 8 129 " --> pdb=" O LEU 8 140 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE 8 152 " --> pdb=" O ILE 8 139 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ARG 8 141 " --> pdb=" O VAL 8 150 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL 8 150 " --> pdb=" O ARG 8 141 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA 8 236 " --> pdb=" O LYS 8 153 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR 8 157 " --> pdb=" O ILE 8 232 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '2' and resid 51 through 59 removed outlier: 6.809A pdb=" N THR 2 62 " --> pdb=" O VAL 2 58 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL 2 80 " --> pdb=" O TYR 2 63 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLU 2 74 " --> pdb=" O ASP 2 69 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '2' and resid 128 through 132 removed outlier: 3.540A pdb=" N TYR 2 137 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE 2 152 " --> pdb=" O ILE 2 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '2' and resid 152 through 159 current: chain '2' and resid 214 through 225 removed outlier: 3.519A pdb=" N GLY 2 221 " --> pdb=" O LEU 2 233 " (cutoff:3.500A) 1317 hydrogen bonds defined for protein. 3663 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: 7.53 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12278 1.34 - 1.46: 9187 1.46 - 1.58: 16930 1.58 - 1.70: 0 1.70 - 1.83: 296 Bond restraints: 38691 Sorted by residual: bond pdb=" N ASP w 225 " pdb=" CA ASP w 225 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.55e+00 bond pdb=" N TYR w 224 " pdb=" CA TYR w 224 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.85e+00 bond pdb=" N SER w 228 " pdb=" CA SER w 228 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.12e+00 bond pdb=" N ASN 8 27 " pdb=" CA ASN 8 27 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.23e-02 6.61e+03 5.92e+00 bond pdb=" N TYR 8 26 " pdb=" CA TYR 8 26 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.17e-02 7.31e+03 5.78e+00 ... (remaining 38686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 51984 2.40 - 4.79: 450 4.79 - 7.19: 60 7.19 - 9.59: 13 9.59 - 11.99: 1 Bond angle restraints: 52508 Sorted by residual: angle pdb=" CA PRO w 231 " pdb=" C PRO w 231 " pdb=" O PRO w 231 " ideal model delta sigma weight residual 121.48 116.62 4.86 1.20e+00 6.94e-01 1.64e+01 angle pdb=" CB MET S 251 " pdb=" CG MET S 251 " pdb=" SD MET S 251 " ideal model delta sigma weight residual 112.70 124.69 -11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CA THR w 227 " pdb=" CB THR w 227 " pdb=" OG1 THR w 227 " ideal model delta sigma weight residual 109.60 103.64 5.96 1.50e+00 4.44e-01 1.58e+01 angle pdb=" N PRO w 231 " pdb=" CD PRO w 231 " pdb=" CG PRO w 231 " ideal model delta sigma weight residual 103.20 97.34 5.86 1.50e+00 4.44e-01 1.53e+01 angle pdb=" CA PRO w 231 " pdb=" C PRO w 231 " pdb=" N THR w 232 " ideal model delta sigma weight residual 115.37 120.43 -5.06 1.32e+00 5.74e-01 1.47e+01 ... (remaining 52503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 19545 17.95 - 35.90: 2735 35.90 - 53.85: 678 53.85 - 71.80: 130 71.80 - 89.75: 43 Dihedral angle restraints: 23131 sinusoidal: 9464 harmonic: 13667 Sorted by residual: dihedral pdb=" CA ASN A 450 " pdb=" C ASN A 450 " pdb=" N LEU A 451 " pdb=" CA LEU A 451 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA PRO A 372 " pdb=" C PRO A 372 " pdb=" N TRP A 373 " pdb=" CA TRP A 373 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLU A 64 " pdb=" C GLU A 64 " pdb=" N ASP A 65 " pdb=" CA ASP A 65 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 23128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4463 0.045 - 0.089: 908 0.089 - 0.134: 340 0.134 - 0.179: 23 0.179 - 0.223: 1 Chirality restraints: 5735 Sorted by residual: chirality pdb=" CA PRO A 68 " pdb=" N PRO A 68 " pdb=" C PRO A 68 " pdb=" CB PRO A 68 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA GLU A 64 " pdb=" N GLU A 64 " pdb=" C GLU A 64 " pdb=" CB GLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CA SER w 228 " pdb=" N SER w 228 " pdb=" C SER w 228 " pdb=" CB SER w 228 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 5732 not shown) Planarity restraints: 6763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP 7 47 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ASP 7 47 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP 7 47 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU 7 48 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 67 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO A 68 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU y 278 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" CD GLU y 278 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU y 278 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU y 278 " -0.013 2.00e-02 2.50e+03 ... (remaining 6760 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 15436 2.91 - 3.41: 34292 3.41 - 3.91: 56902 3.91 - 4.40: 60883 4.40 - 4.90: 106878 Nonbonded interactions: 274391 Sorted by model distance: nonbonded pdb=" O ASP 7 47 " pdb=" OD1 ASP 7 47 " model vdw 2.417 3.040 nonbonded pdb=" O ASN S 84 " pdb=" ND2 ASN S 84 " model vdw 2.486 3.120 nonbonded pdb=" O SER y 212 " pdb=" OG SER y 212 " model vdw 2.515 3.040 nonbonded pdb=" N ASP A 383 " pdb=" OD1 ASP A 383 " model vdw 2.526 3.120 nonbonded pdb=" N GLU 5 85 " pdb=" OE1 GLU 5 85 " model vdw 2.527 3.120 ... (remaining 274386 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 Found NCS groups: ncs_group { reference = (chain '1' and (resid 12 through 20 or resid 23 through 44 or resid 47 through 1 \ 24 or resid 128 through 143 or resid 147 through 160 or resid 181 through 204 or \ resid 206 through 208 or resid 216 through 239)) selection = (chain '2' and (resid 12 through 20 or resid 23 through 44 or resid 47 through 1 \ 24 or resid 128 through 143 or resid 147 through 160 or resid 181 through 204 or \ resid 206 through 208 or resid 216 through 239)) selection = (chain '3' and (resid 12 through 20 or resid 23 through 124 or resid 128 through \ 143 or resid 147 through 160 or resid 181 through 204 or resid 206 through 208 \ or resid 216 through 239)) selection = (chain '4' and (resid 12 through 20 or resid 23 through 124 or resid 128 through \ 143 or resid 147 through 160 or resid 181 through 204 or resid 206 through 208 \ or resid 216 through 239)) selection = (chain '5' and (resid 12 through 20 or resid 23 through 44 or resid 47 through 1 \ 60 or resid 181 through 204 or resid 206 through 208 or resid 216 through 239)) selection = (chain '6' and (resid 12 through 20 or resid 23 through 44 or resid 47 through 1 \ 24 or resid 128 through 143 or resid 147 through 204 or resid 206 through 208 or \ resid 216 through 239)) selection = (chain '7' and (resid 12 through 20 or resid 23 through 44 or resid 47 through 1 \ 24 or resid 128 through 143 or resid 147 through 208 or resid 216 through 239)) selection = (chain '8' and (resid 12 through 44 or resid 47 through 160 or resid 181 through \ 204 or resid 206 through 239)) } ncs_group { reference = (chain 'A' and resid 32 through 468) selection = chain 'B' } ncs_group { reference = chain 'y' selection = (chain 'z' and resid 32 through 281) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 31.770 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.002 0.044 38693 Z= 0.120 Angle : 0.558 11.986 52512 Z= 0.298 Chirality : 0.041 0.223 5735 Planarity : 0.003 0.063 6763 Dihedral : 17.548 89.755 14353 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.91 % Favored : 94.78 % Rotamer: Outliers : 2.97 % Allowed : 29.78 % Favored : 67.25 % 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: -0.37 (0.13), residues: 4562 helix: 2.03 (0.15), residues: 1338 sheet: -0.11 (0.17), residues: 993 loop : -1.82 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG z 208 TYR 0.027 0.001 TYR w 224 PHE 0.011 0.001 PHE 7 33 TRP 0.024 0.001 TRP A 373 HIS 0.009 0.001 HIS 5 18 Details of bonding type rmsd covalent geometry : bond 0.00232 (38691) covalent geometry : angle 0.55838 (52508) SS BOND : bond 0.00709 ( 2) SS BOND : angle 0.97539 ( 4) hydrogen bonds : bond 0.20339 ( 1317) hydrogen bonds : angle 6.60186 ( 3663) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 448 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 382 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8138 (mt-10) REVERT: A 399 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.6963 (ttp-170) REVERT: A 425 TRP cc_start: 0.8607 (OUTLIER) cc_final: 0.8245 (t60) REVERT: A 444 CYS cc_start: 0.8431 (m) cc_final: 0.8211 (p) REVERT: B 182 TYR cc_start: 0.8311 (m-80) cc_final: 0.8103 (m-80) REVERT: B 264 LYS cc_start: 0.8351 (tttt) cc_final: 0.7373 (mptt) REVERT: x 20 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7051 (mtp85) REVERT: y 196 ASN cc_start: 0.9213 (t0) cc_final: 0.8975 (t0) REVERT: z 57 ASP cc_start: 0.8453 (t0) cc_final: 0.8241 (t0) REVERT: z 87 ASP cc_start: 0.8280 (m-30) cc_final: 0.7791 (m-30) REVERT: z 90 GLN cc_start: 0.8801 (pt0) cc_final: 0.7201 (mm-40) REVERT: z 152 LYS cc_start: 0.5326 (mttt) cc_final: 0.3703 (tttm) REVERT: z 216 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7410 (mp10) REVERT: z 256 LYS cc_start: 0.9101 (tttp) cc_final: 0.7598 (mmtt) REVERT: z 259 TRP cc_start: 0.8864 (OUTLIER) cc_final: 0.6663 (p90) REVERT: z 268 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7380 (ttt180) REVERT: w 31 MET cc_start: 0.9196 (mtm) cc_final: 0.8649 (mtp) REVERT: w 46 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8377 (mp10) REVERT: w 66 LYS cc_start: 0.8697 (mmtp) cc_final: 0.7823 (pptt) REVERT: w 227 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.7965 (p) REVERT: w 228 SER cc_start: 0.9062 (m) cc_final: 0.8772 (p) REVERT: w 460 LYS cc_start: 0.9184 (mptt) cc_final: 0.8914 (mmtt) REVERT: w 526 MET cc_start: 0.8819 (mmm) cc_final: 0.8607 (mmm) REVERT: w 540 ARG cc_start: 0.7897 (mmt180) cc_final: 0.6233 (ptt-90) REVERT: 1 24 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7643 (tp40) REVERT: 1 42 ASN cc_start: 0.8839 (t0) cc_final: 0.8554 (t0) REVERT: 1 112 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8973 (mp) REVERT: 3 233 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9062 (pp) REVERT: 5 215 ASN cc_start: 0.7637 (p0) cc_final: 0.7284 (p0) REVERT: 4 74 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6339 (mp0) REVERT: 4 144 ASN cc_start: 0.8884 (p0) cc_final: 0.8432 (p0) REVERT: 4 217 MET cc_start: 0.8747 (mmt) cc_final: 0.8391 (mmt) REVERT: 7 250 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.6850 (t80) REVERT: 8 44 LYS cc_start: 0.8648 (tmtt) cc_final: 0.8395 (tptt) REVERT: S 80 MET cc_start: 0.8998 (tpp) cc_final: 0.8323 (tpp) REVERT: S 115 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: S 162 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.5988 (tmt170) REVERT: S 195 ASP cc_start: 0.8537 (m-30) cc_final: 0.7933 (m-30) outliers start: 123 outliers final: 100 residues processed: 553 average time/residue: 0.2228 time to fit residues: 202.2242 Evaluate side-chains 547 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 433 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 380 GLN Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain x residue 20 ARG Chi-restraints excluded: chain x residue 41 THR Chi-restraints excluded: chain x residue 157 LEU Chi-restraints excluded: chain x residue 216 ILE Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 442 TYR Chi-restraints excluded: chain x residue 454 LEU Chi-restraints excluded: chain x residue 471 LEU Chi-restraints excluded: chain x residue 514 SER Chi-restraints excluded: chain x residue 541 THR Chi-restraints excluded: chain x residue 592 LEU Chi-restraints excluded: chain x residue 614 PHE Chi-restraints excluded: chain x residue 656 ILE Chi-restraints excluded: chain y residue 153 VAL Chi-restraints excluded: chain y residue 158 SER Chi-restraints excluded: chain y residue 162 VAL Chi-restraints excluded: chain y residue 257 LEU Chi-restraints excluded: chain y residue 263 SER Chi-restraints excluded: chain z residue 105 SER Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 153 VAL Chi-restraints excluded: chain z residue 156 ILE Chi-restraints excluded: chain z residue 161 ILE Chi-restraints excluded: chain z residue 179 VAL Chi-restraints excluded: chain z residue 216 GLN Chi-restraints excluded: chain z residue 259 TRP Chi-restraints excluded: chain z residue 268 ARG Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 286 THR Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 46 GLN Chi-restraints excluded: chain w residue 76 THR Chi-restraints excluded: chain w residue 77 TYR Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain w residue 155 THR Chi-restraints excluded: chain w residue 211 LEU Chi-restraints excluded: chain w residue 227 THR Chi-restraints excluded: chain w residue 261 ILE Chi-restraints excluded: chain w residue 281 ILE Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 401 LEU Chi-restraints excluded: chain 1 residue 68 THR Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 115 MET Chi-restraints excluded: chain 3 residue 23 CYS Chi-restraints excluded: chain 3 residue 44 LYS Chi-restraints excluded: chain 3 residue 86 LYS Chi-restraints excluded: chain 3 residue 183 THR Chi-restraints excluded: chain 3 residue 233 LEU Chi-restraints excluded: chain 3 residue 244 ASP Chi-restraints excluded: chain 5 residue 28 HIS Chi-restraints excluded: chain 5 residue 196 PHE Chi-restraints excluded: chain 5 residue 231 VAL Chi-restraints excluded: chain 6 residue 18 HIS Chi-restraints excluded: chain 6 residue 32 MET Chi-restraints excluded: chain 6 residue 80 VAL Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 207 VAL Chi-restraints excluded: chain 6 residue 222 TYR Chi-restraints excluded: chain 4 residue 44 LYS Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 74 GLU Chi-restraints excluded: chain 4 residue 81 THR Chi-restraints excluded: chain 4 residue 172 THR Chi-restraints excluded: chain 4 residue 179 ASP Chi-restraints excluded: chain 4 residue 180 ILE Chi-restraints excluded: chain 7 residue 48 LEU Chi-restraints excluded: chain 7 residue 59 ASP Chi-restraints excluded: chain 7 residue 85 GLU Chi-restraints excluded: chain 7 residue 103 ILE Chi-restraints excluded: chain 7 residue 127 VAL Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 223 THR Chi-restraints excluded: chain 7 residue 231 VAL Chi-restraints excluded: chain 7 residue 233 LEU Chi-restraints excluded: chain 7 residue 250 TYR Chi-restraints excluded: chain 8 residue 98 ILE Chi-restraints excluded: chain 8 residue 164 ILE Chi-restraints excluded: chain 8 residue 171 CYS Chi-restraints excluded: chain 8 residue 181 PHE Chi-restraints excluded: chain 8 residue 183 THR Chi-restraints excluded: chain 2 residue 58 VAL Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 67 LEU Chi-restraints excluded: chain 2 residue 68 THR Chi-restraints excluded: chain 2 residue 180 ILE Chi-restraints excluded: chain 2 residue 217 MET Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 115 GLU Chi-restraints excluded: chain S residue 155 THR Chi-restraints excluded: chain S residue 162 ARG Chi-restraints excluded: chain S residue 167 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.4980 chunk 401 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 190 ASN ** z 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.098264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.081485 restraints weight = 95159.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.083444 restraints weight = 44082.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.084794 restraints weight = 26441.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.085736 restraints weight = 18365.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.086322 restraints weight = 14087.582| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38693 Z= 0.137 Angle : 0.512 7.704 52512 Z= 0.269 Chirality : 0.042 0.227 5735 Planarity : 0.004 0.064 6763 Dihedral : 6.896 67.264 5409 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.29 % Favored : 93.45 % Rotamer: Outliers : 6.55 % Allowed : 25.77 % Favored : 67.68 % 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: -0.21 (0.13), residues: 4562 helix: 2.20 (0.15), residues: 1358 sheet: 0.04 (0.17), residues: 994 loop : -1.83 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 6 40 TYR 0.020 0.001 TYR 4 35 PHE 0.014 0.001 PHE w 432 TRP 0.015 0.001 TRP A 373 HIS 0.004 0.001 HIS w 316 Details of bonding type rmsd covalent geometry : bond 0.00320 (38691) covalent geometry : angle 0.51240 (52508) SS BOND : bond 0.00211 ( 2) SS BOND : angle 0.60449 ( 4) hydrogen bonds : bond 0.04370 ( 1317) hydrogen bonds : angle 4.87365 ( 3663) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 271 poor density : 429 time to evaluate : 1.505 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.7661 (tpp) cc_final: 0.7053 (tpp) REVERT: A 89 ASP cc_start: 0.6413 (p0) cc_final: 0.6205 (p0) REVERT: A 382 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7795 (mt-10) REVERT: A 399 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7054 (ttp-170) REVERT: A 425 TRP cc_start: 0.8588 (OUTLIER) cc_final: 0.8205 (t60) REVERT: B 153 SER cc_start: 0.9135 (OUTLIER) cc_final: 0.8793 (m) REVERT: B 182 TYR cc_start: 0.8297 (m-80) cc_final: 0.8043 (m-80) REVERT: B 264 LYS cc_start: 0.8367 (tttt) cc_final: 0.7380 (mptt) REVERT: B 287 ASP cc_start: 0.8432 (t0) cc_final: 0.8206 (t0) REVERT: x 48 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8993 (p) REVERT: x 365 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8570 (tp) REVERT: z 27 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7255 (tp40) REVERT: z 57 ASP cc_start: 0.8446 (t0) cc_final: 0.8207 (t0) REVERT: z 87 ASP cc_start: 0.8389 (m-30) cc_final: 0.7973 (m-30) REVERT: z 90 GLN cc_start: 0.8804 (pt0) cc_final: 0.7306 (mm110) REVERT: z 152 LYS cc_start: 0.5617 (mttt) cc_final: 0.3909 (tttm) REVERT: z 216 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: z 256 LYS cc_start: 0.9125 (tttp) cc_final: 0.7619 (mmtt) REVERT: z 259 TRP cc_start: 0.8867 (OUTLIER) cc_final: 0.6706 (p90) REVERT: z 268 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7473 (tpt170) REVERT: w 31 MET cc_start: 0.9213 (mtm) cc_final: 0.8698 (mtp) REVERT: w 45 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8598 (t) REVERT: w 46 GLN cc_start: 0.8713 (mt0) cc_final: 0.8396 (mp10) REVERT: w 66 LYS cc_start: 0.8670 (mmtp) cc_final: 0.7753 (pptt) REVERT: w 234 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7912 (pp20) REVERT: w 496 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8096 (m) REVERT: w 526 MET cc_start: 0.8800 (mmm) cc_final: 0.8587 (mmm) REVERT: w 540 ARG cc_start: 0.8007 (mmt180) cc_final: 0.6384 (ptt90) REVERT: 1 24 GLN cc_start: 0.7918 (tp-100) cc_final: 0.7670 (tp40) REVERT: 1 42 ASN cc_start: 0.8741 (t0) cc_final: 0.8535 (t0) REVERT: 1 112 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9061 (mp) REVERT: 3 64 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7961 (tm) REVERT: 3 119 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9063 (mt) REVERT: 3 240 ILE cc_start: 0.5825 (OUTLIER) cc_final: 0.5153 (mp) REVERT: 5 29 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8606 (tp) REVERT: 5 74 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: 5 215 ASN cc_start: 0.7569 (p0) cc_final: 0.7214 (p0) REVERT: 6 87 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.4857 (tp30) REVERT: 4 110 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.7879 (mtm180) REVERT: 4 144 ASN cc_start: 0.8980 (p0) cc_final: 0.8626 (p0) REVERT: 4 217 MET cc_start: 0.8613 (mmt) cc_final: 0.7994 (mmp) REVERT: 7 13 SER cc_start: 0.9060 (OUTLIER) cc_final: 0.8741 (m) REVERT: 7 33 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7772 (t80) REVERT: 7 250 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.6930 (t80) REVERT: 8 44 LYS cc_start: 0.8643 (tmtt) cc_final: 0.8174 (tptt) REVERT: 8 71 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9175 (tt) REVERT: 8 112 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8175 (mp) REVERT: 8 114 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7440 (t0) REVERT: 8 115 MET cc_start: 0.8561 (mmt) cc_final: 0.7996 (mmm) REVERT: 8 142 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7722 (pmt-80) REVERT: 2 132 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8339 (tpt-90) REVERT: 2 195 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7794 (mtt-85) REVERT: 2 217 MET cc_start: 0.7417 (mtp) cc_final: 0.7162 (mtp) REVERT: S 94 MET cc_start: 0.8644 (tpp) cc_final: 0.8421 (tpp) REVERT: S 115 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: S 195 ASP cc_start: 0.8601 (m-30) cc_final: 0.7923 (m-30) outliers start: 271 outliers final: 174 residues processed: 669 average time/residue: 0.2190 time to fit residues: 241.8685 Evaluate side-chains 614 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 410 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 448 TRP Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 49 THR Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 54 SER Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 268 SER Chi-restraints excluded: chain x residue 302 SER Chi-restraints excluded: chain x residue 306 VAL Chi-restraints excluded: chain x residue 323 MET Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain x residue 442 TYR Chi-restraints excluded: chain x residue 445 THR Chi-restraints excluded: chain x residue 451 ASP Chi-restraints excluded: chain x residue 505 VAL Chi-restraints excluded: chain x residue 523 THR Chi-restraints excluded: chain x residue 532 MET Chi-restraints excluded: chain x residue 541 THR Chi-restraints excluded: chain x residue 597 VAL Chi-restraints excluded: chain x residue 614 PHE Chi-restraints excluded: chain x residue 637 VAL Chi-restraints excluded: chain x residue 644 ARG Chi-restraints excluded: chain x residue 668 VAL Chi-restraints excluded: chain x residue 677 THR Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 42 THR Chi-restraints excluded: chain y residue 94 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain y residue 153 VAL Chi-restraints excluded: chain y residue 162 VAL Chi-restraints excluded: chain y residue 188 CYS Chi-restraints excluded: chain y residue 253 ASN Chi-restraints excluded: chain y residue 257 LEU Chi-restraints excluded: chain z residue 27 GLN Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 66 SER Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 153 VAL Chi-restraints excluded: chain z residue 156 ILE Chi-restraints excluded: chain z residue 179 VAL Chi-restraints excluded: chain z residue 188 CYS Chi-restraints excluded: chain z residue 201 THR Chi-restraints excluded: chain z residue 216 GLN Chi-restraints excluded: chain z residue 259 TRP Chi-restraints excluded: chain z residue 268 ARG Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 286 THR Chi-restraints excluded: chain w residue 11 VAL Chi-restraints excluded: chain w residue 37 THR Chi-restraints excluded: chain w residue 45 VAL Chi-restraints excluded: chain w residue 82 ASP Chi-restraints excluded: chain w residue 86 THR Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain w residue 155 THR Chi-restraints excluded: chain w residue 171 ILE Chi-restraints excluded: chain w residue 185 THR Chi-restraints excluded: chain w residue 201 LEU Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 234 GLU Chi-restraints excluded: chain w residue 261 ILE Chi-restraints excluded: chain w residue 290 ARG Chi-restraints excluded: chain w residue 293 SER Chi-restraints excluded: chain w residue 320 ASP Chi-restraints excluded: chain w residue 324 THR Chi-restraints excluded: chain w residue 352 MET Chi-restraints excluded: chain w residue 401 LEU Chi-restraints excluded: chain w residue 423 SER Chi-restraints excluded: chain w residue 429 LEU Chi-restraints excluded: chain w residue 448 THR Chi-restraints excluded: chain w residue 449 ILE Chi-restraints excluded: chain w residue 485 THR Chi-restraints excluded: chain w residue 496 THR Chi-restraints excluded: chain w residue 523 THR Chi-restraints excluded: chain w residue 530 THR Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 31 ASP Chi-restraints excluded: chain 1 residue 67 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 146 GLU Chi-restraints excluded: chain 3 residue 44 LYS Chi-restraints excluded: chain 3 residue 64 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 3 residue 119 LEU Chi-restraints excluded: chain 3 residue 147 LEU Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 240 ILE Chi-restraints excluded: chain 3 residue 248 VAL Chi-restraints excluded: chain 5 residue 13 SER Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 66 VAL Chi-restraints excluded: chain 5 residue 74 GLU Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 158 ILE Chi-restraints excluded: chain 5 residue 164 ILE Chi-restraints excluded: chain 5 residue 227 MET Chi-restraints excluded: chain 5 residue 231 VAL Chi-restraints excluded: chain 6 residue 46 CYS Chi-restraints excluded: chain 6 residue 56 SER Chi-restraints excluded: chain 6 residue 75 THR Chi-restraints excluded: chain 6 residue 77 SER Chi-restraints excluded: chain 6 residue 80 VAL Chi-restraints excluded: chain 6 residue 84 PHE Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 150 VAL Chi-restraints excluded: chain 6 residue 207 VAL Chi-restraints excluded: chain 6 residue 222 TYR Chi-restraints excluded: chain 4 residue 44 LYS Chi-restraints excluded: chain 4 residue 56 SER Chi-restraints excluded: chain 4 residue 68 THR Chi-restraints excluded: chain 4 residue 81 THR Chi-restraints excluded: chain 4 residue 83 GLU Chi-restraints excluded: chain 4 residue 98 ILE Chi-restraints excluded: chain 4 residue 110 ARG Chi-restraints excluded: chain 4 residue 129 LYS Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 164 ILE Chi-restraints excluded: chain 4 residue 180 ILE Chi-restraints excluded: chain 4 residue 234 ASN Chi-restraints excluded: chain 4 residue 241 ASN Chi-restraints excluded: chain 7 residue 12 THR Chi-restraints excluded: chain 7 residue 13 SER Chi-restraints excluded: chain 7 residue 33 PHE Chi-restraints excluded: chain 7 residue 48 LEU Chi-restraints excluded: chain 7 residue 59 ASP Chi-restraints excluded: chain 7 residue 66 VAL Chi-restraints excluded: chain 7 residue 127 VAL Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 7 residue 223 THR Chi-restraints excluded: chain 7 residue 231 VAL Chi-restraints excluded: chain 7 residue 250 TYR Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 98 ILE Chi-restraints excluded: chain 8 residue 112 LEU Chi-restraints excluded: chain 8 residue 114 ASP Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 ARG Chi-restraints excluded: chain 8 residue 181 PHE Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 67 LEU Chi-restraints excluded: chain 2 residue 71 LEU Chi-restraints excluded: chain 2 residue 77 SER Chi-restraints excluded: chain 2 residue 86 LYS Chi-restraints excluded: chain 2 residue 132 ARG Chi-restraints excluded: chain 2 residue 151 ILE Chi-restraints excluded: chain 2 residue 180 ILE Chi-restraints excluded: chain 2 residue 195 ARG Chi-restraints excluded: chain 2 residue 248 VAL Chi-restraints excluded: chain S residue 31 ASP Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 115 GLU Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 167 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 60 optimal weight: 1.9990 chunk 395 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 364 optimal weight: 2.9990 chunk 311 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 330 optimal weight: 0.0470 chunk 285 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS A 94 GLN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN y 196 ASN ** z 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.098559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.081695 restraints weight = 94901.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.083659 restraints weight = 43977.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.085026 restraints weight = 26441.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.085985 restraints weight = 18329.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.086577 restraints weight = 14053.930| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38693 Z= 0.125 Angle : 0.506 10.986 52512 Z= 0.264 Chirality : 0.042 0.226 5735 Planarity : 0.003 0.063 6763 Dihedral : 5.842 59.987 5294 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.12 % Favored : 93.64 % Rotamer: Outliers : 7.03 % Allowed : 25.34 % Favored : 67.63 % 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: -0.18 (0.13), residues: 4562 helix: 2.26 (0.15), residues: 1359 sheet: 0.05 (0.17), residues: 992 loop : -1.83 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 384 TYR 0.017 0.001 TYR 4 35 PHE 0.013 0.001 PHE A 127 TRP 0.015 0.001 TRP A 373 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00295 (38691) covalent geometry : angle 0.50585 (52508) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.40070 ( 4) hydrogen bonds : bond 0.03792 ( 1317) hydrogen bonds : angle 4.54630 ( 3663) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 291 poor density : 427 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.5809 (tmm160) REVERT: A 382 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7797 (mt-10) REVERT: A 399 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7146 (ttp-170) REVERT: A 425 TRP cc_start: 0.8593 (OUTLIER) cc_final: 0.8216 (t60) REVERT: B 153 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8798 (m) REVERT: B 182 TYR cc_start: 0.8386 (m-80) cc_final: 0.8172 (m-80) REVERT: B 264 LYS cc_start: 0.8358 (tttt) cc_final: 0.7366 (mptt) REVERT: x 365 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8582 (tp) REVERT: y 197 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8817 (mtp) REVERT: z 27 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7144 (tp40) REVERT: z 34 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7866 (ptm-80) REVERT: z 36 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8678 (t0) REVERT: z 57 ASP cc_start: 0.8438 (t0) cc_final: 0.8195 (t0) REVERT: z 87 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: z 90 GLN cc_start: 0.8827 (pt0) cc_final: 0.7312 (mm110) REVERT: z 152 LYS cc_start: 0.5615 (mttt) cc_final: 0.3912 (tttm) REVERT: z 216 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: z 256 LYS cc_start: 0.9136 (tttp) cc_final: 0.7622 (mmtt) REVERT: z 259 TRP cc_start: 0.8851 (OUTLIER) cc_final: 0.6714 (p90) REVERT: z 268 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7489 (tpt170) REVERT: w 31 MET cc_start: 0.9165 (mtm) cc_final: 0.8631 (mtp) REVERT: w 45 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8609 (t) REVERT: w 46 GLN cc_start: 0.8699 (mt0) cc_final: 0.8400 (mp10) REVERT: w 66 LYS cc_start: 0.8618 (mmtp) cc_final: 0.7712 (pptt) REVERT: w 234 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7912 (pp20) REVERT: w 496 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8101 (m) REVERT: w 526 MET cc_start: 0.8798 (mmm) cc_final: 0.8588 (mmm) REVERT: w 540 ARG cc_start: 0.7989 (mmt180) cc_final: 0.6310 (ptt-90) REVERT: 1 24 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7624 (tp40) REVERT: 1 42 ASN cc_start: 0.8766 (t0) cc_final: 0.8559 (t0) REVERT: 1 112 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9061 (mp) REVERT: 3 64 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7843 (tm) REVERT: 3 119 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9073 (mt) REVERT: 3 240 ILE cc_start: 0.5815 (OUTLIER) cc_final: 0.5143 (mp) REVERT: 5 29 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8618 (tp) REVERT: 5 74 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: 5 90 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: 5 215 ASN cc_start: 0.7534 (p0) cc_final: 0.7191 (p0) REVERT: 6 63 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.7055 (m-10) REVERT: 6 87 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.4708 (tp30) REVERT: 4 110 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.7909 (mtm180) REVERT: 4 144 ASN cc_start: 0.8986 (p0) cc_final: 0.8618 (p0) REVERT: 4 217 MET cc_start: 0.8606 (mmt) cc_final: 0.8013 (mmt) REVERT: 7 13 SER cc_start: 0.9053 (OUTLIER) cc_final: 0.8750 (m) REVERT: 7 250 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.6927 (t80) REVERT: 8 44 LYS cc_start: 0.8592 (tmtt) cc_final: 0.8215 (tptt) REVERT: 8 71 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9165 (tt) REVERT: 8 112 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8232 (mp) REVERT: 8 114 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.7862 (t70) REVERT: 8 115 MET cc_start: 0.8492 (mmt) cc_final: 0.8072 (mmm) REVERT: 8 142 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7603 (pmt-80) REVERT: 2 195 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7850 (mtt-85) REVERT: 2 217 MET cc_start: 0.7523 (mtp) cc_final: 0.7239 (mtp) REVERT: S 115 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: S 195 ASP cc_start: 0.8625 (m-30) cc_final: 0.7934 (m-30) outliers start: 291 outliers final: 204 residues processed: 679 average time/residue: 0.2128 time to fit residues: 239.9998 Evaluate side-chains 643 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 405 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 448 TRP Chi-restraints excluded: chain x residue 41 THR Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain x residue 49 THR Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 157 LEU Chi-restraints excluded: chain x residue 212 THR Chi-restraints excluded: chain x residue 216 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 268 SER Chi-restraints excluded: chain x residue 302 SER Chi-restraints excluded: chain x residue 306 VAL Chi-restraints excluded: chain x residue 323 MET Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 342 LEU Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 442 TYR Chi-restraints excluded: chain x residue 445 THR Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 451 ASP Chi-restraints excluded: chain x residue 452 SER Chi-restraints excluded: chain x residue 454 LEU Chi-restraints excluded: chain x residue 464 VAL Chi-restraints excluded: chain x residue 484 VAL Chi-restraints excluded: chain x residue 500 THR Chi-restraints excluded: chain x residue 505 VAL Chi-restraints excluded: chain x residue 532 MET Chi-restraints excluded: chain x residue 541 THR Chi-restraints excluded: chain x residue 546 LEU Chi-restraints excluded: chain x residue 592 LEU Chi-restraints excluded: chain x residue 597 VAL Chi-restraints excluded: chain x residue 614 PHE Chi-restraints excluded: chain x residue 637 VAL Chi-restraints excluded: chain x residue 644 ARG Chi-restraints excluded: chain x residue 668 VAL Chi-restraints excluded: chain x residue 677 THR Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 42 THR Chi-restraints excluded: chain y residue 94 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain y residue 153 VAL Chi-restraints excluded: chain y residue 162 VAL Chi-restraints excluded: chain y residue 188 CYS Chi-restraints excluded: chain y residue 195 THR Chi-restraints excluded: chain y residue 197 MET Chi-restraints excluded: chain y residue 228 THR Chi-restraints excluded: chain y residue 253 ASN Chi-restraints excluded: chain y residue 257 LEU Chi-restraints excluded: chain z residue 27 GLN Chi-restraints excluded: chain z residue 34 ARG Chi-restraints excluded: chain z residue 36 ASP Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 66 SER Chi-restraints excluded: chain z residue 87 ASP Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 120 SER Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 153 VAL Chi-restraints excluded: chain z residue 156 ILE Chi-restraints excluded: chain z residue 161 ILE Chi-restraints excluded: chain z residue 164 VAL Chi-restraints excluded: chain z residue 179 VAL Chi-restraints excluded: chain z residue 188 CYS Chi-restraints excluded: chain z residue 201 THR Chi-restraints excluded: chain z residue 216 GLN Chi-restraints excluded: chain z residue 222 VAL Chi-restraints excluded: chain z residue 259 TRP Chi-restraints excluded: chain z residue 268 ARG Chi-restraints excluded: chain z residue 286 THR Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 11 VAL Chi-restraints excluded: chain w residue 37 THR Chi-restraints excluded: chain w residue 45 VAL Chi-restraints excluded: chain w residue 77 TYR Chi-restraints excluded: chain w residue 82 ASP Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain w residue 155 THR Chi-restraints excluded: chain w residue 171 ILE Chi-restraints excluded: chain w residue 185 THR Chi-restraints excluded: chain w residue 198 THR Chi-restraints excluded: chain w residue 201 LEU Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 234 GLU Chi-restraints excluded: chain w residue 261 ILE Chi-restraints excluded: chain w residue 290 ARG Chi-restraints excluded: chain w residue 293 SER Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 307 ARG Chi-restraints excluded: chain w residue 320 ASP Chi-restraints excluded: chain w residue 324 THR Chi-restraints excluded: chain w residue 352 MET Chi-restraints excluded: chain w residue 401 LEU Chi-restraints excluded: chain w residue 423 SER Chi-restraints excluded: chain w residue 448 THR Chi-restraints excluded: chain w residue 449 ILE Chi-restraints excluded: chain w residue 485 THR Chi-restraints excluded: chain w residue 496 THR Chi-restraints excluded: chain w residue 506 VAL Chi-restraints excluded: chain w residue 523 THR Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 67 LEU Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 75 THR Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 115 MET Chi-restraints excluded: chain 1 residue 146 GLU Chi-restraints excluded: chain 1 residue 243 THR Chi-restraints excluded: chain 3 residue 23 CYS Chi-restraints excluded: chain 3 residue 44 LYS Chi-restraints excluded: chain 3 residue 64 LEU Chi-restraints excluded: chain 3 residue 71 LEU Chi-restraints excluded: chain 3 residue 96 ASP Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 119 LEU Chi-restraints excluded: chain 3 residue 147 LEU Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 240 ILE Chi-restraints excluded: chain 3 residue 244 ASP Chi-restraints excluded: chain 3 residue 248 VAL Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 66 VAL Chi-restraints excluded: chain 5 residue 74 GLU Chi-restraints excluded: chain 5 residue 90 GLN Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 158 ILE Chi-restraints excluded: chain 5 residue 160 ARG Chi-restraints excluded: chain 5 residue 164 ILE Chi-restraints excluded: chain 5 residue 196 PHE Chi-restraints excluded: chain 5 residue 227 MET Chi-restraints excluded: chain 5 residue 231 VAL Chi-restraints excluded: chain 6 residue 18 HIS Chi-restraints excluded: chain 6 residue 56 SER Chi-restraints excluded: chain 6 residue 63 TYR Chi-restraints excluded: chain 6 residue 77 SER Chi-restraints excluded: chain 6 residue 80 VAL Chi-restraints excluded: chain 6 residue 84 PHE Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 112 LEU Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 150 VAL Chi-restraints excluded: chain 6 residue 207 VAL Chi-restraints excluded: chain 6 residue 222 TYR Chi-restraints excluded: chain 4 residue 44 LYS Chi-restraints excluded: chain 4 residue 56 SER Chi-restraints excluded: chain 4 residue 68 THR Chi-restraints excluded: chain 4 residue 81 THR Chi-restraints excluded: chain 4 residue 110 ARG Chi-restraints excluded: chain 4 residue 129 LYS Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 164 ILE Chi-restraints excluded: chain 4 residue 180 ILE Chi-restraints excluded: chain 4 residue 234 ASN Chi-restraints excluded: chain 4 residue 241 ASN Chi-restraints excluded: chain 7 residue 12 THR Chi-restraints excluded: chain 7 residue 13 SER Chi-restraints excluded: chain 7 residue 33 PHE Chi-restraints excluded: chain 7 residue 48 LEU Chi-restraints excluded: chain 7 residue 59 ASP Chi-restraints excluded: chain 7 residue 66 VAL Chi-restraints excluded: chain 7 residue 127 VAL Chi-restraints excluded: chain 7 residue 130 LEU Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 223 THR Chi-restraints excluded: chain 7 residue 231 VAL Chi-restraints excluded: chain 7 residue 250 TYR Chi-restraints excluded: chain 8 residue 30 GLN Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 98 ILE Chi-restraints excluded: chain 8 residue 112 LEU Chi-restraints excluded: chain 8 residue 114 ASP Chi-restraints excluded: chain 8 residue 142 ARG Chi-restraints excluded: chain 8 residue 150 VAL Chi-restraints excluded: chain 8 residue 181 PHE Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 67 LEU Chi-restraints excluded: chain 2 residue 71 LEU Chi-restraints excluded: chain 2 residue 77 SER Chi-restraints excluded: chain 2 residue 86 LYS Chi-restraints excluded: chain 2 residue 151 ILE Chi-restraints excluded: chain 2 residue 180 ILE Chi-restraints excluded: chain 2 residue 195 ARG Chi-restraints excluded: chain 2 residue 202 ILE Chi-restraints excluded: chain 2 residue 248 VAL Chi-restraints excluded: chain S residue 31 ASP Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 115 GLU Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 167 ILE Chi-restraints excluded: chain S residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 95 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 303 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 428 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 183 optimal weight: 0.0370 chunk 72 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 133 optimal weight: 0.4980 overall best weight: 1.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS A 94 GLN A 167 GLN A 190 ASN y 196 ASN ** z 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.082221 restraints weight = 94404.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.084190 restraints weight = 43898.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.085567 restraints weight = 26379.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.086537 restraints weight = 18278.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.087112 restraints weight = 13958.768| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38693 Z= 0.107 Angle : 0.499 11.980 52512 Z= 0.259 Chirality : 0.041 0.222 5735 Planarity : 0.003 0.062 6763 Dihedral : 5.716 59.935 5286 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.05 % Favored : 93.71 % Rotamer: Outliers : 6.81 % Allowed : 25.58 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4562 helix: 2.30 (0.15), residues: 1359 sheet: 0.15 (0.17), residues: 976 loop : -1.80 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 384 TYR 0.016 0.001 TYR w 226 PHE 0.013 0.001 PHE A 127 TRP 0.017 0.001 TRP A 373 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00251 (38691) covalent geometry : angle 0.49928 (52508) SS BOND : bond 0.00168 ( 2) SS BOND : angle 0.36838 ( 4) hydrogen bonds : bond 0.03438 ( 1317) hydrogen bonds : angle 4.36363 ( 3663) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 282 poor density : 437 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.6172 (OUTLIER) cc_final: 0.5498 (tmm160) REVERT: A 382 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 399 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7155 (ttp-170) REVERT: A 425 TRP cc_start: 0.8579 (OUTLIER) cc_final: 0.8202 (t60) REVERT: B 153 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8799 (m) REVERT: B 213 GLU cc_start: 0.8172 (tp30) cc_final: 0.7702 (tp30) REVERT: B 264 LYS cc_start: 0.8350 (tttt) cc_final: 0.7155 (mmtt) REVERT: B 287 ASP cc_start: 0.8180 (t0) cc_final: 0.7969 (t0) REVERT: x 365 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8546 (tp) REVERT: y 197 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8812 (mtp) REVERT: z 27 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7202 (tp40) REVERT: z 36 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8627 (t0) REVERT: z 49 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8371 (mmt180) REVERT: z 57 ASP cc_start: 0.8415 (t0) cc_final: 0.8176 (t0) REVERT: z 87 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7940 (m-30) REVERT: z 90 GLN cc_start: 0.8790 (pt0) cc_final: 0.7318 (mm110) REVERT: z 152 LYS cc_start: 0.5595 (mttt) cc_final: 0.3864 (tttt) REVERT: z 216 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: z 256 LYS cc_start: 0.9131 (tttp) cc_final: 0.7609 (mmtt) REVERT: z 259 TRP cc_start: 0.8846 (OUTLIER) cc_final: 0.6671 (p90) REVERT: z 268 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7478 (tpt170) REVERT: w 31 MET cc_start: 0.9156 (mtm) cc_final: 0.8622 (mtp) REVERT: w 45 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8592 (t) REVERT: w 46 GLN cc_start: 0.8699 (mt0) cc_final: 0.8376 (mp10) REVERT: w 66 LYS cc_start: 0.8611 (mmtp) cc_final: 0.7700 (pptt) REVERT: w 194 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7159 (m-80) REVERT: w 234 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7872 (pp20) REVERT: w 464 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8409 (mt-10) REVERT: w 496 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8038 (m) REVERT: w 526 MET cc_start: 0.8800 (mmm) cc_final: 0.8593 (mmm) REVERT: w 540 ARG cc_start: 0.7943 (mmt180) cc_final: 0.6215 (ptt-90) REVERT: 1 24 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7618 (tp40) REVERT: 1 42 ASN cc_start: 0.8763 (t0) cc_final: 0.8560 (t0) REVERT: 1 112 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9056 (mp) REVERT: 3 64 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7842 (tm) REVERT: 3 240 ILE cc_start: 0.5801 (OUTLIER) cc_final: 0.5123 (mp) REVERT: 5 29 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8582 (tp) REVERT: 5 74 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: 5 215 ASN cc_start: 0.7652 (p0) cc_final: 0.7209 (p0) REVERT: 5 217 MET cc_start: 0.8176 (mmm) cc_final: 0.7952 (mmm) REVERT: 6 63 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.7045 (m-10) REVERT: 4 110 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.7965 (mtm180) REVERT: 4 144 ASN cc_start: 0.8950 (p0) cc_final: 0.8620 (p0) REVERT: 4 217 MET cc_start: 0.8570 (mmt) cc_final: 0.7894 (mmt) REVERT: 7 13 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8754 (m) REVERT: 7 250 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.6964 (t80) REVERT: 8 112 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8258 (mp) REVERT: 8 114 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.7793 (t70) REVERT: 8 115 MET cc_start: 0.8457 (mmt) cc_final: 0.8132 (mmm) REVERT: 8 142 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7601 (pmt-80) REVERT: 8 235 MET cc_start: 0.7987 (mtt) cc_final: 0.7786 (mtt) REVERT: 2 132 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8307 (tpt-90) REVERT: 2 195 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7955 (mtt-85) REVERT: 2 217 MET cc_start: 0.7516 (mtp) cc_final: 0.7207 (mtp) REVERT: 2 227 MET cc_start: 0.8503 (tpp) cc_final: 0.8020 (tpt) REVERT: S 115 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: S 195 ASP cc_start: 0.8629 (m-30) cc_final: 0.7929 (m-30) outliers start: 282 outliers final: 204 residues processed: 678 average time/residue: 0.2129 time to fit residues: 239.0559 Evaluate side-chains 654 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 418 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 41 THR Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain x residue 157 LEU Chi-restraints excluded: chain x residue 216 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 268 SER Chi-restraints excluded: chain x residue 302 SER Chi-restraints excluded: chain x residue 323 MET Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 342 LEU Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain x residue 394 ILE Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 442 TYR Chi-restraints excluded: chain x residue 445 THR Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 451 ASP Chi-restraints excluded: chain x residue 452 SER Chi-restraints excluded: chain x residue 454 LEU Chi-restraints excluded: chain x residue 471 LEU Chi-restraints excluded: chain x residue 484 VAL Chi-restraints excluded: chain x residue 500 THR Chi-restraints excluded: chain x residue 505 VAL Chi-restraints excluded: chain x residue 523 THR Chi-restraints excluded: chain x residue 532 MET Chi-restraints excluded: chain x residue 541 THR Chi-restraints excluded: chain x residue 546 LEU Chi-restraints excluded: chain x residue 592 LEU Chi-restraints excluded: chain x residue 597 VAL Chi-restraints excluded: chain x residue 614 PHE Chi-restraints excluded: chain x residue 637 VAL Chi-restraints excluded: chain x residue 644 ARG Chi-restraints excluded: chain x residue 668 VAL Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 42 THR Chi-restraints excluded: chain y residue 94 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain y residue 153 VAL Chi-restraints excluded: chain y residue 162 VAL Chi-restraints excluded: chain y residue 188 CYS Chi-restraints excluded: chain y residue 197 MET Chi-restraints excluded: chain y residue 253 ASN Chi-restraints excluded: chain y residue 257 LEU Chi-restraints excluded: chain z residue 27 GLN Chi-restraints excluded: chain z residue 36 ASP Chi-restraints excluded: chain z residue 49 ARG Chi-restraints excluded: chain z residue 66 SER Chi-restraints excluded: chain z residue 87 ASP Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 153 VAL Chi-restraints excluded: chain z residue 156 ILE Chi-restraints excluded: chain z residue 161 ILE Chi-restraints excluded: chain z residue 164 VAL Chi-restraints excluded: chain z residue 179 VAL Chi-restraints excluded: chain z residue 188 CYS Chi-restraints excluded: chain z residue 201 THR Chi-restraints excluded: chain z residue 216 GLN Chi-restraints excluded: chain z residue 222 VAL Chi-restraints excluded: chain z residue 259 TRP Chi-restraints excluded: chain z residue 268 ARG Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 286 THR Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 11 VAL Chi-restraints excluded: chain w residue 37 THR Chi-restraints excluded: chain w residue 45 VAL Chi-restraints excluded: chain w residue 77 TYR Chi-restraints excluded: chain w residue 82 ASP Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain w residue 155 THR Chi-restraints excluded: chain w residue 171 ILE Chi-restraints excluded: chain w residue 185 THR Chi-restraints excluded: chain w residue 194 PHE Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 234 GLU Chi-restraints excluded: chain w residue 261 ILE Chi-restraints excluded: chain w residue 281 ILE Chi-restraints excluded: chain w residue 290 ARG Chi-restraints excluded: chain w residue 293 SER Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 307 ARG Chi-restraints excluded: chain w residue 320 ASP Chi-restraints excluded: chain w residue 352 MET Chi-restraints excluded: chain w residue 401 LEU Chi-restraints excluded: chain w residue 423 SER Chi-restraints excluded: chain w residue 449 ILE Chi-restraints excluded: chain w residue 485 THR Chi-restraints excluded: chain w residue 496 THR Chi-restraints excluded: chain w residue 506 VAL Chi-restraints excluded: chain w residue 523 THR Chi-restraints excluded: chain 1 residue 67 LEU Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 115 MET Chi-restraints excluded: chain 1 residue 243 THR Chi-restraints excluded: chain 3 residue 23 CYS Chi-restraints excluded: chain 3 residue 44 LYS Chi-restraints excluded: chain 3 residue 57 TYR Chi-restraints excluded: chain 3 residue 64 LEU Chi-restraints excluded: chain 3 residue 68 THR Chi-restraints excluded: chain 3 residue 71 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 96 ASP Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 147 LEU Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 240 ILE Chi-restraints excluded: chain 3 residue 244 ASP Chi-restraints excluded: chain 3 residue 248 VAL Chi-restraints excluded: chain 5 residue 13 SER Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 66 VAL Chi-restraints excluded: chain 5 residue 74 GLU Chi-restraints excluded: chain 5 residue 154 LEU Chi-restraints excluded: chain 5 residue 158 ILE Chi-restraints excluded: chain 5 residue 160 ARG Chi-restraints excluded: chain 5 residue 164 ILE Chi-restraints excluded: chain 5 residue 212 GLN Chi-restraints excluded: chain 5 residue 227 MET Chi-restraints excluded: chain 5 residue 231 VAL Chi-restraints excluded: chain 6 residue 18 HIS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 56 SER Chi-restraints excluded: chain 6 residue 63 TYR Chi-restraints excluded: chain 6 residue 75 THR Chi-restraints excluded: chain 6 residue 77 SER Chi-restraints excluded: chain 6 residue 84 PHE Chi-restraints excluded: chain 6 residue 112 LEU Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 150 VAL Chi-restraints excluded: chain 6 residue 207 VAL Chi-restraints excluded: chain 6 residue 222 TYR Chi-restraints excluded: chain 4 residue 44 LYS Chi-restraints excluded: chain 4 residue 60 SER Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 68 THR Chi-restraints excluded: chain 4 residue 81 THR Chi-restraints excluded: chain 4 residue 110 ARG Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 180 ILE Chi-restraints excluded: chain 4 residue 202 ILE Chi-restraints excluded: chain 4 residue 234 ASN Chi-restraints excluded: chain 4 residue 241 ASN Chi-restraints excluded: chain 4 residue 255 SER Chi-restraints excluded: chain 7 residue 12 THR Chi-restraints excluded: chain 7 residue 13 SER Chi-restraints excluded: chain 7 residue 33 PHE Chi-restraints excluded: chain 7 residue 48 LEU Chi-restraints excluded: chain 7 residue 59 ASP Chi-restraints excluded: chain 7 residue 79 SER Chi-restraints excluded: chain 7 residue 127 VAL Chi-restraints excluded: chain 7 residue 130 LEU Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 223 THR Chi-restraints excluded: chain 7 residue 231 VAL Chi-restraints excluded: chain 7 residue 233 LEU Chi-restraints excluded: chain 7 residue 250 TYR Chi-restraints excluded: chain 8 residue 30 GLN Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 98 ILE Chi-restraints excluded: chain 8 residue 112 LEU Chi-restraints excluded: chain 8 residue 114 ASP Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 ARG Chi-restraints excluded: chain 8 residue 181 PHE Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 67 LEU Chi-restraints excluded: chain 2 residue 71 LEU Chi-restraints excluded: chain 2 residue 77 SER Chi-restraints excluded: chain 2 residue 86 LYS Chi-restraints excluded: chain 2 residue 132 ARG Chi-restraints excluded: chain 2 residue 151 ILE Chi-restraints excluded: chain 2 residue 180 ILE Chi-restraints excluded: chain 2 residue 195 ARG Chi-restraints excluded: chain 2 residue 202 ILE Chi-restraints excluded: chain S residue 31 ASP Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 115 GLU Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 155 THR Chi-restraints excluded: chain S residue 167 ILE Chi-restraints excluded: chain S residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 132 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 324 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 449 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 346 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN B 429 ASN x 660 ASN y 196 ASN ** z 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 274 GLN ** w 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 24 GLN ** 5 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.078524 restraints weight = 95816.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.080430 restraints weight = 45271.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.081740 restraints weight = 27347.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.082631 restraints weight = 19079.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.083291 restraints weight = 14750.005| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 38693 Z= 0.274 Angle : 0.620 8.124 52512 Z= 0.326 Chirality : 0.045 0.237 5735 Planarity : 0.004 0.062 6763 Dihedral : 6.129 59.899 5283 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.04 % Favored : 91.71 % Rotamer: Outliers : 8.41 % Allowed : 24.64 % Favored : 66.96 % 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: -0.43 (0.13), residues: 4562 helix: 2.03 (0.15), residues: 1368 sheet: -0.12 (0.17), residues: 990 loop : -1.98 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 110 TYR 0.023 0.002 TYR 4 35 PHE 0.020 0.002 PHE A 127 TRP 0.011 0.001 TRP A 373 HIS 0.022 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00653 (38691) covalent geometry : angle 0.61961 (52508) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.50713 ( 4) hydrogen bonds : bond 0.04940 ( 1317) hydrogen bonds : angle 4.68129 ( 3663) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 348 poor density : 412 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.5469 (tmm160) REVERT: A 382 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 399 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7318 (ttp-170) REVERT: A 425 TRP cc_start: 0.8530 (OUTLIER) cc_final: 0.8214 (t60) REVERT: B 153 SER cc_start: 0.9184 (OUTLIER) cc_final: 0.8754 (m) REVERT: B 264 LYS cc_start: 0.8368 (tttt) cc_final: 0.7320 (mptt) REVERT: x 365 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8712 (tp) REVERT: x 667 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8290 (p0) REVERT: z 27 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7366 (tp40) REVERT: z 34 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8303 (ptm-80) REVERT: z 57 ASP cc_start: 0.8461 (t0) cc_final: 0.8207 (t0) REVERT: z 87 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: z 152 LYS cc_start: 0.5683 (mttt) cc_final: 0.3902 (tttt) REVERT: z 259 TRP cc_start: 0.8812 (OUTLIER) cc_final: 0.7007 (p90) REVERT: z 268 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7464 (ttt180) REVERT: w 31 MET cc_start: 0.9247 (mtm) cc_final: 0.8463 (mtp) REVERT: w 45 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8622 (t) REVERT: w 46 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8439 (mp10) REVERT: w 66 LYS cc_start: 0.8563 (mmtp) cc_final: 0.7700 (pptt) REVERT: w 184 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: w 320 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8438 (t0) REVERT: w 429 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9301 (mt) REVERT: w 496 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8236 (m) REVERT: w 526 MET cc_start: 0.8776 (mmm) cc_final: 0.8538 (mmm) REVERT: w 540 ARG cc_start: 0.8042 (mmt180) cc_final: 0.6376 (ptt90) REVERT: 1 24 GLN cc_start: 0.7987 (tp40) cc_final: 0.7730 (tp40) REVERT: 1 42 ASN cc_start: 0.8815 (t0) cc_final: 0.8590 (t0) REVERT: 1 71 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9029 (mp) REVERT: 1 246 GLU cc_start: 0.7717 (tt0) cc_final: 0.7483 (tt0) REVERT: 3 64 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7878 (tm) REVERT: 3 203 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8204 (m-10) REVERT: 3 223 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8749 (m) REVERT: 3 240 ILE cc_start: 0.5826 (OUTLIER) cc_final: 0.5114 (mp) REVERT: 5 74 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: 5 215 ASN cc_start: 0.7734 (p0) cc_final: 0.7298 (p0) REVERT: 6 63 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.7175 (m-10) REVERT: 6 87 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.4912 (tp30) REVERT: 4 110 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.7790 (mtm180) REVERT: 4 144 ASN cc_start: 0.9068 (p0) cc_final: 0.8685 (p0) REVERT: 4 217 MET cc_start: 0.8710 (mmt) cc_final: 0.8268 (mmt) REVERT: 7 13 SER cc_start: 0.9193 (OUTLIER) cc_final: 0.8884 (m) REVERT: 7 33 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8030 (t80) REVERT: 7 54 GLN cc_start: 0.8157 (mp10) cc_final: 0.7624 (mm-40) REVERT: 7 250 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.7167 (t80) REVERT: 8 44 LYS cc_start: 0.8691 (tmtt) cc_final: 0.8286 (tptt) REVERT: 8 47 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8665 (t0) REVERT: 8 71 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9234 (tt) REVERT: 8 114 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8391 (m-30) REVERT: 8 115 MET cc_start: 0.8833 (mmt) cc_final: 0.8519 (mmm) REVERT: 8 142 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7776 (pmt-80) REVERT: 2 132 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8336 (tpt-90) REVERT: 2 217 MET cc_start: 0.7649 (mtp) cc_final: 0.7367 (mtp) REVERT: S 195 ASP cc_start: 0.8750 (m-30) cc_final: 0.8077 (m-30) outliers start: 348 outliers final: 264 residues processed: 717 average time/residue: 0.2069 time to fit residues: 247.7981 Evaluate side-chains 699 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 298 poor density : 401 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain x residue 41 THR Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain x residue 49 THR Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 53 ASP Chi-restraints excluded: chain x residue 157 LEU Chi-restraints excluded: chain x residue 212 THR Chi-restraints excluded: chain x residue 216 ILE Chi-restraints excluded: chain x residue 235 GLN Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 257 TYR Chi-restraints excluded: chain x residue 268 SER Chi-restraints excluded: chain x residue 302 SER Chi-restraints excluded: chain x residue 306 VAL Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 342 LEU Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain x residue 401 LYS Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 442 TYR Chi-restraints excluded: chain x residue 445 THR Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 454 LEU Chi-restraints excluded: chain x residue 471 LEU Chi-restraints excluded: chain x residue 484 VAL Chi-restraints excluded: chain x residue 500 THR Chi-restraints excluded: chain x residue 505 VAL Chi-restraints excluded: chain x residue 523 THR Chi-restraints excluded: chain x residue 532 MET Chi-restraints excluded: chain x residue 541 THR Chi-restraints excluded: chain x residue 569 SER Chi-restraints excluded: chain x residue 591 LEU Chi-restraints excluded: chain x residue 592 LEU Chi-restraints excluded: chain x residue 597 VAL Chi-restraints excluded: chain x residue 614 PHE Chi-restraints excluded: chain x residue 637 VAL Chi-restraints excluded: chain x residue 644 ARG Chi-restraints excluded: chain x residue 667 ASN Chi-restraints excluded: chain x residue 668 VAL Chi-restraints excluded: chain x residue 677 THR Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 42 THR Chi-restraints excluded: chain y residue 94 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain y residue 153 VAL Chi-restraints excluded: chain y residue 162 VAL Chi-restraints excluded: chain y residue 188 CYS Chi-restraints excluded: chain y residue 195 THR Chi-restraints excluded: chain y residue 253 ASN Chi-restraints excluded: chain y residue 257 LEU Chi-restraints excluded: chain z residue 27 GLN Chi-restraints excluded: chain z residue 34 ARG Chi-restraints excluded: chain z residue 66 SER Chi-restraints excluded: chain z residue 87 ASP Chi-restraints excluded: chain z residue 105 SER Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 153 VAL Chi-restraints excluded: chain z residue 156 ILE Chi-restraints excluded: chain z residue 161 ILE Chi-restraints excluded: chain z residue 164 VAL Chi-restraints excluded: chain z residue 179 VAL Chi-restraints excluded: chain z residue 188 CYS Chi-restraints excluded: chain z residue 201 THR Chi-restraints excluded: chain z residue 216 GLN Chi-restraints excluded: chain z residue 222 VAL Chi-restraints excluded: chain z residue 228 THR Chi-restraints excluded: chain z residue 259 TRP Chi-restraints excluded: chain z residue 268 ARG Chi-restraints excluded: chain z residue 271 ASN Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 286 THR Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 11 VAL Chi-restraints excluded: chain w residue 37 THR Chi-restraints excluded: chain w residue 45 VAL Chi-restraints excluded: chain w residue 46 GLN Chi-restraints excluded: chain w residue 76 THR Chi-restraints excluded: chain w residue 77 TYR Chi-restraints excluded: chain w residue 86 THR Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain w residue 155 THR Chi-restraints excluded: chain w residue 171 ILE Chi-restraints excluded: chain w residue 184 GLU Chi-restraints excluded: chain w residue 185 THR Chi-restraints excluded: chain w residue 198 THR Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 209 LYS Chi-restraints excluded: chain w residue 210 SER Chi-restraints excluded: chain w residue 259 VAL Chi-restraints excluded: chain w residue 261 ILE Chi-restraints excluded: chain w residue 281 ILE Chi-restraints excluded: chain w residue 290 ARG Chi-restraints excluded: chain w residue 293 SER Chi-restraints excluded: chain w residue 305 LEU Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 320 ASP Chi-restraints excluded: chain w residue 324 THR Chi-restraints excluded: chain w residue 329 ILE Chi-restraints excluded: chain w residue 342 CYS Chi-restraints excluded: chain w residue 344 ASP Chi-restraints excluded: chain w residue 350 THR Chi-restraints excluded: chain w residue 354 PHE Chi-restraints excluded: chain w residue 401 LEU Chi-restraints excluded: chain w residue 423 SER Chi-restraints excluded: chain w residue 429 LEU Chi-restraints excluded: chain w residue 448 THR Chi-restraints excluded: chain w residue 449 ILE Chi-restraints excluded: chain w residue 485 THR Chi-restraints excluded: chain w residue 496 THR Chi-restraints excluded: chain w residue 506 VAL Chi-restraints excluded: chain w residue 523 THR Chi-restraints excluded: chain w residue 530 THR Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 31 ASP Chi-restraints excluded: chain 1 residue 48 LEU Chi-restraints excluded: chain 1 residue 67 LEU Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 75 THR Chi-restraints excluded: chain 1 residue 77 SER Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 115 MET Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 146 GLU Chi-restraints excluded: chain 1 residue 243 THR Chi-restraints excluded: chain 3 residue 23 CYS Chi-restraints excluded: chain 3 residue 44 LYS Chi-restraints excluded: chain 3 residue 57 TYR Chi-restraints excluded: chain 3 residue 64 LEU Chi-restraints excluded: chain 3 residue 68 THR Chi-restraints excluded: chain 3 residue 71 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 96 ASP Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 3 residue 147 LEU Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 3 residue 203 PHE Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 223 THR Chi-restraints excluded: chain 3 residue 240 ILE Chi-restraints excluded: chain 3 residue 244 ASP Chi-restraints excluded: chain 3 residue 248 VAL Chi-restraints excluded: chain 5 residue 13 SER Chi-restraints excluded: chain 5 residue 66 VAL Chi-restraints excluded: chain 5 residue 74 GLU Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 160 ARG Chi-restraints excluded: chain 5 residue 164 ILE Chi-restraints excluded: chain 5 residue 196 PHE Chi-restraints excluded: chain 5 residue 227 MET Chi-restraints excluded: chain 5 residue 231 VAL Chi-restraints excluded: chain 6 residue 12 THR Chi-restraints excluded: chain 6 residue 18 HIS Chi-restraints excluded: chain 6 residue 32 MET Chi-restraints excluded: chain 6 residue 46 CYS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 56 SER Chi-restraints excluded: chain 6 residue 63 TYR Chi-restraints excluded: chain 6 residue 75 THR Chi-restraints excluded: chain 6 residue 77 SER Chi-restraints excluded: chain 6 residue 80 VAL Chi-restraints excluded: chain 6 residue 84 PHE Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 112 LEU Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 150 VAL Chi-restraints excluded: chain 6 residue 207 VAL Chi-restraints excluded: chain 6 residue 214 TYR Chi-restraints excluded: chain 6 residue 222 TYR Chi-restraints excluded: chain 4 residue 44 LYS Chi-restraints excluded: chain 4 residue 56 SER Chi-restraints excluded: chain 4 residue 60 SER Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 68 THR Chi-restraints excluded: chain 4 residue 81 THR Chi-restraints excluded: chain 4 residue 83 GLU Chi-restraints excluded: chain 4 residue 110 ARG Chi-restraints excluded: chain 4 residue 129 LYS Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 164 ILE Chi-restraints excluded: chain 4 residue 180 ILE Chi-restraints excluded: chain 4 residue 183 THR Chi-restraints excluded: chain 4 residue 202 ILE Chi-restraints excluded: chain 4 residue 234 ASN Chi-restraints excluded: chain 4 residue 241 ASN Chi-restraints excluded: chain 4 residue 255 SER Chi-restraints excluded: chain 7 residue 12 THR Chi-restraints excluded: chain 7 residue 13 SER Chi-restraints excluded: chain 7 residue 33 PHE Chi-restraints excluded: chain 7 residue 48 LEU Chi-restraints excluded: chain 7 residue 59 ASP Chi-restraints excluded: chain 7 residue 66 VAL Chi-restraints excluded: chain 7 residue 68 THR Chi-restraints excluded: chain 7 residue 103 ILE Chi-restraints excluded: chain 7 residue 127 VAL Chi-restraints excluded: chain 7 residue 130 LEU Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 223 THR Chi-restraints excluded: chain 7 residue 231 VAL Chi-restraints excluded: chain 7 residue 233 LEU Chi-restraints excluded: chain 7 residue 250 TYR Chi-restraints excluded: chain 8 residue 30 GLN Chi-restraints excluded: chain 8 residue 47 ASP Chi-restraints excluded: chain 8 residue 62 THR Chi-restraints excluded: chain 8 residue 67 LEU Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 98 ILE Chi-restraints excluded: chain 8 residue 114 ASP Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 ARG Chi-restraints excluded: chain 8 residue 150 VAL Chi-restraints excluded: chain 8 residue 181 PHE Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 2 residue 58 VAL Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 67 LEU Chi-restraints excluded: chain 2 residue 68 THR Chi-restraints excluded: chain 2 residue 71 LEU Chi-restraints excluded: chain 2 residue 77 SER Chi-restraints excluded: chain 2 residue 86 LYS Chi-restraints excluded: chain 2 residue 132 ARG Chi-restraints excluded: chain 2 residue 151 ILE Chi-restraints excluded: chain 2 residue 180 ILE Chi-restraints excluded: chain 2 residue 201 VAL Chi-restraints excluded: chain 2 residue 202 ILE Chi-restraints excluded: chain 2 residue 248 VAL Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 106 GLN Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 155 THR Chi-restraints excluded: chain S residue 167 ILE Chi-restraints excluded: chain S residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 372 optimal weight: 9.9990 chunk 403 optimal weight: 4.9990 chunk 302 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS y 196 ASN ** z 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 274 GLN ** 5 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.095793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.079056 restraints weight = 95222.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.080976 restraints weight = 45053.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.082304 restraints weight = 27179.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.083211 restraints weight = 18919.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.083784 restraints weight = 14616.796| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 38693 Z= 0.218 Angle : 0.588 8.779 52512 Z= 0.307 Chirality : 0.044 0.236 5735 Planarity : 0.004 0.060 6763 Dihedral : 6.095 59.406 5280 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.17 % Favored : 92.59 % Rotamer: Outliers : 7.95 % Allowed : 25.19 % Favored : 66.86 % 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: -0.50 (0.13), residues: 4562 helix: 2.03 (0.15), residues: 1362 sheet: -0.19 (0.17), residues: 984 loop : -2.01 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 439 TYR 0.020 0.001 TYR A 57 PHE 0.018 0.001 PHE A 127 TRP 0.020 0.001 TRP A 373 HIS 0.006 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00520 (38691) covalent geometry : angle 0.58790 (52508) SS BOND : bond 0.00233 ( 2) SS BOND : angle 0.47696 ( 4) hydrogen bonds : bond 0.04505 ( 1317) hydrogen bonds : angle 4.57719 ( 3663) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 329 poor density : 413 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5386 (tmm160) REVERT: A 88 MET cc_start: 0.7629 (tpp) cc_final: 0.7138 (tpp) REVERT: A 382 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7941 (mt-10) REVERT: A 399 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7469 (ttp-170) REVERT: A 425 TRP cc_start: 0.8623 (OUTLIER) cc_final: 0.8264 (t60) REVERT: B 51 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8584 (m) REVERT: B 153 SER cc_start: 0.9172 (OUTLIER) cc_final: 0.8752 (m) REVERT: B 264 LYS cc_start: 0.8343 (tttt) cc_final: 0.7302 (mptt) REVERT: x 365 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8638 (tp) REVERT: x 667 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8195 (p0) REVERT: z 27 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7310 (tp40) REVERT: z 34 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8101 (ptm-80) REVERT: z 57 ASP cc_start: 0.8444 (t0) cc_final: 0.8175 (t0) REVERT: z 87 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: z 152 LYS cc_start: 0.5667 (mttt) cc_final: 0.3897 (tttt) REVERT: z 216 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: z 244 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8410 (mttm) REVERT: z 259 TRP cc_start: 0.8803 (OUTLIER) cc_final: 0.7005 (p90) REVERT: z 268 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7435 (tpt170) REVERT: w 31 MET cc_start: 0.9239 (mtm) cc_final: 0.8663 (mtp) REVERT: w 45 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8636 (t) REVERT: w 46 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8445 (mp10) REVERT: w 66 LYS cc_start: 0.8568 (mmtp) cc_final: 0.7705 (pptt) REVERT: w 184 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: w 320 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8393 (t0) REVERT: w 429 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9289 (mt) REVERT: w 496 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8234 (m) REVERT: w 526 MET cc_start: 0.8713 (mmm) cc_final: 0.8472 (mmm) REVERT: w 540 ARG cc_start: 0.8033 (mmt180) cc_final: 0.6417 (ptt90) REVERT: 1 24 GLN cc_start: 0.7937 (tp40) cc_final: 0.7716 (tp40) REVERT: 1 42 ASN cc_start: 0.8826 (t0) cc_final: 0.8599 (t0) REVERT: 1 71 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9022 (mp) REVERT: 3 64 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7870 (tm) REVERT: 3 203 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8184 (m-10) REVERT: 3 223 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8751 (m) REVERT: 3 233 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8765 (pp) REVERT: 3 240 ILE cc_start: 0.5799 (OUTLIER) cc_final: 0.5087 (mp) REVERT: 5 74 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: 5 215 ASN cc_start: 0.7665 (p0) cc_final: 0.7242 (p0) REVERT: 6 63 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.7231 (m-10) REVERT: 6 87 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.4893 (tp30) REVERT: 6 153 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8417 (tppt) REVERT: 4 74 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: 4 110 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.7535 (mtm-85) REVERT: 4 144 ASN cc_start: 0.9039 (p0) cc_final: 0.8685 (p0) REVERT: 4 217 MET cc_start: 0.8711 (mmt) cc_final: 0.8282 (mmt) REVERT: 7 13 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.8944 (m) REVERT: 7 54 GLN cc_start: 0.8178 (mp10) cc_final: 0.7921 (mp10) REVERT: 7 227 MET cc_start: 0.8487 (tpp) cc_final: 0.8281 (tpp) REVERT: 7 250 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.7205 (t80) REVERT: 8 44 LYS cc_start: 0.8715 (tmtt) cc_final: 0.8254 (tptt) REVERT: 8 71 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9231 (tt) REVERT: 8 114 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8394 (m-30) REVERT: 8 115 MET cc_start: 0.8781 (mmt) cc_final: 0.8488 (mmm) REVERT: 8 142 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7823 (pmt-80) REVERT: 2 132 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8375 (tpt-90) REVERT: 2 217 MET cc_start: 0.7643 (mtp) cc_final: 0.7351 (mtp) REVERT: S 189 ARG cc_start: 0.7408 (ptm160) cc_final: 0.7063 (ptm160) outliers start: 329 outliers final: 258 residues processed: 698 average time/residue: 0.2077 time to fit residues: 241.8793 Evaluate side-chains 698 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 295 poor density : 403 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain x residue 41 THR Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain x residue 49 THR Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 53 ASP Chi-restraints excluded: chain x residue 157 LEU Chi-restraints excluded: chain x residue 212 THR Chi-restraints excluded: chain x residue 216 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 257 TYR Chi-restraints excluded: chain x residue 268 SER Chi-restraints excluded: chain x residue 302 SER Chi-restraints excluded: chain x residue 306 VAL Chi-restraints excluded: chain x residue 323 MET Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 342 LEU Chi-restraints excluded: chain x residue 347 VAL Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain x residue 394 ILE Chi-restraints excluded: chain x residue 401 LYS Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 440 LEU Chi-restraints excluded: chain x residue 442 TYR Chi-restraints excluded: chain x residue 445 THR Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 451 ASP Chi-restraints excluded: chain x residue 471 LEU Chi-restraints excluded: chain x residue 484 VAL Chi-restraints excluded: chain x residue 500 THR Chi-restraints excluded: chain x residue 523 THR Chi-restraints excluded: chain x residue 532 MET Chi-restraints excluded: chain x residue 541 THR Chi-restraints excluded: chain x residue 546 LEU Chi-restraints excluded: chain x residue 569 SER Chi-restraints excluded: chain x residue 592 LEU Chi-restraints excluded: chain x residue 597 VAL Chi-restraints excluded: chain x residue 614 PHE Chi-restraints excluded: chain x residue 637 VAL Chi-restraints excluded: chain x residue 644 ARG Chi-restraints excluded: chain x residue 667 ASN Chi-restraints excluded: chain x residue 668 VAL Chi-restraints excluded: chain x residue 677 THR Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 42 THR Chi-restraints excluded: chain y residue 94 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain y residue 153 VAL Chi-restraints excluded: chain y residue 162 VAL Chi-restraints excluded: chain y residue 188 CYS Chi-restraints excluded: chain y residue 195 THR Chi-restraints excluded: chain y residue 253 ASN Chi-restraints excluded: chain y residue 257 LEU Chi-restraints excluded: chain z residue 27 GLN Chi-restraints excluded: chain z residue 34 ARG Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 66 SER Chi-restraints excluded: chain z residue 87 ASP Chi-restraints excluded: chain z residue 105 SER Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 153 VAL Chi-restraints excluded: chain z residue 156 ILE Chi-restraints excluded: chain z residue 161 ILE Chi-restraints excluded: chain z residue 164 VAL Chi-restraints excluded: chain z residue 179 VAL Chi-restraints excluded: chain z residue 188 CYS Chi-restraints excluded: chain z residue 201 THR Chi-restraints excluded: chain z residue 216 GLN Chi-restraints excluded: chain z residue 222 VAL Chi-restraints excluded: chain z residue 228 THR Chi-restraints excluded: chain z residue 259 TRP Chi-restraints excluded: chain z residue 268 ARG Chi-restraints excluded: chain z residue 271 ASN Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 286 THR Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 11 VAL Chi-restraints excluded: chain w residue 37 THR Chi-restraints excluded: chain w residue 45 VAL Chi-restraints excluded: chain w residue 46 GLN Chi-restraints excluded: chain w residue 76 THR Chi-restraints excluded: chain w residue 77 TYR Chi-restraints excluded: chain w residue 86 THR Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain w residue 146 ASN Chi-restraints excluded: chain w residue 155 THR Chi-restraints excluded: chain w residue 171 ILE Chi-restraints excluded: chain w residue 184 GLU Chi-restraints excluded: chain w residue 185 THR Chi-restraints excluded: chain w residue 198 THR Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 209 LYS Chi-restraints excluded: chain w residue 210 SER Chi-restraints excluded: chain w residue 261 ILE Chi-restraints excluded: chain w residue 281 ILE Chi-restraints excluded: chain w residue 290 ARG Chi-restraints excluded: chain w residue 293 SER Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 320 ASP Chi-restraints excluded: chain w residue 324 THR Chi-restraints excluded: chain w residue 342 CYS Chi-restraints excluded: chain w residue 344 ASP Chi-restraints excluded: chain w residue 352 MET Chi-restraints excluded: chain w residue 354 PHE Chi-restraints excluded: chain w residue 401 LEU Chi-restraints excluded: chain w residue 423 SER Chi-restraints excluded: chain w residue 429 LEU Chi-restraints excluded: chain w residue 448 THR Chi-restraints excluded: chain w residue 449 ILE Chi-restraints excluded: chain w residue 485 THR Chi-restraints excluded: chain w residue 496 THR Chi-restraints excluded: chain w residue 506 VAL Chi-restraints excluded: chain w residue 523 THR Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 31 ASP Chi-restraints excluded: chain 1 residue 48 LEU Chi-restraints excluded: chain 1 residue 67 LEU Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 75 THR Chi-restraints excluded: chain 1 residue 77 SER Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 115 MET Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 243 THR Chi-restraints excluded: chain 3 residue 23 CYS Chi-restraints excluded: chain 3 residue 44 LYS Chi-restraints excluded: chain 3 residue 52 SER Chi-restraints excluded: chain 3 residue 57 TYR Chi-restraints excluded: chain 3 residue 64 LEU Chi-restraints excluded: chain 3 residue 68 THR Chi-restraints excluded: chain 3 residue 71 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 86 LYS Chi-restraints excluded: chain 3 residue 96 ASP Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 3 residue 147 LEU Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 3 residue 203 PHE Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 223 THR Chi-restraints excluded: chain 3 residue 233 LEU Chi-restraints excluded: chain 3 residue 240 ILE Chi-restraints excluded: chain 3 residue 244 ASP Chi-restraints excluded: chain 3 residue 248 VAL Chi-restraints excluded: chain 5 residue 13 SER Chi-restraints excluded: chain 5 residue 66 VAL Chi-restraints excluded: chain 5 residue 74 GLU Chi-restraints excluded: chain 5 residue 90 GLN Chi-restraints excluded: chain 5 residue 98 ILE Chi-restraints excluded: chain 5 residue 164 ILE Chi-restraints excluded: chain 5 residue 185 THR Chi-restraints excluded: chain 5 residue 196 PHE Chi-restraints excluded: chain 5 residue 227 MET Chi-restraints excluded: chain 5 residue 231 VAL Chi-restraints excluded: chain 6 residue 12 THR Chi-restraints excluded: chain 6 residue 18 HIS Chi-restraints excluded: chain 6 residue 32 MET Chi-restraints excluded: chain 6 residue 46 CYS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 56 SER Chi-restraints excluded: chain 6 residue 63 TYR Chi-restraints excluded: chain 6 residue 75 THR Chi-restraints excluded: chain 6 residue 77 SER Chi-restraints excluded: chain 6 residue 80 VAL Chi-restraints excluded: chain 6 residue 84 PHE Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 112 LEU Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 150 VAL Chi-restraints excluded: chain 6 residue 153 LYS Chi-restraints excluded: chain 6 residue 207 VAL Chi-restraints excluded: chain 6 residue 214 TYR Chi-restraints excluded: chain 6 residue 222 TYR Chi-restraints excluded: chain 4 residue 44 LYS Chi-restraints excluded: chain 4 residue 56 SER Chi-restraints excluded: chain 4 residue 60 SER Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 68 THR Chi-restraints excluded: chain 4 residue 74 GLU Chi-restraints excluded: chain 4 residue 75 THR Chi-restraints excluded: chain 4 residue 81 THR Chi-restraints excluded: chain 4 residue 83 GLU Chi-restraints excluded: chain 4 residue 98 ILE Chi-restraints excluded: chain 4 residue 110 ARG Chi-restraints excluded: chain 4 residue 129 LYS Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 164 ILE Chi-restraints excluded: chain 4 residue 180 ILE Chi-restraints excluded: chain 4 residue 202 ILE Chi-restraints excluded: chain 4 residue 234 ASN Chi-restraints excluded: chain 4 residue 241 ASN Chi-restraints excluded: chain 4 residue 255 SER Chi-restraints excluded: chain 7 residue 12 THR Chi-restraints excluded: chain 7 residue 13 SER Chi-restraints excluded: chain 7 residue 33 PHE Chi-restraints excluded: chain 7 residue 48 LEU Chi-restraints excluded: chain 7 residue 59 ASP Chi-restraints excluded: chain 7 residue 66 VAL Chi-restraints excluded: chain 7 residue 68 THR Chi-restraints excluded: chain 7 residue 103 ILE Chi-restraints excluded: chain 7 residue 127 VAL Chi-restraints excluded: chain 7 residue 130 LEU Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 223 THR Chi-restraints excluded: chain 7 residue 231 VAL Chi-restraints excluded: chain 7 residue 233 LEU Chi-restraints excluded: chain 7 residue 250 TYR Chi-restraints excluded: chain 8 residue 30 GLN Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 90 GLN Chi-restraints excluded: chain 8 residue 98 ILE Chi-restraints excluded: chain 8 residue 114 ASP Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 ARG Chi-restraints excluded: chain 8 residue 150 VAL Chi-restraints excluded: chain 8 residue 181 PHE Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 67 LEU Chi-restraints excluded: chain 2 residue 68 THR Chi-restraints excluded: chain 2 residue 71 LEU Chi-restraints excluded: chain 2 residue 77 SER Chi-restraints excluded: chain 2 residue 86 LYS Chi-restraints excluded: chain 2 residue 132 ARG Chi-restraints excluded: chain 2 residue 151 ILE Chi-restraints excluded: chain 2 residue 180 ILE Chi-restraints excluded: chain 2 residue 201 VAL Chi-restraints excluded: chain 2 residue 202 ILE Chi-restraints excluded: chain 2 residue 248 VAL Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 155 THR Chi-restraints excluded: chain S residue 167 ILE Chi-restraints excluded: chain S residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 106 optimal weight: 6.9990 chunk 436 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 336 optimal weight: 7.9990 chunk 382 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS A 167 GLN A 190 ASN y 196 ASN ** z 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 274 GLN ** 5 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.080044 restraints weight = 95073.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.081974 restraints weight = 44430.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.083324 restraints weight = 26776.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.084268 restraints weight = 18581.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.084832 restraints weight = 14236.512| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 38693 Z= 0.156 Angle : 0.554 8.291 52512 Z= 0.288 Chirality : 0.043 0.233 5735 Planarity : 0.004 0.059 6763 Dihedral : 6.003 59.403 5280 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.01 % Favored : 92.74 % Rotamer: Outliers : 7.54 % Allowed : 25.80 % Favored : 66.67 % 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: -0.38 (0.13), residues: 4562 helix: 2.16 (0.15), residues: 1356 sheet: -0.13 (0.17), residues: 972 loop : -1.95 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 439 TYR 0.022 0.001 TYR S 147 PHE 0.018 0.001 PHE A 127 TRP 0.021 0.001 TRP A 373 HIS 0.008 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00370 (38691) covalent geometry : angle 0.55408 (52508) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.37910 ( 4) hydrogen bonds : bond 0.03990 ( 1317) hydrogen bonds : angle 4.42393 ( 3663) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 312 poor density : 419 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5450 (tmm160) REVERT: A 88 MET cc_start: 0.7574 (tpp) cc_final: 0.6930 (tpp) REVERT: A 382 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7911 (mt-10) REVERT: A 399 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7612 (ttp-170) REVERT: A 425 TRP cc_start: 0.8597 (OUTLIER) cc_final: 0.8250 (t60) REVERT: B 51 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8588 (m) REVERT: B 153 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8757 (m) REVERT: B 264 LYS cc_start: 0.8399 (tttt) cc_final: 0.7293 (mptt) REVERT: x 107 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8653 (tp) REVERT: x 365 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8621 (tp) REVERT: x 667 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8151 (p0) REVERT: z 27 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7290 (tp40) REVERT: z 34 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7957 (ptm-80) REVERT: z 49 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8001 (mtt-85) REVERT: z 57 ASP cc_start: 0.8360 (t0) cc_final: 0.8115 (t0) REVERT: z 87 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: z 152 LYS cc_start: 0.5650 (mttt) cc_final: 0.3876 (tttt) REVERT: z 216 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: z 244 LYS cc_start: 0.8746 (mmmm) cc_final: 0.8385 (mttm) REVERT: z 259 TRP cc_start: 0.8804 (OUTLIER) cc_final: 0.7030 (p90) REVERT: z 268 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7526 (tpt170) REVERT: w 31 MET cc_start: 0.9218 (mtm) cc_final: 0.8651 (mtp) REVERT: w 45 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8632 (t) REVERT: w 46 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8432 (mp10) REVERT: w 66 LYS cc_start: 0.8558 (mmtp) cc_final: 0.7699 (pptt) REVERT: w 184 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: w 320 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8372 (t0) REVERT: w 464 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8358 (mt-10) REVERT: w 496 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8204 (m) REVERT: w 526 MET cc_start: 0.8710 (mmm) cc_final: 0.8482 (mmm) REVERT: w 540 ARG cc_start: 0.7970 (mmt180) cc_final: 0.6364 (ptt90) REVERT: 1 24 GLN cc_start: 0.7907 (tp40) cc_final: 0.7688 (tp40) REVERT: 1 42 ASN cc_start: 0.8812 (t0) cc_final: 0.8590 (t0) REVERT: 1 71 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9003 (mp) REVERT: 1 112 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9039 (mp) REVERT: 1 145 ASP cc_start: 0.8151 (p0) cc_final: 0.7791 (p0) REVERT: 3 64 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7931 (tm) REVERT: 3 203 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8145 (m-10) REVERT: 3 233 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8730 (pp) REVERT: 3 240 ILE cc_start: 0.5894 (OUTLIER) cc_final: 0.5187 (mp) REVERT: 5 74 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: 5 215 ASN cc_start: 0.7616 (p0) cc_final: 0.7232 (p0) REVERT: 6 87 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.4591 (tp30) REVERT: 4 74 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: 4 110 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.7841 (mtm180) REVERT: 4 144 ASN cc_start: 0.8961 (p0) cc_final: 0.8624 (p0) REVERT: 4 217 MET cc_start: 0.8657 (mmt) cc_final: 0.8087 (mmt) REVERT: 7 13 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8868 (m) REVERT: 7 54 GLN cc_start: 0.8080 (mp10) cc_final: 0.7789 (mp10) REVERT: 7 57 TYR cc_start: 0.7956 (t80) cc_final: 0.7543 (t80) REVERT: 7 227 MET cc_start: 0.8491 (tpp) cc_final: 0.8278 (tpp) REVERT: 7 250 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.7161 (t80) REVERT: 8 44 LYS cc_start: 0.8700 (tmtt) cc_final: 0.8247 (tptt) REVERT: 8 71 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9216 (tt) REVERT: 8 115 MET cc_start: 0.8680 (mmt) cc_final: 0.8438 (mmm) REVERT: 8 142 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7826 (pmt-80) REVERT: 2 217 MET cc_start: 0.7622 (mtp) cc_final: 0.7310 (mtp) REVERT: S 115 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: S 189 ARG cc_start: 0.7212 (ptm160) cc_final: 0.6855 (ptm160) outliers start: 312 outliers final: 245 residues processed: 686 average time/residue: 0.2100 time to fit residues: 239.0168 Evaluate side-chains 696 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 416 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 448 TRP Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain x residue 41 THR Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain x residue 49 THR Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 53 ASP Chi-restraints excluded: chain x residue 107 LEU Chi-restraints excluded: chain x residue 157 LEU Chi-restraints excluded: chain x residue 212 THR Chi-restraints excluded: chain x residue 216 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 257 TYR Chi-restraints excluded: chain x residue 268 SER Chi-restraints excluded: chain x residue 302 SER Chi-restraints excluded: chain x residue 323 MET Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 342 LEU Chi-restraints excluded: chain x residue 347 VAL Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain x residue 394 ILE Chi-restraints excluded: chain x residue 401 LYS Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 440 LEU Chi-restraints excluded: chain x residue 442 TYR Chi-restraints excluded: chain x residue 445 THR Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 451 ASP Chi-restraints excluded: chain x residue 454 LEU Chi-restraints excluded: chain x residue 471 LEU Chi-restraints excluded: chain x residue 484 VAL Chi-restraints excluded: chain x residue 500 THR Chi-restraints excluded: chain x residue 505 VAL Chi-restraints excluded: chain x residue 523 THR Chi-restraints excluded: chain x residue 532 MET Chi-restraints excluded: chain x residue 541 THR Chi-restraints excluded: chain x residue 546 LEU Chi-restraints excluded: chain x residue 569 SER Chi-restraints excluded: chain x residue 592 LEU Chi-restraints excluded: chain x residue 597 VAL Chi-restraints excluded: chain x residue 614 PHE Chi-restraints excluded: chain x residue 637 VAL Chi-restraints excluded: chain x residue 644 ARG Chi-restraints excluded: chain x residue 667 ASN Chi-restraints excluded: chain x residue 668 VAL Chi-restraints excluded: chain x residue 677 THR Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 42 THR Chi-restraints excluded: chain y residue 51 LEU Chi-restraints excluded: chain y residue 94 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain y residue 153 VAL Chi-restraints excluded: chain y residue 162 VAL Chi-restraints excluded: chain y residue 188 CYS Chi-restraints excluded: chain y residue 195 THR Chi-restraints excluded: chain y residue 253 ASN Chi-restraints excluded: chain y residue 257 LEU Chi-restraints excluded: chain z residue 27 GLN Chi-restraints excluded: chain z residue 34 ARG Chi-restraints excluded: chain z residue 49 ARG Chi-restraints excluded: chain z residue 66 SER Chi-restraints excluded: chain z residue 87 ASP Chi-restraints excluded: chain z residue 105 SER Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 153 VAL Chi-restraints excluded: chain z residue 156 ILE Chi-restraints excluded: chain z residue 161 ILE Chi-restraints excluded: chain z residue 164 VAL Chi-restraints excluded: chain z residue 179 VAL Chi-restraints excluded: chain z residue 188 CYS Chi-restraints excluded: chain z residue 201 THR Chi-restraints excluded: chain z residue 216 GLN Chi-restraints excluded: chain z residue 222 VAL Chi-restraints excluded: chain z residue 259 TRP Chi-restraints excluded: chain z residue 268 ARG Chi-restraints excluded: chain z residue 271 ASN Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 286 THR Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 11 VAL Chi-restraints excluded: chain w residue 37 THR Chi-restraints excluded: chain w residue 45 VAL Chi-restraints excluded: chain w residue 46 GLN Chi-restraints excluded: chain w residue 76 THR Chi-restraints excluded: chain w residue 77 TYR Chi-restraints excluded: chain w residue 86 THR Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain w residue 146 ASN Chi-restraints excluded: chain w residue 155 THR Chi-restraints excluded: chain w residue 171 ILE Chi-restraints excluded: chain w residue 184 GLU Chi-restraints excluded: chain w residue 185 THR Chi-restraints excluded: chain w residue 198 THR Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 209 LYS Chi-restraints excluded: chain w residue 261 ILE Chi-restraints excluded: chain w residue 281 ILE Chi-restraints excluded: chain w residue 290 ARG Chi-restraints excluded: chain w residue 293 SER Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 320 ASP Chi-restraints excluded: chain w residue 324 THR Chi-restraints excluded: chain w residue 342 CYS Chi-restraints excluded: chain w residue 344 ASP Chi-restraints excluded: chain w residue 352 MET Chi-restraints excluded: chain w residue 401 LEU Chi-restraints excluded: chain w residue 423 SER Chi-restraints excluded: chain w residue 449 ILE Chi-restraints excluded: chain w residue 485 THR Chi-restraints excluded: chain w residue 496 THR Chi-restraints excluded: chain w residue 523 THR Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 31 ASP Chi-restraints excluded: chain 1 residue 48 LEU Chi-restraints excluded: chain 1 residue 67 LEU Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 75 THR Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 115 MET Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 243 THR Chi-restraints excluded: chain 3 residue 23 CYS Chi-restraints excluded: chain 3 residue 44 LYS Chi-restraints excluded: chain 3 residue 52 SER Chi-restraints excluded: chain 3 residue 57 TYR Chi-restraints excluded: chain 3 residue 64 LEU Chi-restraints excluded: chain 3 residue 68 THR Chi-restraints excluded: chain 3 residue 71 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 86 LYS Chi-restraints excluded: chain 3 residue 96 ASP Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 3 residue 147 LEU Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 3 residue 171 CYS Chi-restraints excluded: chain 3 residue 183 THR Chi-restraints excluded: chain 3 residue 203 PHE Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 233 LEU Chi-restraints excluded: chain 3 residue 240 ILE Chi-restraints excluded: chain 3 residue 244 ASP Chi-restraints excluded: chain 3 residue 248 VAL Chi-restraints excluded: chain 3 residue 249 THR Chi-restraints excluded: chain 5 residue 13 SER Chi-restraints excluded: chain 5 residue 66 VAL Chi-restraints excluded: chain 5 residue 74 GLU Chi-restraints excluded: chain 5 residue 90 GLN Chi-restraints excluded: chain 5 residue 98 ILE Chi-restraints excluded: chain 5 residue 160 ARG Chi-restraints excluded: chain 5 residue 164 ILE Chi-restraints excluded: chain 5 residue 185 THR Chi-restraints excluded: chain 5 residue 196 PHE Chi-restraints excluded: chain 5 residue 212 GLN Chi-restraints excluded: chain 5 residue 227 MET Chi-restraints excluded: chain 5 residue 231 VAL Chi-restraints excluded: chain 6 residue 12 THR Chi-restraints excluded: chain 6 residue 18 HIS Chi-restraints excluded: chain 6 residue 46 CYS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 56 SER Chi-restraints excluded: chain 6 residue 75 THR Chi-restraints excluded: chain 6 residue 77 SER Chi-restraints excluded: chain 6 residue 80 VAL Chi-restraints excluded: chain 6 residue 84 PHE Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 112 LEU Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 150 VAL Chi-restraints excluded: chain 6 residue 207 VAL Chi-restraints excluded: chain 6 residue 214 TYR Chi-restraints excluded: chain 6 residue 222 TYR Chi-restraints excluded: chain 4 residue 44 LYS Chi-restraints excluded: chain 4 residue 56 SER Chi-restraints excluded: chain 4 residue 60 SER Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 68 THR Chi-restraints excluded: chain 4 residue 74 GLU Chi-restraints excluded: chain 4 residue 75 THR Chi-restraints excluded: chain 4 residue 81 THR Chi-restraints excluded: chain 4 residue 110 ARG Chi-restraints excluded: chain 4 residue 129 LYS Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 164 ILE Chi-restraints excluded: chain 4 residue 180 ILE Chi-restraints excluded: chain 4 residue 202 ILE Chi-restraints excluded: chain 4 residue 234 ASN Chi-restraints excluded: chain 4 residue 241 ASN Chi-restraints excluded: chain 4 residue 255 SER Chi-restraints excluded: chain 7 residue 12 THR Chi-restraints excluded: chain 7 residue 13 SER Chi-restraints excluded: chain 7 residue 33 PHE Chi-restraints excluded: chain 7 residue 48 LEU Chi-restraints excluded: chain 7 residue 59 ASP Chi-restraints excluded: chain 7 residue 103 ILE Chi-restraints excluded: chain 7 residue 127 VAL Chi-restraints excluded: chain 7 residue 130 LEU Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 223 THR Chi-restraints excluded: chain 7 residue 231 VAL Chi-restraints excluded: chain 7 residue 233 LEU Chi-restraints excluded: chain 7 residue 250 TYR Chi-restraints excluded: chain 8 residue 62 THR Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 90 GLN Chi-restraints excluded: chain 8 residue 98 ILE Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 ARG Chi-restraints excluded: chain 8 residue 181 PHE Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 68 THR Chi-restraints excluded: chain 2 residue 71 LEU Chi-restraints excluded: chain 2 residue 77 SER Chi-restraints excluded: chain 2 residue 86 LYS Chi-restraints excluded: chain 2 residue 151 ILE Chi-restraints excluded: chain 2 residue 180 ILE Chi-restraints excluded: chain 2 residue 201 VAL Chi-restraints excluded: chain 2 residue 202 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 115 GLU Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 155 THR Chi-restraints excluded: chain S residue 167 ILE Chi-restraints excluded: chain S residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 52 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 416 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 234 optimal weight: 4.9990 chunk 368 optimal weight: 4.9990 chunk 419 optimal weight: 0.0870 chunk 301 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN y 196 ASN ** z 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.097728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.081069 restraints weight = 94204.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.083058 restraints weight = 44785.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.084353 restraints weight = 26689.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.085253 restraints weight = 18446.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.085896 restraints weight = 14167.597| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38693 Z= 0.123 Angle : 0.545 11.000 52512 Z= 0.280 Chirality : 0.042 0.229 5735 Planarity : 0.003 0.058 6763 Dihedral : 5.852 59.761 5278 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.47 % Favored : 93.29 % Rotamer: Outliers : 6.81 % Allowed : 26.62 % Favored : 66.57 % 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: -0.30 (0.13), residues: 4562 helix: 2.22 (0.15), residues: 1362 sheet: -0.07 (0.17), residues: 984 loop : -1.92 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 439 TYR 0.019 0.001 TYR S 147 PHE 0.017 0.001 PHE A 127 TRP 0.021 0.001 TRP A 373 HIS 0.008 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00291 (38691) covalent geometry : angle 0.54497 (52508) SS BOND : bond 0.00206 ( 2) SS BOND : angle 0.42763 ( 4) hydrogen bonds : bond 0.03582 ( 1317) hydrogen bonds : angle 4.29846 ( 3663) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 282 poor density : 420 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.6308 (OUTLIER) cc_final: 0.5685 (tmm160) REVERT: A 75 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8866 (mmm-85) REVERT: A 88 MET cc_start: 0.7579 (tpp) cc_final: 0.6789 (tpp) REVERT: A 98 TYR cc_start: 0.7960 (m-80) cc_final: 0.7729 (m-80) REVERT: A 382 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7901 (mt-10) REVERT: A 399 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7796 (ttp-170) REVERT: A 425 TRP cc_start: 0.8579 (OUTLIER) cc_final: 0.8164 (t60) REVERT: B 153 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8774 (m) REVERT: B 264 LYS cc_start: 0.8376 (tttt) cc_final: 0.8151 (ttmm) REVERT: x 107 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8605 (tp) REVERT: x 365 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8562 (tp) REVERT: x 667 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8120 (p0) REVERT: z 27 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7307 (tp40) REVERT: z 49 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7957 (mtt-85) REVERT: z 57 ASP cc_start: 0.8355 (t0) cc_final: 0.8093 (t0) REVERT: z 87 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: z 152 LYS cc_start: 0.5848 (mttt) cc_final: 0.3996 (tttt) REVERT: z 216 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: z 244 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8354 (mttm) REVERT: z 259 TRP cc_start: 0.8792 (OUTLIER) cc_final: 0.7047 (p90) REVERT: z 268 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7526 (tpt170) REVERT: w 31 MET cc_start: 0.9238 (mtm) cc_final: 0.8719 (mtp) REVERT: w 45 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8618 (t) REVERT: w 46 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8392 (mp10) REVERT: w 66 LYS cc_start: 0.8550 (mmtp) cc_final: 0.7701 (pptt) REVERT: w 234 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7938 (pp20) REVERT: w 320 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8398 (t0) REVERT: w 464 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8331 (mt-10) REVERT: w 496 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8150 (m) REVERT: w 526 MET cc_start: 0.8791 (mmm) cc_final: 0.8576 (mmm) REVERT: w 540 ARG cc_start: 0.7943 (mmt180) cc_final: 0.6261 (ptt-90) REVERT: 1 24 GLN cc_start: 0.7908 (tp40) cc_final: 0.7654 (tp40) REVERT: 1 42 ASN cc_start: 0.8796 (t0) cc_final: 0.8572 (t0) REVERT: 1 71 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8945 (mt) REVERT: 1 112 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9031 (mp) REVERT: 3 64 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7941 (tm) REVERT: 3 233 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8700 (pp) REVERT: 3 240 ILE cc_start: 0.5860 (OUTLIER) cc_final: 0.5162 (mp) REVERT: 5 74 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: 5 215 ASN cc_start: 0.7584 (p0) cc_final: 0.7213 (p0) REVERT: 6 87 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.4748 (tp30) REVERT: 4 74 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: 4 110 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.7921 (mtm180) REVERT: 4 144 ASN cc_start: 0.8950 (p0) cc_final: 0.8607 (p0) REVERT: 4 217 MET cc_start: 0.8603 (mmt) cc_final: 0.7909 (mmt) REVERT: 7 13 SER cc_start: 0.9179 (OUTLIER) cc_final: 0.8886 (m) REVERT: 7 54 GLN cc_start: 0.8067 (mp10) cc_final: 0.7772 (mp10) REVERT: 7 57 TYR cc_start: 0.7949 (t80) cc_final: 0.7576 (t80) REVERT: 7 227 MET cc_start: 0.8411 (tpp) cc_final: 0.8127 (tpp) REVERT: 7 250 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.7167 (t80) REVERT: 8 44 LYS cc_start: 0.8682 (tmtt) cc_final: 0.8211 (tptt) REVERT: 8 142 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7760 (pmt-80) REVERT: 2 72 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8791 (p) REVERT: 2 217 MET cc_start: 0.7586 (mtp) cc_final: 0.7248 (mtp) REVERT: S 115 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: S 195 ASP cc_start: 0.8759 (m-30) cc_final: 0.7826 (m-30) outliers start: 282 outliers final: 233 residues processed: 664 average time/residue: 0.2131 time to fit residues: 235.2726 Evaluate side-chains 681 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 266 poor density : 415 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain x residue 41 THR Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain x residue 49 THR Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 53 ASP Chi-restraints excluded: chain x residue 107 LEU Chi-restraints excluded: chain x residue 157 LEU Chi-restraints excluded: chain x residue 212 THR Chi-restraints excluded: chain x residue 216 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 268 SER Chi-restraints excluded: chain x residue 302 SER Chi-restraints excluded: chain x residue 323 MET Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 342 LEU Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain x residue 394 ILE Chi-restraints excluded: chain x residue 401 LYS Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 440 LEU Chi-restraints excluded: chain x residue 442 TYR Chi-restraints excluded: chain x residue 445 THR Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 451 ASP Chi-restraints excluded: chain x residue 454 LEU Chi-restraints excluded: chain x residue 471 LEU Chi-restraints excluded: chain x residue 484 VAL Chi-restraints excluded: chain x residue 500 THR Chi-restraints excluded: chain x residue 505 VAL Chi-restraints excluded: chain x residue 523 THR Chi-restraints excluded: chain x residue 532 MET Chi-restraints excluded: chain x residue 541 THR Chi-restraints excluded: chain x residue 546 LEU Chi-restraints excluded: chain x residue 569 SER Chi-restraints excluded: chain x residue 592 LEU Chi-restraints excluded: chain x residue 597 VAL Chi-restraints excluded: chain x residue 614 PHE Chi-restraints excluded: chain x residue 637 VAL Chi-restraints excluded: chain x residue 644 ARG Chi-restraints excluded: chain x residue 667 ASN Chi-restraints excluded: chain x residue 668 VAL Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 42 THR Chi-restraints excluded: chain y residue 51 LEU Chi-restraints excluded: chain y residue 94 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain y residue 153 VAL Chi-restraints excluded: chain y residue 162 VAL Chi-restraints excluded: chain y residue 188 CYS Chi-restraints excluded: chain y residue 195 THR Chi-restraints excluded: chain y residue 253 ASN Chi-restraints excluded: chain z residue 27 GLN Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 49 ARG Chi-restraints excluded: chain z residue 66 SER Chi-restraints excluded: chain z residue 87 ASP Chi-restraints excluded: chain z residue 105 SER Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 153 VAL Chi-restraints excluded: chain z residue 156 ILE Chi-restraints excluded: chain z residue 161 ILE Chi-restraints excluded: chain z residue 164 VAL Chi-restraints excluded: chain z residue 179 VAL Chi-restraints excluded: chain z residue 188 CYS Chi-restraints excluded: chain z residue 201 THR Chi-restraints excluded: chain z residue 216 GLN Chi-restraints excluded: chain z residue 222 VAL Chi-restraints excluded: chain z residue 259 TRP Chi-restraints excluded: chain z residue 268 ARG Chi-restraints excluded: chain z residue 271 ASN Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 286 THR Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 11 VAL Chi-restraints excluded: chain w residue 45 VAL Chi-restraints excluded: chain w residue 46 GLN Chi-restraints excluded: chain w residue 76 THR Chi-restraints excluded: chain w residue 77 TYR Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain w residue 155 THR Chi-restraints excluded: chain w residue 171 ILE Chi-restraints excluded: chain w residue 185 THR Chi-restraints excluded: chain w residue 198 THR Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 209 LYS Chi-restraints excluded: chain w residue 234 GLU Chi-restraints excluded: chain w residue 261 ILE Chi-restraints excluded: chain w residue 281 ILE Chi-restraints excluded: chain w residue 290 ARG Chi-restraints excluded: chain w residue 293 SER Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 320 ASP Chi-restraints excluded: chain w residue 352 MET Chi-restraints excluded: chain w residue 401 LEU Chi-restraints excluded: chain w residue 423 SER Chi-restraints excluded: chain w residue 449 ILE Chi-restraints excluded: chain w residue 485 THR Chi-restraints excluded: chain w residue 496 THR Chi-restraints excluded: chain w residue 523 THR Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 31 ASP Chi-restraints excluded: chain 1 residue 67 LEU Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 75 THR Chi-restraints excluded: chain 1 residue 77 SER Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 115 MET Chi-restraints excluded: chain 1 residue 243 THR Chi-restraints excluded: chain 3 residue 23 CYS Chi-restraints excluded: chain 3 residue 44 LYS Chi-restraints excluded: chain 3 residue 52 SER Chi-restraints excluded: chain 3 residue 64 LEU Chi-restraints excluded: chain 3 residue 68 THR Chi-restraints excluded: chain 3 residue 71 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 86 LYS Chi-restraints excluded: chain 3 residue 96 ASP Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 3 residue 147 LEU Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 3 residue 171 CYS Chi-restraints excluded: chain 3 residue 183 THR Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 233 LEU Chi-restraints excluded: chain 3 residue 240 ILE Chi-restraints excluded: chain 3 residue 244 ASP Chi-restraints excluded: chain 3 residue 248 VAL Chi-restraints excluded: chain 3 residue 249 THR Chi-restraints excluded: chain 5 residue 13 SER Chi-restraints excluded: chain 5 residue 66 VAL Chi-restraints excluded: chain 5 residue 74 GLU Chi-restraints excluded: chain 5 residue 90 GLN Chi-restraints excluded: chain 5 residue 98 ILE Chi-restraints excluded: chain 5 residue 160 ARG Chi-restraints excluded: chain 5 residue 164 ILE Chi-restraints excluded: chain 5 residue 185 THR Chi-restraints excluded: chain 5 residue 196 PHE Chi-restraints excluded: chain 5 residue 212 GLN Chi-restraints excluded: chain 5 residue 227 MET Chi-restraints excluded: chain 5 residue 231 VAL Chi-restraints excluded: chain 6 residue 12 THR Chi-restraints excluded: chain 6 residue 18 HIS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 56 SER Chi-restraints excluded: chain 6 residue 75 THR Chi-restraints excluded: chain 6 residue 77 SER Chi-restraints excluded: chain 6 residue 80 VAL Chi-restraints excluded: chain 6 residue 84 PHE Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 112 LEU Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 207 VAL Chi-restraints excluded: chain 6 residue 214 TYR Chi-restraints excluded: chain 6 residue 222 TYR Chi-restraints excluded: chain 4 residue 44 LYS Chi-restraints excluded: chain 4 residue 56 SER Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 68 THR Chi-restraints excluded: chain 4 residue 74 GLU Chi-restraints excluded: chain 4 residue 81 THR Chi-restraints excluded: chain 4 residue 110 ARG Chi-restraints excluded: chain 4 residue 129 LYS Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 180 ILE Chi-restraints excluded: chain 4 residue 183 THR Chi-restraints excluded: chain 4 residue 202 ILE Chi-restraints excluded: chain 4 residue 234 ASN Chi-restraints excluded: chain 4 residue 241 ASN Chi-restraints excluded: chain 4 residue 255 SER Chi-restraints excluded: chain 7 residue 12 THR Chi-restraints excluded: chain 7 residue 13 SER Chi-restraints excluded: chain 7 residue 33 PHE Chi-restraints excluded: chain 7 residue 48 LEU Chi-restraints excluded: chain 7 residue 59 ASP Chi-restraints excluded: chain 7 residue 68 THR Chi-restraints excluded: chain 7 residue 103 ILE Chi-restraints excluded: chain 7 residue 127 VAL Chi-restraints excluded: chain 7 residue 130 LEU Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 223 THR Chi-restraints excluded: chain 7 residue 231 VAL Chi-restraints excluded: chain 7 residue 233 LEU Chi-restraints excluded: chain 7 residue 250 TYR Chi-restraints excluded: chain 8 residue 62 THR Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 90 GLN Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 ARG Chi-restraints excluded: chain 8 residue 181 PHE Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 67 LEU Chi-restraints excluded: chain 2 residue 68 THR Chi-restraints excluded: chain 2 residue 71 LEU Chi-restraints excluded: chain 2 residue 72 THR Chi-restraints excluded: chain 2 residue 77 SER Chi-restraints excluded: chain 2 residue 86 LYS Chi-restraints excluded: chain 2 residue 151 ILE Chi-restraints excluded: chain 2 residue 180 ILE Chi-restraints excluded: chain 2 residue 202 ILE Chi-restraints excluded: chain S residue 31 ASP Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 115 GLU Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 155 THR Chi-restraints excluded: chain S residue 167 ILE Chi-restraints excluded: chain S residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 328 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 262 optimal weight: 10.0000 chunk 265 optimal weight: 3.9990 chunk 320 optimal weight: 4.9990 chunk 360 optimal weight: 7.9990 chunk 286 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 275 optimal weight: 0.7980 chunk 204 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN y 196 ASN ** z 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.080898 restraints weight = 95001.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.082857 restraints weight = 44413.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.084174 restraints weight = 26711.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.085131 restraints weight = 18582.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.085714 restraints weight = 14270.738| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38693 Z= 0.133 Angle : 0.544 10.283 52512 Z= 0.281 Chirality : 0.042 0.226 5735 Planarity : 0.003 0.057 6763 Dihedral : 5.808 59.766 5274 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.62 % Favored : 93.14 % Rotamer: Outliers : 6.93 % Allowed : 26.47 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 4562 helix: 2.22 (0.15), residues: 1362 sheet: -0.05 (0.17), residues: 984 loop : -1.92 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 439 TYR 0.021 0.001 TYR S 147 PHE 0.016 0.001 PHE A 127 TRP 0.021 0.001 TRP A 373 HIS 0.005 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00316 (38691) covalent geometry : angle 0.54445 (52508) SS BOND : bond 0.00187 ( 2) SS BOND : angle 0.36647 ( 4) hydrogen bonds : bond 0.03599 ( 1317) hydrogen bonds : angle 4.27594 ( 3663) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 287 poor density : 421 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5755 (tmm160) REVERT: A 88 MET cc_start: 0.7587 (tpp) cc_final: 0.7036 (tpp) REVERT: A 98 TYR cc_start: 0.7974 (m-80) cc_final: 0.7296 (m-80) REVERT: A 382 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7896 (mt-10) REVERT: A 399 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7814 (ttp-170) REVERT: A 425 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.8180 (t60) REVERT: B 51 SER cc_start: 0.8965 (OUTLIER) cc_final: 0.8575 (m) REVERT: B 153 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8782 (m) REVERT: B 264 LYS cc_start: 0.8384 (tttt) cc_final: 0.8149 (ttmm) REVERT: x 365 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8564 (tp) REVERT: x 667 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8110 (p0) REVERT: y 197 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8787 (mtp) REVERT: z 27 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7379 (tp40) REVERT: z 34 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.7904 (ptm-80) REVERT: z 49 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7795 (mtt-85) REVERT: z 57 ASP cc_start: 0.8346 (t0) cc_final: 0.8096 (t0) REVERT: z 87 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: z 152 LYS cc_start: 0.5846 (mttt) cc_final: 0.3999 (tttt) REVERT: z 216 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7698 (mp10) REVERT: z 229 ASP cc_start: 0.7944 (t0) cc_final: 0.7660 (t70) REVERT: z 244 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8347 (mttm) REVERT: z 259 TRP cc_start: 0.8788 (OUTLIER) cc_final: 0.7055 (p90) REVERT: z 268 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7505 (tpt170) REVERT: w 31 MET cc_start: 0.9242 (mtm) cc_final: 0.8731 (mtp) REVERT: w 45 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8622 (t) REVERT: w 46 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8389 (mp10) REVERT: w 66 LYS cc_start: 0.8547 (mmtp) cc_final: 0.7695 (pptt) REVERT: w 234 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7935 (pp20) REVERT: w 320 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8406 (t0) REVERT: w 464 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8320 (mt-10) REVERT: w 496 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8150 (m) REVERT: w 526 MET cc_start: 0.8792 (mmm) cc_final: 0.8573 (mmm) REVERT: w 540 ARG cc_start: 0.7950 (mmt180) cc_final: 0.6334 (ptt90) REVERT: 1 24 GLN cc_start: 0.7910 (tp40) cc_final: 0.7653 (tp40) REVERT: 1 42 ASN cc_start: 0.8797 (t0) cc_final: 0.8567 (t0) REVERT: 1 71 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8973 (mp) REVERT: 1 112 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9044 (mp) REVERT: 3 64 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7959 (tm) REVERT: 3 203 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8190 (m-10) REVERT: 3 233 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8713 (pp) REVERT: 3 240 ILE cc_start: 0.5861 (OUTLIER) cc_final: 0.5158 (mp) REVERT: 5 74 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: 5 215 ASN cc_start: 0.7587 (p0) cc_final: 0.7224 (p0) REVERT: 6 87 GLU cc_start: 0.5972 (OUTLIER) cc_final: 0.4746 (tp30) REVERT: 4 74 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6414 (mp0) REVERT: 4 110 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.7889 (mtm180) REVERT: 4 144 ASN cc_start: 0.8955 (p0) cc_final: 0.8613 (p0) REVERT: 4 217 MET cc_start: 0.8604 (mmt) cc_final: 0.7919 (mmt) REVERT: 7 13 SER cc_start: 0.9181 (OUTLIER) cc_final: 0.8887 (m) REVERT: 7 54 GLN cc_start: 0.8076 (mp10) cc_final: 0.7772 (mp10) REVERT: 7 57 TYR cc_start: 0.7961 (t80) cc_final: 0.7587 (t80) REVERT: 7 227 MET cc_start: 0.8433 (tpp) cc_final: 0.8205 (tpp) REVERT: 7 250 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.7167 (t80) REVERT: 8 44 LYS cc_start: 0.8680 (tmtt) cc_final: 0.8332 (tptt) REVERT: 8 71 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9178 (tt) REVERT: 8 142 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7576 (pmt-80) REVERT: 8 235 MET cc_start: 0.8001 (mtt) cc_final: 0.7783 (mtt) REVERT: 2 72 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8798 (p) REVERT: 2 217 MET cc_start: 0.7592 (mtp) cc_final: 0.7244 (mtp) REVERT: S 115 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: S 195 ASP cc_start: 0.8754 (m-30) cc_final: 0.7822 (m-30) outliers start: 287 outliers final: 241 residues processed: 668 average time/residue: 0.2092 time to fit residues: 232.3466 Evaluate side-chains 688 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 277 poor density : 411 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain x residue 41 THR Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain x residue 49 THR Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 53 ASP Chi-restraints excluded: chain x residue 157 LEU Chi-restraints excluded: chain x residue 212 THR Chi-restraints excluded: chain x residue 216 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 268 SER Chi-restraints excluded: chain x residue 302 SER Chi-restraints excluded: chain x residue 323 MET Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 342 LEU Chi-restraints excluded: chain x residue 347 VAL Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain x residue 394 ILE Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 440 LEU Chi-restraints excluded: chain x residue 442 TYR Chi-restraints excluded: chain x residue 445 THR Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 451 ASP Chi-restraints excluded: chain x residue 454 LEU Chi-restraints excluded: chain x residue 471 LEU Chi-restraints excluded: chain x residue 484 VAL Chi-restraints excluded: chain x residue 500 THR Chi-restraints excluded: chain x residue 505 VAL Chi-restraints excluded: chain x residue 523 THR Chi-restraints excluded: chain x residue 532 MET Chi-restraints excluded: chain x residue 541 THR Chi-restraints excluded: chain x residue 546 LEU Chi-restraints excluded: chain x residue 569 SER Chi-restraints excluded: chain x residue 592 LEU Chi-restraints excluded: chain x residue 597 VAL Chi-restraints excluded: chain x residue 614 PHE Chi-restraints excluded: chain x residue 637 VAL Chi-restraints excluded: chain x residue 644 ARG Chi-restraints excluded: chain x residue 667 ASN Chi-restraints excluded: chain x residue 668 VAL Chi-restraints excluded: chain x residue 677 THR Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 42 THR Chi-restraints excluded: chain y residue 51 LEU Chi-restraints excluded: chain y residue 94 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain y residue 153 VAL Chi-restraints excluded: chain y residue 162 VAL Chi-restraints excluded: chain y residue 188 CYS Chi-restraints excluded: chain y residue 195 THR Chi-restraints excluded: chain y residue 196 ASN Chi-restraints excluded: chain y residue 197 MET Chi-restraints excluded: chain y residue 253 ASN Chi-restraints excluded: chain z residue 27 GLN Chi-restraints excluded: chain z residue 34 ARG Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 49 ARG Chi-restraints excluded: chain z residue 66 SER Chi-restraints excluded: chain z residue 87 ASP Chi-restraints excluded: chain z residue 105 SER Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 153 VAL Chi-restraints excluded: chain z residue 156 ILE Chi-restraints excluded: chain z residue 161 ILE Chi-restraints excluded: chain z residue 164 VAL Chi-restraints excluded: chain z residue 179 VAL Chi-restraints excluded: chain z residue 188 CYS Chi-restraints excluded: chain z residue 201 THR Chi-restraints excluded: chain z residue 216 GLN Chi-restraints excluded: chain z residue 222 VAL Chi-restraints excluded: chain z residue 259 TRP Chi-restraints excluded: chain z residue 268 ARG Chi-restraints excluded: chain z residue 271 ASN Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 286 THR Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 11 VAL Chi-restraints excluded: chain w residue 37 THR Chi-restraints excluded: chain w residue 45 VAL Chi-restraints excluded: chain w residue 46 GLN Chi-restraints excluded: chain w residue 76 THR Chi-restraints excluded: chain w residue 77 TYR Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain w residue 155 THR Chi-restraints excluded: chain w residue 171 ILE Chi-restraints excluded: chain w residue 185 THR Chi-restraints excluded: chain w residue 198 THR Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 209 LYS Chi-restraints excluded: chain w residue 234 GLU Chi-restraints excluded: chain w residue 261 ILE Chi-restraints excluded: chain w residue 281 ILE Chi-restraints excluded: chain w residue 290 ARG Chi-restraints excluded: chain w residue 293 SER Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 320 ASP Chi-restraints excluded: chain w residue 352 MET Chi-restraints excluded: chain w residue 401 LEU Chi-restraints excluded: chain w residue 423 SER Chi-restraints excluded: chain w residue 449 ILE Chi-restraints excluded: chain w residue 485 THR Chi-restraints excluded: chain w residue 496 THR Chi-restraints excluded: chain w residue 523 THR Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 31 ASP Chi-restraints excluded: chain 1 residue 67 LEU Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 75 THR Chi-restraints excluded: chain 1 residue 77 SER Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 115 MET Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 243 THR Chi-restraints excluded: chain 3 residue 23 CYS Chi-restraints excluded: chain 3 residue 44 LYS Chi-restraints excluded: chain 3 residue 52 SER Chi-restraints excluded: chain 3 residue 64 LEU Chi-restraints excluded: chain 3 residue 68 THR Chi-restraints excluded: chain 3 residue 71 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 86 LYS Chi-restraints excluded: chain 3 residue 96 ASP Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 3 residue 147 LEU Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 3 residue 171 CYS Chi-restraints excluded: chain 3 residue 183 THR Chi-restraints excluded: chain 3 residue 203 PHE Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 233 LEU Chi-restraints excluded: chain 3 residue 240 ILE Chi-restraints excluded: chain 3 residue 244 ASP Chi-restraints excluded: chain 3 residue 248 VAL Chi-restraints excluded: chain 3 residue 249 THR Chi-restraints excluded: chain 5 residue 13 SER Chi-restraints excluded: chain 5 residue 66 VAL Chi-restraints excluded: chain 5 residue 74 GLU Chi-restraints excluded: chain 5 residue 90 GLN Chi-restraints excluded: chain 5 residue 98 ILE Chi-restraints excluded: chain 5 residue 160 ARG Chi-restraints excluded: chain 5 residue 164 ILE Chi-restraints excluded: chain 5 residue 185 THR Chi-restraints excluded: chain 5 residue 196 PHE Chi-restraints excluded: chain 5 residue 212 GLN Chi-restraints excluded: chain 5 residue 227 MET Chi-restraints excluded: chain 5 residue 231 VAL Chi-restraints excluded: chain 6 residue 12 THR Chi-restraints excluded: chain 6 residue 18 HIS Chi-restraints excluded: chain 6 residue 32 MET Chi-restraints excluded: chain 6 residue 46 CYS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 56 SER Chi-restraints excluded: chain 6 residue 75 THR Chi-restraints excluded: chain 6 residue 77 SER Chi-restraints excluded: chain 6 residue 80 VAL Chi-restraints excluded: chain 6 residue 84 PHE Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 112 LEU Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 207 VAL Chi-restraints excluded: chain 6 residue 214 TYR Chi-restraints excluded: chain 6 residue 222 TYR Chi-restraints excluded: chain 4 residue 44 LYS Chi-restraints excluded: chain 4 residue 56 SER Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 68 THR Chi-restraints excluded: chain 4 residue 74 GLU Chi-restraints excluded: chain 4 residue 75 THR Chi-restraints excluded: chain 4 residue 81 THR Chi-restraints excluded: chain 4 residue 83 GLU Chi-restraints excluded: chain 4 residue 110 ARG Chi-restraints excluded: chain 4 residue 129 LYS Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 180 ILE Chi-restraints excluded: chain 4 residue 183 THR Chi-restraints excluded: chain 4 residue 202 ILE Chi-restraints excluded: chain 4 residue 234 ASN Chi-restraints excluded: chain 4 residue 241 ASN Chi-restraints excluded: chain 4 residue 255 SER Chi-restraints excluded: chain 7 residue 12 THR Chi-restraints excluded: chain 7 residue 13 SER Chi-restraints excluded: chain 7 residue 33 PHE Chi-restraints excluded: chain 7 residue 48 LEU Chi-restraints excluded: chain 7 residue 59 ASP Chi-restraints excluded: chain 7 residue 68 THR Chi-restraints excluded: chain 7 residue 103 ILE Chi-restraints excluded: chain 7 residue 127 VAL Chi-restraints excluded: chain 7 residue 130 LEU Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 223 THR Chi-restraints excluded: chain 7 residue 231 VAL Chi-restraints excluded: chain 7 residue 233 LEU Chi-restraints excluded: chain 7 residue 250 TYR Chi-restraints excluded: chain 8 residue 62 THR Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 90 GLN Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 ARG Chi-restraints excluded: chain 8 residue 164 ILE Chi-restraints excluded: chain 8 residue 181 PHE Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 67 LEU Chi-restraints excluded: chain 2 residue 68 THR Chi-restraints excluded: chain 2 residue 71 LEU Chi-restraints excluded: chain 2 residue 72 THR Chi-restraints excluded: chain 2 residue 77 SER Chi-restraints excluded: chain 2 residue 86 LYS Chi-restraints excluded: chain 2 residue 151 ILE Chi-restraints excluded: chain 2 residue 180 ILE Chi-restraints excluded: chain 2 residue 201 VAL Chi-restraints excluded: chain 2 residue 202 ILE Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 115 GLU Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 155 THR Chi-restraints excluded: chain S residue 167 ILE Chi-restraints excluded: chain S residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 24 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 277 optimal weight: 8.9990 chunk 300 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 390 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN B 429 ASN y 196 ASN ** z 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 27 ASN S 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.095390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.078617 restraints weight = 95888.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080536 restraints weight = 45326.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.081858 restraints weight = 27287.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.082769 restraints weight = 19018.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.083393 restraints weight = 14623.971| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 38693 Z= 0.259 Angle : 0.630 9.339 52512 Z= 0.328 Chirality : 0.045 0.234 5735 Planarity : 0.004 0.057 6763 Dihedral : 6.074 59.126 5274 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.13 % Favored : 91.63 % Rotamer: Outliers : 6.98 % Allowed : 26.45 % Favored : 66.57 % 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: -0.52 (0.13), residues: 4562 helix: 2.04 (0.15), residues: 1362 sheet: -0.24 (0.17), residues: 988 loop : -2.04 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 439 TYR 0.025 0.002 TYR S 147 PHE 0.017 0.002 PHE A 127 TRP 0.018 0.001 TRP A 373 HIS 0.006 0.001 HIS w 316 Details of bonding type rmsd covalent geometry : bond 0.00617 (38691) covalent geometry : angle 0.62967 (52508) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.42580 ( 4) hydrogen bonds : bond 0.04654 ( 1317) hydrogen bonds : angle 4.54815 ( 3663) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9124 Ramachandran restraints generated. 4562 Oldfield, 0 Emsley, 4562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 289 poor density : 405 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.6354 (OUTLIER) cc_final: 0.5485 (tmm160) REVERT: A 47 TRP cc_start: 0.8536 (t-100) cc_final: 0.8260 (t-100) REVERT: A 88 MET cc_start: 0.7586 (tpp) cc_final: 0.7066 (tpp) REVERT: A 382 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7914 (mt-10) REVERT: A 425 TRP cc_start: 0.8597 (OUTLIER) cc_final: 0.8229 (t60) REVERT: B 51 SER cc_start: 0.8988 (OUTLIER) cc_final: 0.8582 (m) REVERT: B 153 SER cc_start: 0.9161 (OUTLIER) cc_final: 0.8758 (m) REVERT: B 264 LYS cc_start: 0.8422 (tttt) cc_final: 0.8203 (ttmm) REVERT: x 365 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8744 (tp) REVERT: x 667 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8311 (p0) REVERT: z 27 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7354 (tp40) REVERT: z 34 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.7998 (ptm-80) REVERT: z 49 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7828 (mtt-85) REVERT: z 57 ASP cc_start: 0.8440 (t0) cc_final: 0.8189 (t0) REVERT: z 87 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: z 152 LYS cc_start: 0.5672 (mttt) cc_final: 0.3898 (tttt) REVERT: z 244 LYS cc_start: 0.8782 (mmmm) cc_final: 0.8399 (mttm) REVERT: z 259 TRP cc_start: 0.8808 (OUTLIER) cc_final: 0.7070 (p90) REVERT: z 268 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7388 (tpt170) REVERT: w 31 MET cc_start: 0.9259 (mtm) cc_final: 0.8683 (mtp) REVERT: w 45 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8635 (t) REVERT: w 46 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8436 (mp10) REVERT: w 66 LYS cc_start: 0.8573 (mmtp) cc_final: 0.7713 (pptt) REVERT: w 320 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8418 (t0) REVERT: w 464 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8360 (mt-10) REVERT: w 526 MET cc_start: 0.8742 (mmm) cc_final: 0.8506 (mmm) REVERT: w 540 ARG cc_start: 0.8019 (mmt180) cc_final: 0.6384 (ptt90) REVERT: 1 24 GLN cc_start: 0.7986 (tp40) cc_final: 0.7784 (tp40) REVERT: 1 42 ASN cc_start: 0.8838 (t0) cc_final: 0.8598 (t0) REVERT: 1 71 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9057 (mp) REVERT: 3 64 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7900 (tm) REVERT: 3 203 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8257 (m-10) REVERT: 3 233 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8771 (pp) REVERT: 3 240 ILE cc_start: 0.5832 (OUTLIER) cc_final: 0.5120 (mp) REVERT: 5 74 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: 5 215 ASN cc_start: 0.7639 (p0) cc_final: 0.7243 (p0) REVERT: 6 87 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.4756 (tp30) REVERT: 4 74 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: 4 110 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.7425 (mtm-85) REVERT: 4 144 ASN cc_start: 0.9057 (p0) cc_final: 0.8706 (p0) REVERT: 4 217 MET cc_start: 0.8731 (mmt) cc_final: 0.8274 (mmt) REVERT: 7 13 SER cc_start: 0.9254 (OUTLIER) cc_final: 0.8947 (m) REVERT: 7 54 GLN cc_start: 0.8108 (mp10) cc_final: 0.7802 (mp10) REVERT: 7 57 TYR cc_start: 0.8011 (t80) cc_final: 0.7716 (t80) REVERT: 7 250 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.7238 (t80) REVERT: 8 71 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9217 (tt) REVERT: 8 142 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7741 (pmt-80) REVERT: 2 72 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8870 (p) REVERT: 2 217 MET cc_start: 0.7666 (mtp) cc_final: 0.7358 (mtp) outliers start: 289 outliers final: 244 residues processed: 655 average time/residue: 0.2129 time to fit residues: 231.4997 Evaluate side-chains 674 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 273 poor density : 401 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 TRP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 TRP Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain x residue 41 THR Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain x residue 49 THR Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 53 ASP Chi-restraints excluded: chain x residue 157 LEU Chi-restraints excluded: chain x residue 212 THR Chi-restraints excluded: chain x residue 216 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 257 TYR Chi-restraints excluded: chain x residue 268 SER Chi-restraints excluded: chain x residue 302 SER Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 342 LEU Chi-restraints excluded: chain x residue 347 VAL Chi-restraints excluded: chain x residue 365 ILE Chi-restraints excluded: chain x residue 394 ILE Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 440 LEU Chi-restraints excluded: chain x residue 442 TYR Chi-restraints excluded: chain x residue 445 THR Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 454 LEU Chi-restraints excluded: chain x residue 471 LEU Chi-restraints excluded: chain x residue 484 VAL Chi-restraints excluded: chain x residue 500 THR Chi-restraints excluded: chain x residue 505 VAL Chi-restraints excluded: chain x residue 523 THR Chi-restraints excluded: chain x residue 532 MET Chi-restraints excluded: chain x residue 541 THR Chi-restraints excluded: chain x residue 569 SER Chi-restraints excluded: chain x residue 592 LEU Chi-restraints excluded: chain x residue 597 VAL Chi-restraints excluded: chain x residue 614 PHE Chi-restraints excluded: chain x residue 637 VAL Chi-restraints excluded: chain x residue 644 ARG Chi-restraints excluded: chain x residue 667 ASN Chi-restraints excluded: chain x residue 668 VAL Chi-restraints excluded: chain x residue 677 THR Chi-restraints excluded: chain y residue 40 LEU Chi-restraints excluded: chain y residue 42 THR Chi-restraints excluded: chain y residue 94 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain y residue 153 VAL Chi-restraints excluded: chain y residue 162 VAL Chi-restraints excluded: chain y residue 188 CYS Chi-restraints excluded: chain y residue 253 ASN Chi-restraints excluded: chain z residue 27 GLN Chi-restraints excluded: chain z residue 34 ARG Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 49 ARG Chi-restraints excluded: chain z residue 66 SER Chi-restraints excluded: chain z residue 87 ASP Chi-restraints excluded: chain z residue 105 SER Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 151 THR Chi-restraints excluded: chain z residue 153 VAL Chi-restraints excluded: chain z residue 156 ILE Chi-restraints excluded: chain z residue 161 ILE Chi-restraints excluded: chain z residue 164 VAL Chi-restraints excluded: chain z residue 179 VAL Chi-restraints excluded: chain z residue 188 CYS Chi-restraints excluded: chain z residue 201 THR Chi-restraints excluded: chain z residue 216 GLN Chi-restraints excluded: chain z residue 222 VAL Chi-restraints excluded: chain z residue 259 TRP Chi-restraints excluded: chain z residue 268 ARG Chi-restraints excluded: chain z residue 271 ASN Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 286 THR Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 11 VAL Chi-restraints excluded: chain w residue 37 THR Chi-restraints excluded: chain w residue 45 VAL Chi-restraints excluded: chain w residue 46 GLN Chi-restraints excluded: chain w residue 76 THR Chi-restraints excluded: chain w residue 77 TYR Chi-restraints excluded: chain w residue 86 THR Chi-restraints excluded: chain w residue 116 VAL Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain w residue 155 THR Chi-restraints excluded: chain w residue 171 ILE Chi-restraints excluded: chain w residue 185 THR Chi-restraints excluded: chain w residue 198 THR Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 209 LYS Chi-restraints excluded: chain w residue 261 ILE Chi-restraints excluded: chain w residue 281 ILE Chi-restraints excluded: chain w residue 290 ARG Chi-restraints excluded: chain w residue 293 SER Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 320 ASP Chi-restraints excluded: chain w residue 342 CYS Chi-restraints excluded: chain w residue 344 ASP Chi-restraints excluded: chain w residue 352 MET Chi-restraints excluded: chain w residue 401 LEU Chi-restraints excluded: chain w residue 423 SER Chi-restraints excluded: chain w residue 448 THR Chi-restraints excluded: chain w residue 449 ILE Chi-restraints excluded: chain w residue 485 THR Chi-restraints excluded: chain w residue 496 THR Chi-restraints excluded: chain w residue 523 THR Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 1 residue 31 ASP Chi-restraints excluded: chain 1 residue 48 LEU Chi-restraints excluded: chain 1 residue 67 LEU Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 75 THR Chi-restraints excluded: chain 1 residue 77 SER Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 115 MET Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 243 THR Chi-restraints excluded: chain 3 residue 23 CYS Chi-restraints excluded: chain 3 residue 44 LYS Chi-restraints excluded: chain 3 residue 52 SER Chi-restraints excluded: chain 3 residue 64 LEU Chi-restraints excluded: chain 3 residue 68 THR Chi-restraints excluded: chain 3 residue 71 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 86 LYS Chi-restraints excluded: chain 3 residue 96 ASP Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 3 residue 147 LEU Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 3 residue 171 CYS Chi-restraints excluded: chain 3 residue 183 THR Chi-restraints excluded: chain 3 residue 203 PHE Chi-restraints excluded: chain 3 residue 220 THR Chi-restraints excluded: chain 3 residue 233 LEU Chi-restraints excluded: chain 3 residue 240 ILE Chi-restraints excluded: chain 3 residue 244 ASP Chi-restraints excluded: chain 3 residue 248 VAL Chi-restraints excluded: chain 3 residue 249 THR Chi-restraints excluded: chain 5 residue 13 SER Chi-restraints excluded: chain 5 residue 66 VAL Chi-restraints excluded: chain 5 residue 74 GLU Chi-restraints excluded: chain 5 residue 90 GLN Chi-restraints excluded: chain 5 residue 160 ARG Chi-restraints excluded: chain 5 residue 164 ILE Chi-restraints excluded: chain 5 residue 185 THR Chi-restraints excluded: chain 5 residue 196 PHE Chi-restraints excluded: chain 5 residue 227 MET Chi-restraints excluded: chain 5 residue 231 VAL Chi-restraints excluded: chain 6 residue 12 THR Chi-restraints excluded: chain 6 residue 18 HIS Chi-restraints excluded: chain 6 residue 32 MET Chi-restraints excluded: chain 6 residue 46 CYS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 56 SER Chi-restraints excluded: chain 6 residue 75 THR Chi-restraints excluded: chain 6 residue 77 SER Chi-restraints excluded: chain 6 residue 80 VAL Chi-restraints excluded: chain 6 residue 84 PHE Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 112 LEU Chi-restraints excluded: chain 6 residue 207 VAL Chi-restraints excluded: chain 6 residue 214 TYR Chi-restraints excluded: chain 6 residue 222 TYR Chi-restraints excluded: chain 4 residue 44 LYS Chi-restraints excluded: chain 4 residue 56 SER Chi-restraints excluded: chain 4 residue 64 LEU Chi-restraints excluded: chain 4 residue 68 THR Chi-restraints excluded: chain 4 residue 74 GLU Chi-restraints excluded: chain 4 residue 75 THR Chi-restraints excluded: chain 4 residue 81 THR Chi-restraints excluded: chain 4 residue 83 GLU Chi-restraints excluded: chain 4 residue 110 ARG Chi-restraints excluded: chain 4 residue 129 LYS Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 164 ILE Chi-restraints excluded: chain 4 residue 180 ILE Chi-restraints excluded: chain 4 residue 183 THR Chi-restraints excluded: chain 4 residue 202 ILE Chi-restraints excluded: chain 4 residue 234 ASN Chi-restraints excluded: chain 4 residue 241 ASN Chi-restraints excluded: chain 4 residue 255 SER Chi-restraints excluded: chain 7 residue 12 THR Chi-restraints excluded: chain 7 residue 13 SER Chi-restraints excluded: chain 7 residue 33 PHE Chi-restraints excluded: chain 7 residue 48 LEU Chi-restraints excluded: chain 7 residue 59 ASP Chi-restraints excluded: chain 7 residue 68 THR Chi-restraints excluded: chain 7 residue 103 ILE Chi-restraints excluded: chain 7 residue 127 VAL Chi-restraints excluded: chain 7 residue 130 LEU Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 223 THR Chi-restraints excluded: chain 7 residue 231 VAL Chi-restraints excluded: chain 7 residue 233 LEU Chi-restraints excluded: chain 7 residue 250 TYR Chi-restraints excluded: chain 8 residue 62 THR Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 90 GLN Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 ARG Chi-restraints excluded: chain 8 residue 150 VAL Chi-restraints excluded: chain 8 residue 164 ILE Chi-restraints excluded: chain 8 residue 181 PHE Chi-restraints excluded: chain 8 residue 193 VAL Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 232 ILE Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 67 LEU Chi-restraints excluded: chain 2 residue 68 THR Chi-restraints excluded: chain 2 residue 71 LEU Chi-restraints excluded: chain 2 residue 72 THR Chi-restraints excluded: chain 2 residue 77 SER Chi-restraints excluded: chain 2 residue 86 LYS Chi-restraints excluded: chain 2 residue 151 ILE Chi-restraints excluded: chain 2 residue 180 ILE Chi-restraints excluded: chain 2 residue 201 VAL Chi-restraints excluded: chain 2 residue 202 ILE Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 155 THR Chi-restraints excluded: chain S residue 167 ILE Chi-restraints excluded: chain S residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 208 optimal weight: 0.0470 chunk 277 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 408 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 292 optimal weight: 9.9990 chunk 450 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 341 optimal weight: 20.0000 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 139 GLN y 196 ASN ** z 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 27 ASN S 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.080690 restraints weight = 94828.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.082665 restraints weight = 44698.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.084014 restraints weight = 26915.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.084964 restraints weight = 18766.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.085568 restraints weight = 14445.071| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38693 Z= 0.131 Angle : 0.564 12.332 52512 Z= 0.290 Chirality : 0.042 0.230 5735 Planarity : 0.004 0.055 6763 Dihedral : 5.841 59.500 5270 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.18 % Favored : 93.60 % Rotamer: Outliers : 6.50 % Allowed : 26.96 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 4562 helix: 2.20 (0.15), residues: 1350 sheet: -0.10 (0.17), residues: 973 loop : -1.95 (0.13), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 439 TYR 0.018 0.001 TYR S 147 PHE 0.019 0.001 PHE A 127 TRP 0.022 0.001 TRP A 373 HIS 0.005 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00307 (38691) covalent geometry : angle 0.56364 (52508) SS BOND : bond 0.00204 ( 2) SS BOND : angle 0.42002 ( 4) hydrogen bonds : bond 0.03744 ( 1317) hydrogen bonds : angle 4.32463 ( 3663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6966.23 seconds wall clock time: 120 minutes 42.29 seconds (7242.29 seconds total)