Starting phenix.real_space_refine on Sat Jan 25 05:48:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9avj_43903/01_2025/9avj_43903.cif Found real_map, /net/cci-nas-00/data/ceres_data/9avj_43903/01_2025/9avj_43903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9avj_43903/01_2025/9avj_43903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9avj_43903/01_2025/9avj_43903.map" model { file = "/net/cci-nas-00/data/ceres_data/9avj_43903/01_2025/9avj_43903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9avj_43903/01_2025/9avj_43903.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.037 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 72 5.16 5 C 14601 2.51 5 N 4058 2.21 5 O 4437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 23188 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3598 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Chain breaks: 1 Chain: "B" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3542 Classifications: {'peptide': 462} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 439} Chain breaks: 1 Chain: "C" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3534 Classifications: {'peptide': 461} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 439} Chain breaks: 2 Chain: "D" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3611 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "E" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3589 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 441} Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3614 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Chain: "G" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1540 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.52, per 1000 atoms: 0.58 Number of scatterers: 23188 At special positions: 0 Unit cell: (137.054, 126.208, 127.194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 15 15.00 Mg 5 11.99 O 4437 8.00 N 4058 7.00 C 14601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 2.6 seconds 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5448 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 24 sheets defined 46.7% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.639A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.578A pdb=" N ALA A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 4.118A pdb=" N VAL A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 215 through 219 removed outlier: 5.962A pdb=" N LEU A 218 " --> pdb=" O HIS A 215 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 219' Processing helix chain 'A' and resid 231 through 252 removed outlier: 3.824A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 4.458A pdb=" N GLY A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.739A pdb=" N ALA A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 removed outlier: 4.043A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 removed outlier: 3.582A pdb=" N SER A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.893A pdb=" N PHE A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.593A pdb=" N LYS A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 397 removed outlier: 3.652A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ALA A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 452 through 468 removed outlier: 4.053A pdb=" N LYS A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 479 Processing helix chain 'A' and resid 483 through 496 removed outlier: 4.345A pdb=" N LYS A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA A 490 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.892A pdb=" N GLY B 81 " --> pdb=" O PRO B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.787A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.561A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.584A pdb=" N ASN B 190 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 252 removed outlier: 3.598A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.819A pdb=" N GLY B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 4.085A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.961A pdb=" N ILE B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 352 removed outlier: 3.927A pdb=" N GLY B 352 " --> pdb=" O PHE B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.561A pdb=" N LYS B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 396 removed outlier: 3.584A pdb=" N TYR B 389 " --> pdb=" O ASP B 385 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 419 removed outlier: 3.690A pdb=" N ALA B 411 " --> pdb=" O GLN B 407 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 413 " --> pdb=" O LYS B 409 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.686A pdb=" N LYS B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP B 465 " --> pdb=" O TYR B 461 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 removed outlier: 4.162A pdb=" N LEU B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 495 removed outlier: 3.829A pdb=" N ILE B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU B 492 " --> pdb=" O ASN B 488 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 493 " --> pdb=" O LYS B 489 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 156 removed outlier: 3.783A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 4.000A pdb=" N ALA C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 204 through 216 removed outlier: 4.392A pdb=" N VAL C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.578A pdb=" N PHE C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 250 removed outlier: 4.108A pdb=" N GLY C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 243 " --> pdb=" O PRO C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 4.136A pdb=" N LEU C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.713A pdb=" N GLU C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 325 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.503A pdb=" N PHE C 349 " --> pdb=" O GLN C 345 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 345 through 350' Processing helix chain 'C' and resid 372 through 380 removed outlier: 3.991A pdb=" N LYS C 376 " --> pdb=" O ILE C 372 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 397 removed outlier: 3.595A pdb=" N ASP C 385 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 420 removed outlier: 3.558A pdb=" N LEU C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 441 removed outlier: 4.109A pdb=" N VAL C 434 " --> pdb=" O VAL C 430 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.523A pdb=" N LYS C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 4.172A pdb=" N HIS C 474 " --> pdb=" O HIS C 470 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 479 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 497 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 139 through 146 removed outlier: 3.531A pdb=" N LEU D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.658A pdb=" N LEU D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN D 177 " --> pdb=" O HIS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 206 removed outlier: 3.526A pdb=" N TYR D 199 " --> pdb=" O GLY D 195 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.651A pdb=" N ARG D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY D 232 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.697A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.657A pdb=" N GLN D 287 " --> pdb=" O THR D 283 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.582A pdb=" N GLY D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 3.507A pdb=" N TYR D 364 " --> pdb=" O GLY D 360 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL D 366 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.695A pdb=" N VAL D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 400 " --> pdb=" O ASP D 396 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.574A pdb=" N ARG D 454 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 4.159A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 22 removed outlier: 3.896A pdb=" N HIS E 22 " --> pdb=" O GLU E 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 19 through 22' Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.681A pdb=" N GLU E 127 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 146 Processing helix chain 'E' and resid 165 through 179 removed outlier: 3.951A pdb=" N LEU E 171 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 172 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS E 173 " --> pdb=" O GLN E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 204 removed outlier: 3.621A pdb=" N GLY E 195 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN E 196 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 206 No H-bonds generated for 'chain 'E' and resid 205 through 206' Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 227 through 242 removed outlier: 3.561A pdb=" N THR E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET E 235 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG E 240 " --> pdb=" O ALA E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.871A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 277 Processing helix chain 'E' and resid 280 through 285 removed outlier: 3.607A pdb=" N MET E 285 " --> pdb=" O LEU E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 315 through 323 removed outlier: 4.125A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 385 removed outlier: 3.662A pdb=" N VAL E 370 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN E 371 " --> pdb=" O ALA E 367 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG E 376 " --> pdb=" O GLN E 372 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR E 377 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 4.110A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE E 408 " --> pdb=" O ARG E 404 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU E 410 " --> pdb=" O ILE E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 420 removed outlier: 3.554A pdb=" N GLU E 418 " --> pdb=" O HIS E 415 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 443 removed outlier: 3.811A pdb=" N VAL E 434 " --> pdb=" O VAL E 430 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG E 435 " --> pdb=" O LYS E 431 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY E 443 " --> pdb=" O GLU E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 466 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 139 through 146 removed outlier: 3.753A pdb=" N LEU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 175 Processing helix chain 'F' and resid 191 through 204 removed outlier: 3.556A pdb=" N TYR F 199 " --> pdb=" O GLY F 195 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS F 200 " --> pdb=" O ASN F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 209 removed outlier: 4.076A pdb=" N SER F 209 " --> pdb=" O GLY F 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 206 through 209' Processing helix chain 'F' and resid 223 through 242 removed outlier: 4.454A pdb=" N ARG F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 4.239A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 315 through 320 Processing helix chain 'F' and resid 321 through 324 Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 removed outlier: 3.861A pdb=" N VAL F 366 " --> pdb=" O GLU F 362 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG F 376 " --> pdb=" O GLN F 372 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR F 377 " --> pdb=" O THR F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.587A pdb=" N VAL F 399 " --> pdb=" O GLU F 395 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG F 402 " --> pdb=" O LEU F 398 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA F 403 " --> pdb=" O VAL F 399 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG F 404 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 418 removed outlier: 3.567A pdb=" N GLU F 418 " --> pdb=" O HIS F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 442 removed outlier: 4.084A pdb=" N PHE F 437 " --> pdb=" O THR F 433 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS F 438 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU F 439 " --> pdb=" O ARG F 435 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE F 440 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 469 removed outlier: 3.848A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 51 Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 87 through 90 removed outlier: 3.854A pdb=" N TYR G 90 " --> pdb=" O ALA G 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 87 through 90' Processing helix chain 'G' and resid 91 through 105 removed outlier: 3.954A pdb=" N LEU G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG G 105 " --> pdb=" O THR G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 127 removed outlier: 3.506A pdb=" N PHE G 125 " --> pdb=" O GLY G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 283 removed outlier: 4.258A pdb=" N ASP G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN G 249 " --> pdb=" O ASN G 245 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASN G 251 " --> pdb=" O THR G 247 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU G 252 " --> pdb=" O ASP G 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 35 removed outlier: 6.670A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.166A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 3.596A pdb=" N ALA A 226 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA5, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.532A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA7, first strand: chain 'B' and resid 113 through 114 removed outlier: 3.705A pdb=" N GLN B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR B 225 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.825A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 341 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 363 " --> pdb=" O GLN B 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.493A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU C 66 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.598A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL C 256 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU C 316 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL C 258 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE C 318 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR C 260 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N GLU C 320 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE C 167 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 9 removed outlier: 5.780A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 49 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 87 removed outlier: 4.387A pdb=" N ARG D 114 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.702A pdb=" N SER D 183 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VAL D 214 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N PHE D 185 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.630A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 4 through 10 removed outlier: 5.580A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 52 " --> pdb=" O ARG E 60 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.424A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER E 183 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL E 214 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE E 185 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY E 216 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY E 187 " --> pdb=" O GLY E 216 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE E 182 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N PHE E 250 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N THR E 328 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N LEU E 347 " --> pdb=" O THR E 328 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASN E 330 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.556A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 4 through 9 removed outlier: 5.453A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN F 28 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALA F 29 " --> pdb=" O THR F 79 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 84 through 86 removed outlier: 3.852A pdb=" N VAL F 85 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP F 116 " --> pdb=" O VAL F 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 95 through 96 removed outlier: 7.091A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL F 214 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 134 through 135 removed outlier: 3.928A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 116 through 117 removed outlier: 6.792A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU G 78 " --> pdb=" O TYR G 170 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ILE G 80 " --> pdb=" O ASN G 172 " (cutoff:3.500A) 898 hydrogen bonds defined for protein. 2559 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: 8.30 Time building geometry restraints manager: 6.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.30: 3989 1.30 - 1.62: 19416 1.62 - 1.94: 159 1.94 - 2.26: 0 2.26 - 2.58: 1 Bond restraints: 23565 Sorted by residual: bond pdb=" CB PRO F 117 " pdb=" CG PRO F 117 " ideal model delta sigma weight residual 1.492 2.579 -1.087 5.00e-02 4.00e+02 4.73e+02 bond pdb=" CG PRO F 117 " pdb=" CD PRO F 117 " ideal model delta sigma weight residual 1.503 0.986 0.517 3.40e-02 8.65e+02 2.31e+02 bond pdb=" O3A ANP F 500 " pdb=" PB ANP F 500 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP A 600 " pdb=" PB ANP A 600 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP D 500 " pdb=" PB ANP D 500 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 ... (remaining 23560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.34: 31929 19.34 - 38.68: 2 38.68 - 58.02: 0 58.02 - 77.37: 0 77.37 - 96.71: 1 Bond angle restraints: 31932 Sorted by residual: angle pdb=" CB PRO F 117 " pdb=" CG PRO F 117 " pdb=" CD PRO F 117 " ideal model delta sigma weight residual 106.10 9.39 96.71 3.20e+00 9.77e-02 9.13e+02 angle pdb=" N PRO F 117 " pdb=" CA PRO F 117 " pdb=" CB PRO F 117 " ideal model delta sigma weight residual 103.35 86.44 16.91 8.70e-01 1.32e+00 3.78e+02 angle pdb=" CA PRO F 117 " pdb=" N PRO F 117 " pdb=" CD PRO F 117 " ideal model delta sigma weight residual 112.00 85.51 26.49 1.40e+00 5.10e-01 3.58e+02 angle pdb=" CA PRO F 117 " pdb=" CB PRO F 117 " pdb=" CG PRO F 117 " ideal model delta sigma weight residual 104.50 75.98 28.52 1.90e+00 2.77e-01 2.25e+02 angle pdb=" CA PRO A 449 " pdb=" N PRO A 449 " pdb=" CD PRO A 449 " ideal model delta sigma weight residual 112.00 93.92 18.08 1.40e+00 5.10e-01 1.67e+02 ... (remaining 31927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.33: 13536 26.33 - 52.66: 760 52.66 - 78.99: 81 78.99 - 105.32: 26 105.32 - 131.65: 2 Dihedral angle restraints: 14405 sinusoidal: 5896 harmonic: 8509 Sorted by residual: dihedral pdb=" N PRO F 117 " pdb=" C PRO F 117 " pdb=" CA PRO F 117 " pdb=" CB PRO F 117 " ideal model delta harmonic sigma weight residual 115.10 97.65 17.45 0 2.50e+00 1.60e-01 4.87e+01 dihedral pdb=" CA PRO F 117 " pdb=" CB PRO F 117 " pdb=" CG PRO F 117 " pdb=" CD PRO F 117 " ideal model delta sinusoidal sigma weight residual 38.00 169.65 -131.65 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" CA ILE G 178 " pdb=" C ILE G 178 " pdb=" N GLN G 179 " pdb=" CA GLN G 179 " ideal model delta harmonic sigma weight residual 180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 14402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3013 0.062 - 0.124: 589 0.124 - 0.186: 61 0.186 - 0.247: 4 0.247 - 0.309: 9 Chirality restraints: 3676 Sorted by residual: chirality pdb=" CB ILE B 184 " pdb=" CA ILE B 184 " pdb=" CG1 ILE B 184 " pdb=" CG2 ILE B 184 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3' ANP D 500 " pdb=" C2' ANP D 500 " pdb=" C4' ANP D 500 " pdb=" O3' ANP D 500 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C3' ANP C 600 " pdb=" C2' ANP C 600 " pdb=" C4' ANP C 600 " pdb=" O3' ANP C 600 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 3673 not shown) Planarity restraints: 4160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 85 " -0.117 5.00e-02 4.00e+02 1.63e-01 4.23e+01 pdb=" N PRO F 86 " 0.281 5.00e-02 4.00e+02 pdb=" CA PRO F 86 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO F 86 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 280 " -0.111 5.00e-02 4.00e+02 1.60e-01 4.10e+01 pdb=" N PRO A 281 " 0.277 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 448 " -0.110 5.00e-02 4.00e+02 1.51e-01 3.65e+01 pdb=" N PRO F 449 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO F 449 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO F 449 " -0.079 5.00e-02 4.00e+02 ... (remaining 4157 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 114 2.51 - 3.11: 17128 3.11 - 3.71: 34233 3.71 - 4.30: 46914 4.30 - 4.90: 78236 Nonbonded interactions: 176625 Sorted by model distance: nonbonded pdb=" O2B ANP F 500 " pdb="MG MG F 501 " model vdw 1.914 2.170 nonbonded pdb=" O1G ANP D 500 " pdb="MG MG D 501 " model vdw 1.928 2.170 nonbonded pdb=" O2B ANP D 500 " pdb="MG MG D 501 " model vdw 1.939 2.170 nonbonded pdb=" O2B ANP C 600 " pdb="MG MG C 601 " model vdw 1.972 2.170 nonbonded pdb=" O1G ANP B 600 " pdb="MG MG B 601 " model vdw 1.975 2.170 ... (remaining 176620 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 'A' and (resid 28 through 396 or resid 404 through 444 or resid 450 throu \ gh 495 or resid 600 through 601)) selection = (chain 'B' and (resid 28 through 444 or resid 450 through 495 or resid 600 throu \ gh 601)) selection = (chain 'C' and (resid 28 through 396 or resid 404 through 495 or resid 600 throu \ gh 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 189 or resid 191 through 466)) selection = (chain 'E' and (resid 2 through 189 or resid 191 through 466)) selection = (chain 'F' and (resid 2 through 189 or resid 191 through 466)) } 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: 1.510 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: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 51.400 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.110 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 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 : 0.010 1.087 23565 Z= 0.734 Angle : 1.084 96.707 31932 Z= 0.530 Chirality : 0.050 0.309 3676 Planarity : 0.009 0.163 4160 Dihedral : 15.997 131.646 8957 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 0.37 % Allowed : 16.05 % Favored : 83.58 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 2956 helix: -0.38 (0.15), residues: 1070 sheet: 0.46 (0.23), residues: 455 loop : -0.43 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS F 363 PHE 0.047 0.003 PHE D 255 TYR 0.032 0.002 TYR G 90 ARG 0.014 0.001 ARG F 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 687 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ILE cc_start: 0.5764 (pt) cc_final: 0.5519 (pt) REVERT: B 463 PHE cc_start: 0.7128 (t80) cc_final: 0.6807 (t80) REVERT: C 46 ASN cc_start: 0.7052 (m-40) cc_final: 0.6494 (m-40) REVERT: D 128 LEU cc_start: 0.7006 (mt) cc_final: 0.6104 (mt) REVERT: D 400 VAL cc_start: 0.7444 (t) cc_final: 0.7055 (p) outliers start: 9 outliers final: 2 residues processed: 695 average time/residue: 0.3757 time to fit residues: 397.3282 Evaluate side-chains 458 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 456 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain D residue 30 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 3.9990 chunk 223 optimal weight: 0.0070 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 overall best weight: 2.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 333 ASN A 469 GLN A 474 HIS ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN B 469 GLN B 483 ASN C 143 HIS C 185 ASN C 422 GLN C 474 HIS D 371 GLN E 33 GLN E 53 HIS E 415 HIS E 447 HIS G 37 ASN G 100 GLN G 103 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.116585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098579 restraints weight = 72711.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.101070 restraints weight = 43375.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.102734 restraints weight = 30120.514| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 23565 Z= 0.255 Angle : 0.726 13.997 31932 Z= 0.373 Chirality : 0.048 0.192 3676 Planarity : 0.006 0.101 4160 Dihedral : 7.632 104.925 3411 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.41 % Allowed : 19.98 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 2956 helix: 0.01 (0.15), residues: 1088 sheet: 0.68 (0.24), residues: 436 loop : -0.52 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 474 PHE 0.021 0.002 PHE A 494 TYR 0.020 0.002 TYR E 148 ARG 0.006 0.001 ARG G 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 491 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.7354 (mtp) cc_final: 0.7129 (mtm) REVERT: A 491 ILE cc_start: 0.8681 (mt) cc_final: 0.8419 (tt) REVERT: B 48 MET cc_start: 0.8275 (ptp) cc_final: 0.7952 (ptp) REVERT: B 62 MET cc_start: 0.4108 (ppp) cc_final: 0.3632 (ppp) REVERT: B 284 GLU cc_start: 0.8752 (mp0) cc_final: 0.8347 (mp0) REVERT: B 286 TYR cc_start: 0.8127 (m-80) cc_final: 0.7890 (m-10) REVERT: B 299 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7287 (mm-30) REVERT: B 483 ASN cc_start: 0.9117 (t0) cc_final: 0.8805 (t0) REVERT: B 491 ILE cc_start: 0.9511 (mm) cc_final: 0.9290 (tt) REVERT: C 33 GLN cc_start: 0.6757 (tm-30) cc_final: 0.6535 (tm-30) REVERT: C 245 MET cc_start: 0.7721 (mtt) cc_final: 0.7472 (mmt) REVERT: C 273 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9501 (pp) REVERT: C 391 GLU cc_start: 0.9285 (tp30) cc_final: 0.9052 (mm-30) REVERT: D 52 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6250 (tp) REVERT: D 191 ARG cc_start: 0.7276 (mtm110) cc_final: 0.6758 (mpp80) REVERT: D 213 MET cc_start: 0.7150 (mmm) cc_final: 0.6803 (mmm) REVERT: D 226 MET cc_start: 0.8123 (mtt) cc_final: 0.7833 (mmm) REVERT: D 253 ASN cc_start: 0.7363 (m110) cc_final: 0.7083 (m-40) REVERT: D 400 VAL cc_start: 0.8449 (t) cc_final: 0.8156 (p) REVERT: E 218 MET cc_start: 0.9145 (mtp) cc_final: 0.8508 (mmm) REVERT: E 354 LEU cc_start: 0.8190 (tp) cc_final: 0.7774 (tt) REVERT: E 364 TYR cc_start: 0.8725 (t80) cc_final: 0.8409 (t80) REVERT: F 23 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.7659 (tp) REVERT: F 54 LEU cc_start: 0.9040 (mm) cc_final: 0.8756 (mm) REVERT: F 218 MET cc_start: 0.7957 (mtm) cc_final: 0.7488 (mtm) REVERT: F 219 ASN cc_start: 0.7817 (p0) cc_final: 0.6105 (p0) REVERT: F 220 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8140 (mt-10) REVERT: F 271 MET cc_start: 0.8738 (mmt) cc_final: 0.8528 (mpp) REVERT: F 361 GLU cc_start: 0.8704 (mp0) cc_final: 0.7541 (tm-30) REVERT: F 389 MET cc_start: 0.7924 (ppp) cc_final: 0.7408 (ppp) REVERT: G 36 GLN cc_start: 0.9582 (OUTLIER) cc_final: 0.9191 (mp10) REVERT: G 225 TYR cc_start: 0.9338 (t80) cc_final: 0.9095 (t80) REVERT: G 243 MET cc_start: 0.8749 (mmm) cc_final: 0.8485 (mmm) outliers start: 108 outliers final: 53 residues processed: 563 average time/residue: 0.3751 time to fit residues: 325.1015 Evaluate side-chains 479 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 422 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 22 HIS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 248 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 5 optimal weight: 0.2980 chunk 124 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 289 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN F 28 ASN ** F 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.117333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.098240 restraints weight = 73096.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.100862 restraints weight = 43103.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.102705 restraints weight = 29510.804| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23565 Z= 0.204 Angle : 0.672 13.553 31932 Z= 0.336 Chirality : 0.047 0.245 3676 Planarity : 0.005 0.072 4160 Dihedral : 7.145 102.289 3411 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.88 % Allowed : 21.36 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2956 helix: 0.23 (0.16), residues: 1090 sheet: 0.71 (0.24), residues: 444 loop : -0.43 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 363 PHE 0.028 0.002 PHE A 318 TYR 0.015 0.001 TYR E 148 ARG 0.011 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 454 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8870 (mtp) cc_final: 0.8300 (mpp) REVERT: A 191 MET cc_start: 0.7794 (tpt) cc_final: 0.7264 (tpp) REVERT: A 272 GLU cc_start: 0.8804 (tt0) cc_final: 0.8591 (tt0) REVERT: B 48 MET cc_start: 0.8379 (ptp) cc_final: 0.8001 (ptp) REVERT: B 62 MET cc_start: 0.4092 (ppp) cc_final: 0.3580 (ppp) REVERT: B 137 MET cc_start: 0.6585 (mmt) cc_final: 0.5642 (mmp) REVERT: B 284 GLU cc_start: 0.8807 (mp0) cc_final: 0.8206 (mp0) REVERT: B 286 TYR cc_start: 0.8031 (m-80) cc_final: 0.7744 (m-80) REVERT: B 375 MET cc_start: 0.8103 (tmm) cc_final: 0.7819 (tmm) REVERT: B 491 ILE cc_start: 0.9502 (mm) cc_final: 0.9247 (tt) REVERT: C 33 GLN cc_start: 0.6923 (tm-30) cc_final: 0.6615 (tm-30) REVERT: C 101 GLU cc_start: 0.8981 (mp0) cc_final: 0.8780 (mp0) REVERT: C 270 TYR cc_start: 0.8568 (t80) cc_final: 0.8121 (t80) REVERT: C 273 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9516 (pp) REVERT: C 391 GLU cc_start: 0.9346 (tp30) cc_final: 0.9077 (tt0) REVERT: D 52 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6361 (tp) REVERT: D 213 MET cc_start: 0.7262 (mmm) cc_final: 0.6956 (mmm) REVERT: D 226 MET cc_start: 0.8176 (mtt) cc_final: 0.7788 (mmm) REVERT: D 253 ASN cc_start: 0.7455 (m110) cc_final: 0.6983 (m110) REVERT: D 400 VAL cc_start: 0.8413 (t) cc_final: 0.8165 (p) REVERT: E 15 ASP cc_start: 0.7661 (m-30) cc_final: 0.7431 (m-30) REVERT: E 218 MET cc_start: 0.9017 (mtp) cc_final: 0.8650 (mmm) REVERT: E 338 MET cc_start: 0.8164 (tmm) cc_final: 0.7859 (ppp) REVERT: E 364 TYR cc_start: 0.8639 (t80) cc_final: 0.8332 (t80) REVERT: F 28 ASN cc_start: 0.3436 (OUTLIER) cc_final: 0.2677 (m110) REVERT: F 220 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8224 (mt-10) REVERT: F 226 MET cc_start: 0.7819 (mtt) cc_final: 0.6598 (mmt) REVERT: G 21 LYS cc_start: 0.9365 (tptp) cc_final: 0.9124 (tptp) REVERT: G 243 MET cc_start: 0.8853 (mmm) cc_final: 0.8569 (mmm) REVERT: G 265 ARG cc_start: 0.8785 (mtp-110) cc_final: 0.8442 (mtm180) outliers start: 95 outliers final: 61 residues processed: 521 average time/residue: 0.3644 time to fit residues: 293.1554 Evaluate side-chains 471 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 407 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 22 HIS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 248 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 14 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 176 optimal weight: 30.0000 chunk 107 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN B 189 GLN B 294 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN D 174 ASN D 324 HIS D 372 GLN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 53 HIS ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN G 266 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.111281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093246 restraints weight = 76878.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.095698 restraints weight = 44948.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.097440 restraints weight = 30829.597| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 23565 Z= 0.335 Angle : 0.722 12.489 31932 Z= 0.368 Chirality : 0.047 0.199 3676 Planarity : 0.005 0.067 4160 Dihedral : 7.221 97.794 3411 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.76 % Allowed : 21.08 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 2956 helix: 0.06 (0.15), residues: 1102 sheet: 0.43 (0.23), residues: 444 loop : -0.62 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 236 PHE 0.046 0.002 PHE G 41 TYR 0.026 0.002 TYR G 90 ARG 0.006 0.001 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 413 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8807 (mtp) cc_final: 0.8594 (mtm) REVERT: A 245 MET cc_start: 0.7866 (mtm) cc_final: 0.7564 (mtm) REVERT: B 48 MET cc_start: 0.8262 (ptp) cc_final: 0.8035 (ptp) REVERT: B 51 GLU cc_start: 0.5634 (OUTLIER) cc_final: 0.5270 (tt0) REVERT: B 60 MET cc_start: 0.8628 (mmm) cc_final: 0.8372 (mmm) REVERT: B 62 MET cc_start: 0.5077 (ppp) cc_final: 0.4600 (ppp) REVERT: B 137 MET cc_start: 0.6614 (mmt) cc_final: 0.5749 (mmp) REVERT: B 284 GLU cc_start: 0.8997 (mp0) cc_final: 0.8315 (mp0) REVERT: B 320 GLU cc_start: 0.7637 (tp30) cc_final: 0.7395 (tp30) REVERT: C 101 GLU cc_start: 0.8939 (mp0) cc_final: 0.8711 (mp0) REVERT: C 137 MET cc_start: 0.5478 (mpp) cc_final: 0.4916 (mpp) REVERT: C 391 GLU cc_start: 0.9363 (tp30) cc_final: 0.9091 (mm-30) REVERT: D 226 MET cc_start: 0.8362 (mtt) cc_final: 0.7956 (mmm) REVERT: D 253 ASN cc_start: 0.7749 (m110) cc_final: 0.7350 (m-40) REVERT: E 213 MET cc_start: 0.7664 (mtm) cc_final: 0.7304 (mtm) REVERT: E 364 TYR cc_start: 0.8770 (t80) cc_final: 0.8474 (t80) REVERT: F 28 ASN cc_start: 0.3428 (OUTLIER) cc_final: 0.2003 (m110) REVERT: F 389 MET cc_start: 0.7863 (ppp) cc_final: 0.7328 (ppp) REVERT: G 9 ARG cc_start: 0.9191 (mtp180) cc_final: 0.8884 (mtp180) REVERT: G 18 GLN cc_start: 0.9437 (mt0) cc_final: 0.9200 (mp10) REVERT: G 21 LYS cc_start: 0.9336 (tptp) cc_final: 0.9052 (tptp) REVERT: G 25 MET cc_start: 0.8988 (ppp) cc_final: 0.8648 (ppp) REVERT: G 243 MET cc_start: 0.8859 (mmm) cc_final: 0.8497 (mmt) REVERT: G 265 ARG cc_start: 0.8746 (mtp-110) cc_final: 0.8310 (mtm180) REVERT: G 266 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8835 (mp-120) outliers start: 141 outliers final: 101 residues processed: 508 average time/residue: 0.3482 time to fit residues: 275.7694 Evaluate side-chains 492 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 388 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 266 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 18 optimal weight: 9.9990 chunk 197 optimal weight: 0.0770 chunk 251 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 140 optimal weight: 0.0040 chunk 96 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 263 optimal weight: 3.9990 chunk 165 optimal weight: 0.1980 overall best weight: 2.4554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN D 365 GLN ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.114644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095476 restraints weight = 75069.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.098044 restraints weight = 44033.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.099873 restraints weight = 30036.804| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23565 Z= 0.214 Angle : 0.654 12.818 31932 Z= 0.331 Chirality : 0.046 0.255 3676 Planarity : 0.005 0.062 4160 Dihedral : 7.027 96.728 3411 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.45 % Allowed : 23.57 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 2956 helix: 0.15 (0.15), residues: 1110 sheet: 0.68 (0.24), residues: 424 loop : -0.55 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 324 PHE 0.050 0.002 PHE G 41 TYR 0.016 0.001 TYR G 90 ARG 0.008 0.000 ARG D 435 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 419 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8008 (tpt) cc_final: 0.7512 (tpp) REVERT: A 201 LYS cc_start: 0.7279 (ptmt) cc_final: 0.6722 (pttm) REVERT: A 245 MET cc_start: 0.7860 (mtm) cc_final: 0.7520 (mtm) REVERT: A 277 LEU cc_start: 0.8313 (mm) cc_final: 0.8084 (mm) REVERT: B 48 MET cc_start: 0.8361 (ptp) cc_final: 0.8096 (ptp) REVERT: B 51 GLU cc_start: 0.5427 (OUTLIER) cc_final: 0.4783 (tt0) REVERT: B 60 MET cc_start: 0.8534 (mmm) cc_final: 0.8207 (mmm) REVERT: B 62 MET cc_start: 0.5019 (ppp) cc_final: 0.3972 (ppp) REVERT: B 137 MET cc_start: 0.6641 (mmt) cc_final: 0.5822 (mmp) REVERT: B 283 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7819 (ttm-80) REVERT: B 284 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: C 101 GLU cc_start: 0.9019 (mp0) cc_final: 0.8733 (mm-30) REVERT: C 137 MET cc_start: 0.6000 (mpp) cc_final: 0.5293 (mpp) REVERT: C 372 ILE cc_start: 0.9336 (mm) cc_final: 0.9093 (tp) REVERT: C 391 GLU cc_start: 0.9353 (tp30) cc_final: 0.9071 (mm-30) REVERT: C 456 PHE cc_start: 0.9219 (t80) cc_final: 0.8825 (m-80) REVERT: D 52 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6942 (tp) REVERT: D 226 MET cc_start: 0.8149 (mtt) cc_final: 0.7831 (mmm) REVERT: D 253 ASN cc_start: 0.7700 (m110) cc_final: 0.7250 (m110) REVERT: E 218 MET cc_start: 0.8986 (mtp) cc_final: 0.8654 (mmm) REVERT: E 235 MET cc_start: 0.7152 (mmt) cc_final: 0.6924 (mmt) REVERT: E 237 GLU cc_start: 0.8122 (tt0) cc_final: 0.7342 (tp30) REVERT: E 338 MET cc_start: 0.8182 (ppp) cc_final: 0.7830 (ppp) REVERT: F 148 TYR cc_start: 0.7855 (m-80) cc_final: 0.7132 (m-80) REVERT: F 226 MET cc_start: 0.7499 (mtt) cc_final: 0.7249 (mmt) REVERT: F 389 MET cc_start: 0.7786 (ppp) cc_final: 0.7227 (ppp) REVERT: G 9 ARG cc_start: 0.9271 (mtp180) cc_final: 0.8923 (mtp180) REVERT: G 21 LYS cc_start: 0.9360 (tptp) cc_final: 0.9033 (tptp) REVERT: G 25 MET cc_start: 0.9045 (ppp) cc_final: 0.8634 (ppp) REVERT: G 243 MET cc_start: 0.8924 (mmm) cc_final: 0.8558 (mmt) outliers start: 109 outliers final: 82 residues processed: 491 average time/residue: 0.3627 time to fit residues: 279.1407 Evaluate side-chains 467 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 382 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 248 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 289 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 260 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 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 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.108433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.090606 restraints weight = 78074.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.093010 restraints weight = 46108.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094632 restraints weight = 31723.688| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.147 23565 Z= 0.378 Angle : 0.754 12.183 31932 Z= 0.384 Chirality : 0.048 0.260 3676 Planarity : 0.005 0.068 4160 Dihedral : 7.293 93.557 3411 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.88 % Allowed : 23.28 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 2956 helix: -0.01 (0.15), residues: 1109 sheet: 0.33 (0.24), residues: 411 loop : -0.75 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 363 PHE 0.041 0.002 PHE G 41 TYR 0.020 0.002 TYR B 220 ARG 0.015 0.001 ARG G 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 395 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.5757 (OUTLIER) cc_final: 0.5425 (mt) REVERT: A 137 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7912 (mmm) REVERT: A 165 GLU cc_start: 0.7962 (tp30) cc_final: 0.7590 (tp30) REVERT: A 191 MET cc_start: 0.7964 (tpt) cc_final: 0.7763 (tpt) REVERT: A 201 LYS cc_start: 0.7504 (ptmt) cc_final: 0.6998 (pttm) REVERT: A 272 GLU cc_start: 0.8790 (tt0) cc_final: 0.8495 (tt0) REVERT: A 462 LEU cc_start: 0.9781 (mm) cc_final: 0.9465 (pp) REVERT: B 48 MET cc_start: 0.8322 (ptp) cc_final: 0.8041 (ptp) REVERT: B 51 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5471 (tt0) REVERT: B 60 MET cc_start: 0.8411 (mmm) cc_final: 0.8021 (mmm) REVERT: B 62 MET cc_start: 0.5426 (ppp) cc_final: 0.5131 (ppp) REVERT: B 196 VAL cc_start: 0.9048 (t) cc_final: 0.8831 (p) REVERT: B 202 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: B 284 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: C 137 MET cc_start: 0.6301 (mpp) cc_final: 0.5805 (mpp) REVERT: C 322 GLN cc_start: 0.7574 (mm-40) cc_final: 0.6969 (mm-40) REVERT: C 391 GLU cc_start: 0.9345 (tp30) cc_final: 0.9140 (mm-30) REVERT: C 456 PHE cc_start: 0.9245 (t80) cc_final: 0.8795 (m-80) REVERT: D 52 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7066 (tp) REVERT: D 226 MET cc_start: 0.8382 (mtt) cc_final: 0.8145 (mmm) REVERT: D 253 ASN cc_start: 0.7728 (m110) cc_final: 0.7414 (m110) REVERT: D 315 ASP cc_start: 0.7659 (t0) cc_final: 0.7398 (t0) REVERT: E 213 MET cc_start: 0.7153 (mtm) cc_final: 0.6727 (mtp) REVERT: E 218 MET cc_start: 0.8992 (mtp) cc_final: 0.8665 (mmm) REVERT: E 237 GLU cc_start: 0.8304 (tt0) cc_final: 0.7493 (tp30) REVERT: E 455 LEU cc_start: 0.9531 (tp) cc_final: 0.9244 (pp) REVERT: F 226 MET cc_start: 0.7521 (mtt) cc_final: 0.7221 (mmt) REVERT: F 389 MET cc_start: 0.7819 (ppp) cc_final: 0.7303 (ppp) REVERT: G 9 ARG cc_start: 0.9182 (mtp180) cc_final: 0.8832 (mtp180) REVERT: G 15 LYS cc_start: 0.9526 (mmtt) cc_final: 0.9308 (mmtm) REVERT: G 21 LYS cc_start: 0.9365 (tptp) cc_final: 0.9079 (tptp) REVERT: G 243 MET cc_start: 0.9010 (mmm) cc_final: 0.8793 (mmm) REVERT: G 265 ARG cc_start: 0.8715 (mtp180) cc_final: 0.8285 (mtm180) outliers start: 144 outliers final: 112 residues processed: 493 average time/residue: 0.3455 time to fit residues: 267.9323 Evaluate side-chains 485 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 367 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 248 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 217 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 255 optimal weight: 0.0060 chunk 6 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 overall best weight: 4.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 HIS ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN D 253 ASN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.108814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.090977 restraints weight = 78017.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093399 restraints weight = 46114.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.095044 restraints weight = 31788.609| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 23565 Z= 0.303 Angle : 0.716 12.303 31932 Z= 0.362 Chirality : 0.047 0.356 3676 Planarity : 0.005 0.069 4160 Dihedral : 7.276 94.439 3411 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.51 % Allowed : 24.55 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 2956 helix: -0.00 (0.15), residues: 1111 sheet: 0.45 (0.25), residues: 396 loop : -0.77 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 474 PHE 0.060 0.002 PHE G 41 TYR 0.018 0.002 TYR B 220 ARG 0.007 0.001 ARG G 4 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 392 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.5698 (OUTLIER) cc_final: 0.5402 (mt) REVERT: A 137 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7916 (mmm) REVERT: A 165 GLU cc_start: 0.7927 (tp30) cc_final: 0.7517 (tp30) REVERT: A 191 MET cc_start: 0.7960 (tpt) cc_final: 0.7461 (tpt) REVERT: A 201 LYS cc_start: 0.7460 (ptmt) cc_final: 0.6879 (pttm) REVERT: A 245 MET cc_start: 0.7878 (mtm) cc_final: 0.7595 (mtm) REVERT: A 277 LEU cc_start: 0.8396 (mm) cc_final: 0.8041 (mm) REVERT: A 462 LEU cc_start: 0.9781 (mm) cc_final: 0.9487 (pp) REVERT: B 48 MET cc_start: 0.8300 (ptp) cc_final: 0.8036 (ptp) REVERT: B 51 GLU cc_start: 0.5462 (OUTLIER) cc_final: 0.4862 (tt0) REVERT: B 60 MET cc_start: 0.8443 (mmm) cc_final: 0.8130 (mmm) REVERT: B 62 MET cc_start: 0.5374 (ppp) cc_final: 0.4485 (ppp) REVERT: B 137 MET cc_start: 0.6318 (mmt) cc_final: 0.5570 (mtm) REVERT: B 196 VAL cc_start: 0.9045 (t) cc_final: 0.8766 (p) REVERT: B 202 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: B 284 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: C 137 MET cc_start: 0.6160 (mpp) cc_final: 0.5693 (mpp) REVERT: C 201 LYS cc_start: 0.6795 (OUTLIER) cc_final: 0.6538 (ptpt) REVERT: C 202 GLU cc_start: 0.8218 (tp30) cc_final: 0.7984 (tp30) REVERT: C 322 GLN cc_start: 0.7530 (mm-40) cc_final: 0.6938 (mm-40) REVERT: C 391 GLU cc_start: 0.9373 (tp30) cc_final: 0.9089 (tt0) REVERT: C 456 PHE cc_start: 0.9297 (t80) cc_final: 0.8838 (m-80) REVERT: D 52 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6981 (tp) REVERT: D 226 MET cc_start: 0.8306 (mtt) cc_final: 0.7897 (mmm) REVERT: D 253 ASN cc_start: 0.7792 (m-40) cc_final: 0.7398 (m110) REVERT: E 64 MET cc_start: 0.4802 (mmp) cc_final: 0.3828 (mmm) REVERT: E 237 GLU cc_start: 0.8257 (tt0) cc_final: 0.7452 (tp30) REVERT: E 455 LEU cc_start: 0.9546 (tp) cc_final: 0.9275 (pp) REVERT: F 226 MET cc_start: 0.7382 (mtt) cc_final: 0.7178 (mmt) REVERT: F 389 MET cc_start: 0.7824 (ppp) cc_final: 0.7278 (ppp) REVERT: G 7 LYS cc_start: 0.9590 (tptp) cc_final: 0.9382 (tptp) REVERT: G 21 LYS cc_start: 0.9357 (tptp) cc_final: 0.9132 (tptp) REVERT: G 243 MET cc_start: 0.9059 (mmm) cc_final: 0.8812 (mmm) REVERT: G 265 ARG cc_start: 0.8726 (mtp180) cc_final: 0.8438 (mtm180) outliers start: 135 outliers final: 106 residues processed: 483 average time/residue: 0.3585 time to fit residues: 273.1032 Evaluate side-chains 481 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 368 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 248 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 152 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 270 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN B 294 HIS ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.108117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.090378 restraints weight = 78249.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.092778 restraints weight = 46231.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.094403 restraints weight = 31773.951| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 23565 Z= 0.300 Angle : 0.722 12.046 31932 Z= 0.365 Chirality : 0.048 0.439 3676 Planarity : 0.005 0.128 4160 Dihedral : 7.258 93.251 3411 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.72 % Allowed : 25.04 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 2956 helix: 0.02 (0.15), residues: 1112 sheet: 0.37 (0.25), residues: 396 loop : -0.79 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 474 PHE 0.063 0.002 PHE G 41 TYR 0.018 0.002 TYR B 220 ARG 0.010 0.001 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 376 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8683 (mmm) cc_final: 0.8386 (mmm) REVERT: A 76 LEU cc_start: 0.5723 (OUTLIER) cc_final: 0.5337 (mt) REVERT: A 137 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7875 (mmm) REVERT: A 165 GLU cc_start: 0.7937 (tp30) cc_final: 0.7540 (tp30) REVERT: A 191 MET cc_start: 0.7988 (tpt) cc_final: 0.7443 (tpp) REVERT: A 201 LYS cc_start: 0.7486 (ptmt) cc_final: 0.6497 (pttm) REVERT: A 277 LEU cc_start: 0.8397 (mm) cc_final: 0.8026 (mm) REVERT: A 462 LEU cc_start: 0.9781 (mm) cc_final: 0.9488 (pp) REVERT: B 48 MET cc_start: 0.8302 (ptp) cc_final: 0.8030 (ptp) REVERT: B 51 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.4894 (tt0) REVERT: B 62 MET cc_start: 0.5547 (ppp) cc_final: 0.4675 (ppp) REVERT: B 137 MET cc_start: 0.6165 (mmt) cc_final: 0.5508 (mtm) REVERT: B 196 VAL cc_start: 0.9051 (t) cc_final: 0.8765 (p) REVERT: B 202 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: B 284 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: C 137 MET cc_start: 0.5973 (mpp) cc_final: 0.5572 (mpp) REVERT: C 391 GLU cc_start: 0.9384 (tp30) cc_final: 0.9126 (tt0) REVERT: C 456 PHE cc_start: 0.9297 (t80) cc_final: 0.8835 (m-80) REVERT: D 52 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7019 (tp) REVERT: D 226 MET cc_start: 0.8317 (mtt) cc_final: 0.7937 (mmm) REVERT: D 253 ASN cc_start: 0.7758 (m-40) cc_final: 0.7363 (m110) REVERT: D 284 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: D 315 ASP cc_start: 0.7662 (t0) cc_final: 0.7428 (t0) REVERT: E 237 GLU cc_start: 0.8337 (tt0) cc_final: 0.7604 (tp30) REVERT: E 364 TYR cc_start: 0.8666 (t80) cc_final: 0.8313 (t80) REVERT: F 226 MET cc_start: 0.7500 (mtt) cc_final: 0.7211 (mmt) REVERT: F 253 ASN cc_start: 0.6619 (t0) cc_final: 0.6380 (t0) REVERT: F 389 MET cc_start: 0.7773 (ppp) cc_final: 0.7226 (ppp) REVERT: G 9 ARG cc_start: 0.9237 (mtp180) cc_final: 0.8966 (mtp180) REVERT: G 15 LYS cc_start: 0.9529 (mmtt) cc_final: 0.9307 (mmtm) REVERT: G 243 MET cc_start: 0.9000 (mmm) cc_final: 0.8776 (mmm) REVERT: G 265 ARG cc_start: 0.8725 (mtp180) cc_final: 0.8429 (mtm180) outliers start: 140 outliers final: 114 residues processed: 470 average time/residue: 0.3526 time to fit residues: 265.6714 Evaluate side-chains 483 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 362 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 248 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 166 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 254 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN B 294 HIS ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.109556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.091458 restraints weight = 79961.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.093933 restraints weight = 45678.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.095642 restraints weight = 30991.198| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 23565 Z= 0.345 Angle : 0.767 11.887 31932 Z= 0.384 Chirality : 0.049 0.433 3676 Planarity : 0.005 0.085 4160 Dihedral : 7.378 92.683 3411 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.68 % Allowed : 25.16 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 2956 helix: -0.12 (0.15), residues: 1124 sheet: 0.18 (0.25), residues: 402 loop : -0.94 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 425 PHE 0.064 0.002 PHE G 41 TYR 0.020 0.002 TYR B 220 ARG 0.009 0.001 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 379 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8720 (mmm) cc_final: 0.8455 (mmm) REVERT: A 76 LEU cc_start: 0.5720 (OUTLIER) cc_final: 0.5303 (mt) REVERT: A 137 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7856 (mmm) REVERT: A 165 GLU cc_start: 0.7958 (tp30) cc_final: 0.7571 (tp30) REVERT: A 191 MET cc_start: 0.8007 (tpt) cc_final: 0.7445 (tpp) REVERT: A 277 LEU cc_start: 0.8430 (mm) cc_final: 0.8046 (mm) REVERT: A 462 LEU cc_start: 0.9789 (mm) cc_final: 0.9489 (pp) REVERT: B 48 MET cc_start: 0.8282 (ptp) cc_final: 0.8024 (ptp) REVERT: B 51 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.5072 (tt0) REVERT: B 62 MET cc_start: 0.5883 (ppp) cc_final: 0.4958 (ppp) REVERT: B 137 MET cc_start: 0.6015 (mmt) cc_final: 0.5398 (mtm) REVERT: B 202 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: B 245 MET cc_start: 0.7269 (mmm) cc_final: 0.7022 (mmt) REVERT: B 284 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: C 202 GLU cc_start: 0.8430 (tp30) cc_final: 0.8203 (mm-30) REVERT: C 456 PHE cc_start: 0.9307 (t80) cc_final: 0.8798 (m-80) REVERT: C 461 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: D 52 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7122 (tp) REVERT: D 226 MET cc_start: 0.8185 (mtt) cc_final: 0.7851 (mmm) REVERT: D 253 ASN cc_start: 0.7759 (m-40) cc_final: 0.7373 (m110) REVERT: D 284 GLU cc_start: 0.8327 (tt0) cc_final: 0.7749 (tt0) REVERT: D 315 ASP cc_start: 0.7711 (t0) cc_final: 0.7469 (t0) REVERT: E 64 MET cc_start: 0.4969 (mmp) cc_final: 0.4229 (mmm) REVERT: E 237 GLU cc_start: 0.8422 (tt0) cc_final: 0.7806 (tp30) REVERT: E 455 LEU cc_start: 0.9495 (tp) cc_final: 0.9238 (pp) REVERT: F 202 MET cc_start: 0.8986 (mmm) cc_final: 0.8751 (mmt) REVERT: F 226 MET cc_start: 0.7552 (mtt) cc_final: 0.7277 (mmt) REVERT: F 253 ASN cc_start: 0.6620 (t0) cc_final: 0.6381 (t0) REVERT: F 389 MET cc_start: 0.7764 (ppp) cc_final: 0.7248 (ppp) REVERT: G 9 ARG cc_start: 0.9236 (mtp180) cc_final: 0.8978 (mtp180) REVERT: G 15 LYS cc_start: 0.9539 (mmtt) cc_final: 0.9326 (mmtm) REVERT: G 243 MET cc_start: 0.9018 (mmm) cc_final: 0.8810 (mmm) REVERT: G 265 ARG cc_start: 0.8757 (mtp180) cc_final: 0.8426 (mtm110) REVERT: G 266 GLN cc_start: 0.9319 (mp10) cc_final: 0.8971 (mp10) outliers start: 139 outliers final: 121 residues processed: 472 average time/residue: 0.3344 time to fit residues: 253.3437 Evaluate side-chains 491 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 363 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 248 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 2 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 161 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 276 optimal weight: 5.9990 chunk 270 optimal weight: 6.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 HIS ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.110291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.092481 restraints weight = 79375.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.094996 restraints weight = 44655.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.096723 restraints weight = 30004.599| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 23565 Z= 0.291 Angle : 0.748 13.467 31932 Z= 0.372 Chirality : 0.048 0.411 3676 Planarity : 0.005 0.068 4160 Dihedral : 7.302 93.420 3409 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.11 % Allowed : 25.69 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 2956 helix: -0.03 (0.15), residues: 1117 sheet: 0.19 (0.25), residues: 403 loop : -0.92 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 22 PHE 0.062 0.002 PHE G 41 TYR 0.017 0.001 TYR B 220 ARG 0.010 0.001 ARG C 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 374 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8664 (mmm) cc_final: 0.8402 (mmm) REVERT: A 76 LEU cc_start: 0.5716 (OUTLIER) cc_final: 0.5317 (mt) REVERT: A 137 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7857 (mmm) REVERT: A 165 GLU cc_start: 0.8002 (tp30) cc_final: 0.7621 (tp30) REVERT: A 191 MET cc_start: 0.7983 (tpt) cc_final: 0.7436 (tpp) REVERT: A 277 LEU cc_start: 0.8417 (mm) cc_final: 0.8038 (mm) REVERT: A 410 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9090 (pp) REVERT: A 462 LEU cc_start: 0.9788 (mm) cc_final: 0.9493 (pp) REVERT: B 48 MET cc_start: 0.8288 (ptp) cc_final: 0.8036 (ptp) REVERT: B 51 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.4986 (tt0) REVERT: B 62 MET cc_start: 0.5875 (ppp) cc_final: 0.4987 (ppp) REVERT: B 137 MET cc_start: 0.5898 (mmt) cc_final: 0.5269 (mtm) REVERT: B 191 MET cc_start: 0.7069 (mtp) cc_final: 0.6567 (mmm) REVERT: B 202 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: B 245 MET cc_start: 0.7306 (mmm) cc_final: 0.7064 (mmt) REVERT: B 284 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: B 343 PHE cc_start: 0.8759 (t80) cc_final: 0.8440 (t80) REVERT: B 462 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9044 (pp) REVERT: C 46 ASN cc_start: 0.8756 (m-40) cc_final: 0.8527 (m110) REVERT: C 456 PHE cc_start: 0.9307 (t80) cc_final: 0.8781 (m-80) REVERT: C 461 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.7059 (m-80) REVERT: D 52 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7152 (tp) REVERT: D 64 MET cc_start: 0.6867 (pmm) cc_final: 0.6548 (pmm) REVERT: D 226 MET cc_start: 0.8162 (mtt) cc_final: 0.7870 (mmm) REVERT: D 253 ASN cc_start: 0.7741 (m-40) cc_final: 0.7337 (m110) REVERT: D 284 GLU cc_start: 0.8274 (tt0) cc_final: 0.7809 (tt0) REVERT: E 64 MET cc_start: 0.4823 (mmp) cc_final: 0.4061 (mmm) REVERT: E 237 GLU cc_start: 0.8415 (tt0) cc_final: 0.7807 (tp30) REVERT: E 364 TYR cc_start: 0.8788 (t80) cc_final: 0.8477 (t80) REVERT: E 455 LEU cc_start: 0.9486 (tp) cc_final: 0.9244 (pp) REVERT: F 202 MET cc_start: 0.8978 (mmm) cc_final: 0.8718 (mmt) REVERT: F 226 MET cc_start: 0.7531 (mtt) cc_final: 0.7289 (mmt) REVERT: F 253 ASN cc_start: 0.6643 (t0) cc_final: 0.6418 (t0) REVERT: F 389 MET cc_start: 0.7681 (ppp) cc_final: 0.7206 (ppp) REVERT: G 243 MET cc_start: 0.9002 (mmm) cc_final: 0.8771 (mmm) REVERT: G 266 GLN cc_start: 0.9285 (mp10) cc_final: 0.9024 (mp10) outliers start: 125 outliers final: 111 residues processed: 460 average time/residue: 0.3305 time to fit residues: 242.3706 Evaluate side-chains 482 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 362 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 248 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 273 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 218 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 205 optimal weight: 0.2980 chunk 186 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.113502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.094780 restraints weight = 78715.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097416 restraints weight = 44715.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.099224 restraints weight = 30197.317| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23565 Z= 0.217 Angle : 0.717 13.725 31932 Z= 0.355 Chirality : 0.047 0.383 3676 Planarity : 0.005 0.069 4160 Dihedral : 7.129 92.736 3409 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.08 % Allowed : 26.63 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 2956 helix: 0.18 (0.15), residues: 1121 sheet: 0.28 (0.25), residues: 421 loop : -0.75 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.066 0.002 PHE G 41 TYR 0.016 0.001 TYR G 90 ARG 0.009 0.001 ARG C 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7851.50 seconds wall clock time: 141 minutes 58.48 seconds (8518.48 seconds total)