Starting phenix.real_space_refine on Fri Sep 19 04:02:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9avj_43903/09_2025/9avj_43903.cif Found real_map, /net/cci-nas-00/data/ceres_data/9avj_43903/09_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_43903/09_2025/9avj_43903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9avj_43903/09_2025/9avj_43903.map" model { file = "/net/cci-nas-00/data/ceres_data/9avj_43903/09_2025/9avj_43903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9avj_43903/09_2025/9avj_43903.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.037 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.93, per 1000 atoms: 0.26 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: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.11 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: 4.60 Time building geometry restraints manager: 2.63 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 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.320 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.570 ------------------------------------------------------------------------------- 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= 0.305 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.001 ARG F 115 TYR 0.032 0.002 TYR G 90 PHE 0.047 0.003 PHE D 255 HIS 0.010 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00974 (23565) covalent geometry : angle 1.08360 (31932) hydrogen bonds : bond 0.18137 ( 898) hydrogen bonds : angle 6.97303 ( 2559) *********************** 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 : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.5424 (pt) REVERT: B 346 SER cc_start: 0.8253 (p) cc_final: 0.8052 (p) 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: 0.6489 (m-40) REVERT: D 128 LEU cc_start: 0.7006 (mt) cc_final: 0.6085 (mt) REVERT: D 400 VAL cc_start: 0.7444 (t) cc_final: 0.7056 (p) REVERT: E 87 VAL cc_start: 0.7001 (m) cc_final: 0.6798 (m) outliers start: 9 outliers final: 2 residues processed: 695 average time/residue: 0.1745 time to fit residues: 185.3662 Evaluate side-chains 454 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 452 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.4980 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 345 GLN 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.116441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.098435 restraints weight = 73295.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.100928 restraints weight = 43692.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.102639 restraints weight = 30230.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.103841 restraints weight = 22991.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.104795 restraints weight = 18671.453| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2701 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= 0.167 Angle : 0.727 12.852 31932 Z= 0.373 Chirality : 0.048 0.197 3676 Planarity : 0.006 0.100 4160 Dihedral : 7.642 104.974 3411 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.62 % Allowed : 19.61 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.15), residues: 2956 helix: 0.01 (0.15), residues: 1091 sheet: 0.70 (0.24), residues: 436 loop : -0.49 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 435 TYR 0.021 0.002 TYR E 148 PHE 0.021 0.002 PHE A 494 HIS 0.004 0.001 HIS B 425 Details of bonding type rmsd covalent geometry : bond 0.00388 (23565) covalent geometry : angle 0.72739 (31932) hydrogen bonds : bond 0.04792 ( 898) hydrogen bonds : angle 5.33959 ( 2559) *********************** 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 595 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 482 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.7349 (mtp) cc_final: 0.7121 (mtm) REVERT: A 491 ILE cc_start: 0.8700 (mt) cc_final: 0.8434 (tt) REVERT: B 48 MET cc_start: 0.8240 (ptp) cc_final: 0.7906 (ptp) REVERT: B 62 MET cc_start: 0.3949 (ppp) cc_final: 0.3480 (ppp) REVERT: B 272 GLU cc_start: 0.8253 (tt0) cc_final: 0.8009 (tt0) REVERT: B 284 GLU cc_start: 0.8765 (mp0) cc_final: 0.8263 (mp0) REVERT: B 286 TYR cc_start: 0.8109 (m-80) cc_final: 0.7868 (m-10) REVERT: B 299 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7115 (mm-30) REVERT: B 418 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: B 483 ASN cc_start: 0.9095 (t0) cc_final: 0.8779 (t0) REVERT: B 491 ILE cc_start: 0.9518 (mm) cc_final: 0.9295 (tt) REVERT: C 245 MET cc_start: 0.7726 (mtt) cc_final: 0.7477 (mmt) REVERT: C 273 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9502 (pp) REVERT: C 350 PHE cc_start: 0.8838 (m-80) cc_final: 0.8634 (m-80) REVERT: C 391 GLU cc_start: 0.9274 (tp30) cc_final: 0.9047 (mm-30) REVERT: D 52 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6210 (tp) REVERT: D 213 MET cc_start: 0.7072 (mmm) cc_final: 0.6719 (mmm) REVERT: D 226 MET cc_start: 0.8029 (ttm) cc_final: 0.6977 (ttm) REVERT: D 253 ASN cc_start: 0.7466 (m110) cc_final: 0.7157 (m-40) REVERT: D 400 VAL cc_start: 0.8444 (t) cc_final: 0.8143 (p) REVERT: E 218 MET cc_start: 0.9172 (mtp) cc_final: 0.8538 (mmm) REVERT: E 354 LEU cc_start: 0.8210 (tp) cc_final: 0.7787 (tt) REVERT: E 364 TYR cc_start: 0.8727 (t80) cc_final: 0.8387 (t80) REVERT: F 23 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.7616 (tp) REVERT: F 54 LEU cc_start: 0.9029 (mm) cc_final: 0.8740 (mm) REVERT: F 218 MET cc_start: 0.7952 (mtm) cc_final: 0.7377 (mtm) REVERT: F 219 ASN cc_start: 0.7800 (p0) cc_final: 0.6085 (p0) REVERT: F 220 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8116 (mt-10) REVERT: F 256 ARG cc_start: 0.8739 (mmt-90) cc_final: 0.8427 (mpt180) REVERT: F 271 MET cc_start: 0.8732 (mmt) cc_final: 0.8520 (mpp) REVERT: F 361 GLU cc_start: 0.8680 (mp0) cc_final: 0.7527 (tm-30) REVERT: F 389 MET cc_start: 0.7875 (ppp) cc_final: 0.7362 (ppp) REVERT: G 225 TYR cc_start: 0.9332 (t80) cc_final: 0.9078 (t80) REVERT: G 243 MET cc_start: 0.8750 (mmm) cc_final: 0.8483 (mmm) REVERT: G 265 ARG cc_start: 0.8765 (mtm110) cc_final: 0.8232 (mtm110) outliers start: 113 outliers final: 56 residues processed: 560 average time/residue: 0.1499 time to fit residues: 132.1212 Evaluate side-chains 480 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 420 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE 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 418 GLU 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 225 THR 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 260 optimal weight: 0.3980 chunk 246 optimal weight: 0.0060 chunk 225 optimal weight: 5.9990 chunk 122 optimal weight: 0.0370 chunk 207 optimal weight: 4.9990 chunk 265 optimal weight: 0.0170 chunk 292 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 259 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.2312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 GLN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.118144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.100033 restraints weight = 71252.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.102643 restraints weight = 42018.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104471 restraints weight = 28755.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.105681 restraints weight = 21687.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.106641 restraints weight = 17561.036| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23565 Z= 0.128 Angle : 0.676 14.092 31932 Z= 0.338 Chirality : 0.047 0.253 3676 Planarity : 0.005 0.069 4160 Dihedral : 7.076 101.899 3411 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 3.27 % Allowed : 21.69 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.15), residues: 2956 helix: 0.15 (0.15), residues: 1096 sheet: 0.82 (0.24), residues: 444 loop : -0.42 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 89 TYR 0.017 0.001 TYR E 148 PHE 0.026 0.002 PHE A 318 HIS 0.005 0.000 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00278 (23565) covalent geometry : angle 0.67645 (31932) hydrogen bonds : bond 0.04119 ( 898) hydrogen bonds : angle 5.09355 ( 2559) *********************** 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 545 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 465 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8525 (mtp) cc_final: 0.8169 (mpp) REVERT: A 191 MET cc_start: 0.7741 (tpt) cc_final: 0.7092 (tpp) REVERT: A 272 GLU cc_start: 0.8671 (tt0) cc_final: 0.8452 (tt0) REVERT: A 457 GLU cc_start: 0.8145 (pt0) cc_final: 0.7931 (pt0) REVERT: B 48 MET cc_start: 0.8254 (ptp) cc_final: 0.7904 (ptp) REVERT: B 62 MET cc_start: 0.4180 (ppp) cc_final: 0.3698 (ppp) REVERT: B 137 MET cc_start: 0.6332 (mmt) cc_final: 0.5365 (mmp) REVERT: B 284 GLU cc_start: 0.8857 (mp0) cc_final: 0.8241 (mp0) REVERT: B 286 TYR cc_start: 0.8008 (m-80) cc_final: 0.7724 (m-80) REVERT: B 375 MET cc_start: 0.8203 (tmm) cc_final: 0.7943 (tmm) REVERT: B 462 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8988 (pp) REVERT: B 491 ILE cc_start: 0.9504 (mm) cc_final: 0.9206 (tt) REVERT: C 49 SER cc_start: 0.9078 (m) cc_final: 0.8628 (t) REVERT: C 65 ASN cc_start: 0.8393 (t0) cc_final: 0.8075 (t0) REVERT: C 66 LEU cc_start: 0.8908 (mp) cc_final: 0.8437 (mt) REVERT: C 191 MET cc_start: 0.8881 (ptt) cc_final: 0.8496 (ptt) REVERT: C 245 MET cc_start: 0.7776 (mtt) cc_final: 0.7411 (mmt) REVERT: C 270 TYR cc_start: 0.8456 (t80) cc_final: 0.8042 (t80) REVERT: C 350 PHE cc_start: 0.8842 (m-80) cc_final: 0.8629 (m-80) REVERT: C 386 LEU cc_start: 0.8684 (tp) cc_final: 0.8450 (tt) REVERT: C 391 GLU cc_start: 0.9267 (tp30) cc_final: 0.9052 (mm-30) REVERT: D 54 LEU cc_start: 0.8980 (tp) cc_final: 0.8457 (mp) REVERT: D 213 MET cc_start: 0.7154 (mmm) cc_final: 0.6848 (mmm) REVERT: D 226 MET cc_start: 0.7953 (ttm) cc_final: 0.6627 (tpp) REVERT: D 253 ASN cc_start: 0.7683 (m110) cc_final: 0.7337 (m-40) REVERT: D 400 VAL cc_start: 0.8447 (t) cc_final: 0.8173 (p) REVERT: E 201 GLU cc_start: 0.9043 (tp30) cc_final: 0.8532 (tp30) REVERT: E 218 MET cc_start: 0.8997 (mtp) cc_final: 0.8653 (mmm) REVERT: E 281 LEU cc_start: 0.7342 (tt) cc_final: 0.7134 (tt) REVERT: E 338 MET cc_start: 0.8141 (tmm) cc_final: 0.7914 (ppp) REVERT: E 364 TYR cc_start: 0.8608 (t80) cc_final: 0.8285 (t80) REVERT: F 28 ASN cc_start: 0.3232 (OUTLIER) cc_final: 0.2462 (m110) REVERT: F 226 MET cc_start: 0.7548 (mtt) cc_final: 0.6823 (mmt) REVERT: F 263 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7219 (mt-10) REVERT: F 271 MET cc_start: 0.8711 (mmt) cc_final: 0.8471 (mmp) REVERT: G 9 ARG cc_start: 0.9087 (mtp180) cc_final: 0.8839 (ptm160) REVERT: G 95 LEU cc_start: 0.8777 (pp) cc_final: 0.8427 (mt) REVERT: G 225 TYR cc_start: 0.9314 (t80) cc_final: 0.9096 (t80) REVERT: G 243 MET cc_start: 0.8738 (mmm) cc_final: 0.8399 (mmm) REVERT: G 265 ARG cc_start: 0.8636 (mtm110) cc_final: 0.8354 (mtp180) outliers start: 80 outliers final: 44 residues processed: 520 average time/residue: 0.1568 time to fit residues: 127.7394 Evaluate side-chains 458 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 412 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 297 LEU 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 473 GLU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 327 SER 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 462 LEU 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 314 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 410 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 58 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 168 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 28 ASN 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 428 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 31 LEU 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 148 optimal weight: 0.0770 chunk 258 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 130 optimal weight: 0.0270 chunk 3 optimal weight: 0.4980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 322 GLN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 HIS ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN F 219 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.117465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.099097 restraints weight = 72271.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.101662 restraints weight = 43210.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.103455 restraints weight = 29688.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.104636 restraints weight = 22610.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.105556 restraints weight = 18472.085| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23565 Z= 0.118 Angle : 0.654 12.541 31932 Z= 0.326 Chirality : 0.046 0.302 3676 Planarity : 0.005 0.063 4160 Dihedral : 6.775 98.751 3411 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 3.59 % Allowed : 22.55 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 2956 helix: 0.20 (0.16), residues: 1098 sheet: 0.79 (0.24), residues: 455 loop : -0.41 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 435 TYR 0.019 0.001 TYR G 90 PHE 0.050 0.002 PHE G 41 HIS 0.003 0.000 HIS G 236 Details of bonding type rmsd covalent geometry : bond 0.00266 (23565) covalent geometry : angle 0.65412 (31932) hydrogen bonds : bond 0.03931 ( 898) hydrogen bonds : angle 4.97637 ( 2559) *********************** 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 522 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 434 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8560 (mtp) cc_final: 0.8194 (mpp) REVERT: A 191 MET cc_start: 0.7815 (tpt) cc_final: 0.7360 (tpp) REVERT: A 272 GLU cc_start: 0.8698 (tt0) cc_final: 0.8446 (tt0) REVERT: B 48 MET cc_start: 0.8287 (ptp) cc_final: 0.8056 (ptp) REVERT: B 51 GLU cc_start: 0.4909 (OUTLIER) cc_final: 0.4586 (tt0) REVERT: B 62 MET cc_start: 0.4145 (ppp) cc_final: 0.3751 (ppp) REVERT: B 137 MET cc_start: 0.6397 (mmt) cc_final: 0.5912 (mtm) REVERT: B 284 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8254 (mp0) REVERT: B 286 TYR cc_start: 0.8026 (m-80) cc_final: 0.7750 (m-80) REVERT: B 375 MET cc_start: 0.8275 (tmm) cc_final: 0.8067 (tmm) REVERT: B 462 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9013 (pp) REVERT: B 491 ILE cc_start: 0.9489 (mm) cc_final: 0.9190 (tt) REVERT: C 49 SER cc_start: 0.9053 (m) cc_final: 0.8528 (t) REVERT: C 65 ASN cc_start: 0.8205 (t0) cc_final: 0.7909 (t0) REVERT: C 66 LEU cc_start: 0.8828 (mp) cc_final: 0.8313 (mt) REVERT: C 137 MET cc_start: 0.5239 (mpp) cc_final: 0.4493 (mpp) REVERT: C 350 PHE cc_start: 0.8871 (m-80) cc_final: 0.8628 (m-80) REVERT: C 386 LEU cc_start: 0.8702 (tp) cc_final: 0.8488 (tt) REVERT: C 391 GLU cc_start: 0.9289 (tp30) cc_final: 0.9043 (tt0) REVERT: D 52 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6381 (tp) REVERT: D 202 MET cc_start: 0.8795 (tpp) cc_final: 0.8285 (mmm) REVERT: D 218 MET cc_start: 0.8495 (ptp) cc_final: 0.8217 (ptp) REVERT: D 226 MET cc_start: 0.8064 (ttm) cc_final: 0.6672 (tpp) REVERT: D 253 ASN cc_start: 0.7569 (m110) cc_final: 0.7231 (m-40) REVERT: D 400 VAL cc_start: 0.8434 (t) cc_final: 0.8125 (p) REVERT: D 413 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8480 (p0) REVERT: D 432 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7663 (tp30) REVERT: E 15 ASP cc_start: 0.7516 (m-30) cc_final: 0.7282 (m-30) REVERT: E 201 GLU cc_start: 0.9110 (tp30) cc_final: 0.8616 (tp30) REVERT: E 218 MET cc_start: 0.8983 (mtp) cc_final: 0.8712 (mmm) REVERT: E 226 MET cc_start: 0.9031 (ttm) cc_final: 0.8458 (tmm) REVERT: E 364 TYR cc_start: 0.8557 (t80) cc_final: 0.8235 (t80) REVERT: F 38 ASN cc_start: 0.7311 (p0) cc_final: 0.6728 (p0) REVERT: F 106 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8269 (mp0) REVERT: F 226 MET cc_start: 0.7492 (mtt) cc_final: 0.6736 (mmt) REVERT: F 271 MET cc_start: 0.8740 (mmt) cc_final: 0.8485 (mmp) REVERT: F 389 MET cc_start: 0.7725 (ppp) cc_final: 0.7150 (ppp) REVERT: G 18 GLN cc_start: 0.9369 (mt0) cc_final: 0.9115 (mp10) REVERT: G 243 MET cc_start: 0.8785 (mmm) cc_final: 0.8512 (mmm) REVERT: G 265 ARG cc_start: 0.8676 (mtm110) cc_final: 0.8318 (mtm180) outliers start: 88 outliers final: 62 residues processed: 496 average time/residue: 0.1390 time to fit residues: 111.2043 Evaluate side-chains 470 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 403 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE 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 471 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 193 SER 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 364 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 462 LEU 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 153 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 271 ARG 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 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 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 233 LEU Chi-restraints excluded: chain D residue 271 MET 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 D residue 413 ASN 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 258 THR Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 456 VAL 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 248 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 200 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 288 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 292 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS D 174 ASN E 381 GLN ** F 375 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 = 0.3868 r_free = 0.3868 target = 0.113723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.096176 restraints weight = 73403.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.098553 restraints weight = 44089.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.100229 restraints weight = 30693.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101376 restraints weight = 23401.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.102270 restraints weight = 19108.796| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 23565 Z= 0.180 Angle : 0.677 12.199 31932 Z= 0.344 Chirality : 0.046 0.196 3676 Planarity : 0.005 0.060 4160 Dihedral : 6.850 96.215 3411 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.86 % Allowed : 22.26 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.15), residues: 2956 helix: 0.23 (0.15), residues: 1107 sheet: 0.67 (0.24), residues: 431 loop : -0.46 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 435 TYR 0.017 0.001 TYR A 220 PHE 0.034 0.002 PHE A 318 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00416 (23565) covalent geometry : angle 0.67734 (31932) hydrogen bonds : bond 0.04240 ( 898) hydrogen bonds : angle 5.06452 ( 2559) *********************** 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 540 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 421 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8593 (mtp) cc_final: 0.8090 (mpp) REVERT: B 48 MET cc_start: 0.8315 (ptp) cc_final: 0.8059 (ptp) REVERT: B 51 GLU cc_start: 0.5619 (OUTLIER) cc_final: 0.5000 (tt0) REVERT: B 62 MET cc_start: 0.5081 (ppp) cc_final: 0.3981 (ppp) REVERT: B 137 MET cc_start: 0.6266 (mmt) cc_final: 0.5874 (mpp) REVERT: B 245 MET cc_start: 0.7070 (mpp) cc_final: 0.6566 (mmm) REVERT: B 284 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: B 286 TYR cc_start: 0.8132 (m-80) cc_final: 0.7909 (m-80) REVERT: B 456 PHE cc_start: 0.8689 (m-80) cc_final: 0.8477 (m-10) REVERT: C 137 MET cc_start: 0.5951 (mpp) cc_final: 0.5252 (mpp) REVERT: C 272 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: C 283 ARG cc_start: 0.7828 (ttp80) cc_final: 0.6762 (ttp80) REVERT: C 391 GLU cc_start: 0.9285 (tp30) cc_final: 0.9052 (mm-30) REVERT: C 456 PHE cc_start: 0.9191 (t80) cc_final: 0.8818 (m-80) REVERT: C 496 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8681 (ptpp) REVERT: D 52 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6668 (tp) REVERT: D 202 MET cc_start: 0.8856 (tpp) cc_final: 0.8436 (mmm) REVERT: D 207 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8356 (t) REVERT: D 218 MET cc_start: 0.8450 (ptp) cc_final: 0.8240 (ptp) REVERT: D 226 MET cc_start: 0.8273 (ttm) cc_final: 0.7007 (tpp) REVERT: D 253 ASN cc_start: 0.7813 (m110) cc_final: 0.7479 (m-40) REVERT: D 256 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8714 (tpp80) REVERT: D 413 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8472 (p0) REVERT: D 432 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7342 (tp30) REVERT: D 435 ARG cc_start: 0.7579 (ttp80) cc_final: 0.7312 (ttp80) REVERT: E 15 ASP cc_start: 0.7645 (m-30) cc_final: 0.7426 (m-30) REVERT: E 201 GLU cc_start: 0.9129 (tp30) cc_final: 0.8661 (tp30) REVERT: E 218 MET cc_start: 0.9028 (mtp) cc_final: 0.8815 (mmm) REVERT: E 226 MET cc_start: 0.9039 (ttm) cc_final: 0.8412 (tmm) REVERT: E 235 MET cc_start: 0.7007 (mmt) cc_final: 0.6774 (mmt) REVERT: E 364 TYR cc_start: 0.8634 (t80) cc_final: 0.8334 (t80) REVERT: E 455 LEU cc_start: 0.9448 (tp) cc_final: 0.9185 (pp) REVERT: F 8 GLN cc_start: 0.7902 (mp10) cc_final: 0.7642 (mp10) REVERT: F 271 MET cc_start: 0.8842 (mmt) cc_final: 0.8625 (mpp) REVERT: F 389 MET cc_start: 0.7720 (ppp) cc_final: 0.7188 (ppp) REVERT: G 243 MET cc_start: 0.8908 (mmm) cc_final: 0.8614 (mmm) REVERT: G 265 ARG cc_start: 0.8705 (mtm110) cc_final: 0.8359 (mtp180) outliers start: 119 outliers final: 82 residues processed: 498 average time/residue: 0.1397 time to fit residues: 110.2898 Evaluate side-chains 477 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 387 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU 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 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 471 LEU Chi-restraints excluded: chain A residue 473 GLU 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 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 247 GLU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 378 VAL 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 109 ASN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 153 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 243 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 272 GLU 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 C residue 496 LYS 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 142 VAL Chi-restraints excluded: chain D residue 207 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 256 ARG 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 D residue 397 LYS Chi-restraints excluded: chain D residue 413 ASN 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 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 162 VAL 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 350 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 248 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 216 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 176 optimal weight: 0.1980 chunk 292 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 270 optimal weight: 0.2980 chunk 28 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS D 53 HIS ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 103 GLN ** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.114206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.095452 restraints weight = 73624.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.097981 restraints weight = 43921.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.099680 restraints weight = 30314.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.100907 restraints weight = 23182.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101817 restraints weight = 18846.559| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23565 Z= 0.134 Angle : 0.655 12.221 31932 Z= 0.330 Chirality : 0.046 0.291 3676 Planarity : 0.004 0.061 4160 Dihedral : 6.754 93.401 3411 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.17 % Allowed : 24.10 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 2956 helix: 0.27 (0.15), residues: 1120 sheet: 0.79 (0.25), residues: 420 loop : -0.46 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG G 4 TYR 0.012 0.001 TYR A 251 PHE 0.033 0.002 PHE A 318 HIS 0.006 0.001 HIS F 324 Details of bonding type rmsd covalent geometry : bond 0.00309 (23565) covalent geometry : angle 0.65512 (31932) hydrogen bonds : bond 0.03931 ( 898) hydrogen bonds : angle 4.98596 ( 2559) *********************** 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 503 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 401 time to evaluate : 0.786 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 48 MET cc_start: 0.8334 (mtp) cc_final: 0.8062 (mpp) REVERT: A 462 LEU cc_start: 0.9748 (mm) cc_final: 0.9436 (pp) REVERT: B 48 MET cc_start: 0.8294 (ptp) cc_final: 0.8057 (ptp) REVERT: B 51 GLU cc_start: 0.5322 (OUTLIER) cc_final: 0.4645 (tt0) REVERT: B 62 MET cc_start: 0.5069 (ppp) cc_final: 0.4108 (ppp) REVERT: B 137 MET cc_start: 0.6367 (mmt) cc_final: 0.5657 (mmp) REVERT: B 245 MET cc_start: 0.7220 (mpp) cc_final: 0.6701 (mmm) REVERT: B 284 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: B 299 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8084 (mm-30) REVERT: C 137 MET cc_start: 0.6085 (mpp) cc_final: 0.5437 (mpp) REVERT: C 272 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8310 (mt-10) REVERT: C 391 GLU cc_start: 0.9315 (tp30) cc_final: 0.9049 (mm-30) REVERT: C 456 PHE cc_start: 0.9191 (t80) cc_final: 0.8812 (m-80) REVERT: D 52 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6901 (tp) REVERT: D 202 MET cc_start: 0.8855 (tpp) cc_final: 0.8491 (mmm) REVERT: D 207 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8255 (t) REVERT: D 218 MET cc_start: 0.8450 (ptp) cc_final: 0.8141 (ptp) REVERT: D 226 MET cc_start: 0.8303 (ttm) cc_final: 0.7006 (tpp) REVERT: D 253 ASN cc_start: 0.7790 (m110) cc_final: 0.7460 (m-40) REVERT: D 256 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8596 (tpp80) REVERT: D 413 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8473 (p0) REVERT: D 432 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7222 (tp30) REVERT: D 435 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7375 (ttp80) REVERT: E 15 ASP cc_start: 0.7703 (m-30) cc_final: 0.7471 (m-30) REVERT: E 201 GLU cc_start: 0.9177 (tp30) cc_final: 0.8733 (tp30) REVERT: E 218 MET cc_start: 0.9075 (mtp) cc_final: 0.8817 (mmm) REVERT: E 226 MET cc_start: 0.8966 (ttm) cc_final: 0.8337 (tmm) REVERT: E 455 LEU cc_start: 0.9435 (tp) cc_final: 0.9190 (pp) REVERT: F 8 GLN cc_start: 0.7942 (mp10) cc_final: 0.7715 (mp10) REVERT: F 106 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8302 (mp0) REVERT: F 148 TYR cc_start: 0.7705 (m-80) cc_final: 0.7328 (m-80) REVERT: F 271 MET cc_start: 0.8844 (mmt) cc_final: 0.8622 (mpp) REVERT: F 389 MET cc_start: 0.7674 (ppp) cc_final: 0.7124 (ppp) REVERT: G 5 ASP cc_start: 0.9257 (t0) cc_final: 0.8390 (t0) REVERT: G 9 ARG cc_start: 0.9160 (ptm160) cc_final: 0.8671 (ptt180) REVERT: G 243 MET cc_start: 0.8916 (mmm) cc_final: 0.8593 (mmm) REVERT: G 265 ARG cc_start: 0.8666 (mtm110) cc_final: 0.8282 (mtp180) outliers start: 102 outliers final: 74 residues processed: 473 average time/residue: 0.1493 time to fit residues: 110.9168 Evaluate side-chains 462 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 381 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE 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 473 GLU Chi-restraints excluded: chain A residue 484 GLU 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 247 GLU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 109 ASN 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 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 272 GLU Chi-restraints excluded: chain C residue 298 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 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 58 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 256 ARG 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 D residue 397 LYS Chi-restraints excluded: chain D residue 413 ASN 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 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 350 THR 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 6 ILE Chi-restraints excluded: chain G residue 36 GLN 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 233 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 225 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 287 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS C 407 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 HIS ** 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** F 375 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.113297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.095002 restraints weight = 73870.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.097483 restraints weight = 43883.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.099161 restraints weight = 30201.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.100399 restraints weight = 22961.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.101252 restraints weight = 18615.003| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23565 Z= 0.151 Angle : 0.665 12.835 31932 Z= 0.336 Chirality : 0.046 0.321 3676 Planarity : 0.005 0.061 4160 Dihedral : 6.712 90.200 3411 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.62 % Allowed : 24.10 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.15), residues: 2956 helix: 0.30 (0.15), residues: 1111 sheet: 0.72 (0.25), residues: 412 loop : -0.47 (0.17), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 4 TYR 0.013 0.001 TYR C 461 PHE 0.029 0.002 PHE B 291 HIS 0.008 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00345 (23565) covalent geometry : angle 0.66535 (31932) hydrogen bonds : bond 0.04021 ( 898) hydrogen bonds : angle 4.98963 ( 2559) *********************** 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 511 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 398 time to evaluate : 0.780 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: 0.8297 (mtp) cc_final: 0.7964 (mpp) REVERT: A 76 LEU cc_start: 0.5745 (OUTLIER) cc_final: 0.5378 (mt) REVERT: A 165 GLU cc_start: 0.7732 (tp30) cc_final: 0.7405 (tp30) REVERT: A 191 MET cc_start: 0.7799 (tpt) cc_final: 0.7377 (tpt) REVERT: A 462 LEU cc_start: 0.9743 (mm) cc_final: 0.9433 (pp) REVERT: B 48 MET cc_start: 0.8312 (ptp) cc_final: 0.8053 (ptp) REVERT: B 51 GLU cc_start: 0.5468 (OUTLIER) cc_final: 0.4854 (tt0) REVERT: B 62 MET cc_start: 0.5267 (ppp) cc_final: 0.4324 (ppp) REVERT: B 245 MET cc_start: 0.7240 (mpp) cc_final: 0.6690 (mmm) REVERT: B 284 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: B 320 GLU cc_start: 0.7431 (tp30) cc_final: 0.7217 (tp30) REVERT: B 363 VAL cc_start: 0.8854 (t) cc_final: 0.8603 (p) REVERT: B 418 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: C 137 MET cc_start: 0.6021 (mpp) cc_final: 0.5381 (mpp) REVERT: C 272 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8303 (mt-10) REVERT: C 391 GLU cc_start: 0.9294 (tp30) cc_final: 0.9050 (mm-30) REVERT: C 456 PHE cc_start: 0.9212 (t80) cc_final: 0.8843 (m-80) REVERT: D 52 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6952 (tp) REVERT: D 202 MET cc_start: 0.8930 (tpp) cc_final: 0.8541 (mmm) REVERT: D 207 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8311 (t) REVERT: D 218 MET cc_start: 0.8550 (ptp) cc_final: 0.8235 (ptp) REVERT: D 226 MET cc_start: 0.8310 (ttm) cc_final: 0.7048 (tpp) REVERT: D 253 ASN cc_start: 0.7850 (m110) cc_final: 0.7442 (m110) REVERT: D 256 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8769 (tpp80) REVERT: D 413 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8469 (p0) REVERT: D 432 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7305 (tp30) REVERT: D 435 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7636 (ttp80) REVERT: E 15 ASP cc_start: 0.7728 (m-30) cc_final: 0.7504 (m-30) REVERT: E 226 MET cc_start: 0.8932 (ttm) cc_final: 0.8308 (tmm) REVERT: E 237 GLU cc_start: 0.7917 (tt0) cc_final: 0.7203 (tp30) REVERT: F 8 GLN cc_start: 0.7948 (mp10) cc_final: 0.7647 (mp10) REVERT: F 148 TYR cc_start: 0.7844 (m-80) cc_final: 0.7459 (m-80) REVERT: F 226 MET cc_start: 0.7514 (mmt) cc_final: 0.6626 (mmt) REVERT: F 251 ILE cc_start: 0.6279 (mm) cc_final: 0.6031 (mm) REVERT: F 271 MET cc_start: 0.8867 (mmt) cc_final: 0.8631 (mpp) REVERT: F 389 MET cc_start: 0.7704 (ppp) cc_final: 0.7226 (ppp) REVERT: G 243 MET cc_start: 0.8933 (mmm) cc_final: 0.8630 (mmm) REVERT: G 265 ARG cc_start: 0.8661 (mtm110) cc_final: 0.8316 (mtp180) outliers start: 113 outliers final: 87 residues processed: 477 average time/residue: 0.1507 time to fit residues: 113.6608 Evaluate side-chains 473 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 377 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 473 GLU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 GLU 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 247 GLU 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 418 GLU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 109 ASN 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 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 272 GLU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 339 ASP 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 C residue 461 TYR 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 142 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 256 ARG 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 D residue 389 MET Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain E residue 46 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 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 46 LEU 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 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 333 ARG 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 248 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 191 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 141 optimal weight: 0.0970 chunk 231 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS D 40 ASN D 365 GLN E 169 GLN E 259 GLN ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.108043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.090332 restraints weight = 79465.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.092983 restraints weight = 44317.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.094846 restraints weight = 29299.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.096143 restraints weight = 21450.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.097129 restraints weight = 16898.822| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23565 Z= 0.173 Angle : 0.706 12.156 31932 Z= 0.355 Chirality : 0.047 0.271 3676 Planarity : 0.005 0.091 4160 Dihedral : 6.822 89.178 3411 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.70 % Allowed : 24.31 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.15), residues: 2956 helix: 0.21 (0.15), residues: 1110 sheet: 0.70 (0.25), residues: 412 loop : -0.55 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 4 TYR 0.017 0.001 TYR D 377 PHE 0.031 0.002 PHE B 291 HIS 0.005 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00399 (23565) covalent geometry : angle 0.70590 (31932) hydrogen bonds : bond 0.04166 ( 898) hydrogen bonds : angle 5.10674 ( 2559) *********************** 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 508 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 393 time to evaluate : 0.867 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: 0.8201 (mtp) cc_final: 0.7924 (mpp) REVERT: A 76 LEU cc_start: 0.5874 (OUTLIER) cc_final: 0.5507 (mt) REVERT: A 191 MET cc_start: 0.7853 (tpt) cc_final: 0.7475 (tpt) REVERT: A 462 LEU cc_start: 0.9741 (mm) cc_final: 0.9432 (pp) REVERT: B 48 MET cc_start: 0.8252 (ptp) cc_final: 0.8021 (ptp) REVERT: B 51 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.4956 (tt0) REVERT: B 62 MET cc_start: 0.5406 (ppp) cc_final: 0.4482 (ppp) REVERT: B 245 MET cc_start: 0.7325 (mpp) cc_final: 0.6754 (mmm) REVERT: B 284 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: B 299 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7954 (mm-30) REVERT: B 363 VAL cc_start: 0.8922 (t) cc_final: 0.8656 (p) REVERT: B 418 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: C 137 MET cc_start: 0.6143 (mpp) cc_final: 0.5565 (mpp) REVERT: C 272 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: C 391 GLU cc_start: 0.9338 (tp30) cc_final: 0.9077 (mm-30) REVERT: C 393 GLU cc_start: 0.9282 (tt0) cc_final: 0.8858 (mt-10) REVERT: C 456 PHE cc_start: 0.9247 (t80) cc_final: 0.8830 (m-80) REVERT: D 52 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6937 (tp) REVERT: D 202 MET cc_start: 0.8937 (tpp) cc_final: 0.8569 (mmm) REVERT: D 207 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8312 (t) REVERT: D 218 MET cc_start: 0.8395 (ptp) cc_final: 0.8079 (ptp) REVERT: D 226 MET cc_start: 0.8400 (ttm) cc_final: 0.7220 (tpp) REVERT: D 253 ASN cc_start: 0.7772 (m110) cc_final: 0.7412 (m110) REVERT: D 256 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8779 (tpp80) REVERT: D 432 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7403 (tp30) REVERT: D 435 ARG cc_start: 0.8070 (ttp80) cc_final: 0.7816 (ttp80) REVERT: E 15 ASP cc_start: 0.7727 (m-30) cc_final: 0.7509 (m-30) REVERT: E 169 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8053 (mm-40) REVERT: E 237 GLU cc_start: 0.7925 (tt0) cc_final: 0.7196 (tp30) REVERT: E 338 MET cc_start: 0.8472 (pmm) cc_final: 0.7892 (ppp) REVERT: E 364 TYR cc_start: 0.8630 (t80) cc_final: 0.8284 (t80) REVERT: E 455 LEU cc_start: 0.9419 (tp) cc_final: 0.9210 (pp) REVERT: F 8 GLN cc_start: 0.7908 (mp10) cc_final: 0.7620 (mp10) REVERT: F 64 MET cc_start: 0.8466 (mmm) cc_final: 0.7305 (mmm) REVERT: F 226 MET cc_start: 0.7545 (mmt) cc_final: 0.6644 (mmt) REVERT: F 271 MET cc_start: 0.8878 (mmt) cc_final: 0.8623 (mpp) REVERT: F 300 ILE cc_start: 0.8166 (mt) cc_final: 0.7945 (mm) REVERT: F 389 MET cc_start: 0.7835 (ppp) cc_final: 0.7212 (ppp) REVERT: G 5 ASP cc_start: 0.9439 (t0) cc_final: 0.8841 (t0) REVERT: G 9 ARG cc_start: 0.9242 (ptm160) cc_final: 0.8787 (ptt180) REVERT: G 130 MET cc_start: 0.6889 (mmp) cc_final: 0.6202 (tpt) REVERT: G 243 MET cc_start: 0.9019 (mmm) cc_final: 0.8707 (mmm) REVERT: G 252 GLU cc_start: 0.9197 (mp0) cc_final: 0.8934 (mp0) REVERT: G 265 ARG cc_start: 0.8809 (mtm110) cc_final: 0.8390 (mtm110) outliers start: 115 outliers final: 93 residues processed: 471 average time/residue: 0.1432 time to fit residues: 108.4715 Evaluate side-chains 474 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 372 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 122 GLU 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 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 473 GLU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 51 GLU 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 247 GLU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 109 ASN 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 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 272 GLU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 339 ASP 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 C residue 461 TYR 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 207 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 256 ARG 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 46 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 169 GLN Chi-restraints excluded: chain E residue 171 LEU 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 F residue 46 LEU 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 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 333 ARG 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 248 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 291 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN E 381 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.112984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.094186 restraints weight = 76133.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.096683 restraints weight = 44947.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.098428 restraints weight = 30853.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.099602 restraints weight = 23494.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.100486 restraints weight = 19276.621| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 23565 Z= 0.191 Angle : 0.725 11.856 31932 Z= 0.366 Chirality : 0.047 0.306 3676 Planarity : 0.005 0.108 4160 Dihedral : 6.959 89.860 3411 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.45 % Allowed : 25.08 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.15), residues: 2956 helix: 0.19 (0.15), residues: 1103 sheet: 0.57 (0.25), residues: 409 loop : -0.61 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 4 TYR 0.018 0.002 TYR B 220 PHE 0.031 0.002 PHE B 291 HIS 0.005 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00439 (23565) covalent geometry : angle 0.72545 (31932) hydrogen bonds : bond 0.04294 ( 898) hydrogen bonds : angle 5.18157 ( 2559) *********************** 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 491 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 382 time to evaluate : 0.947 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: 0.8199 (mtp) cc_final: 0.7938 (mpp) REVERT: A 76 LEU cc_start: 0.5744 (OUTLIER) cc_final: 0.5369 (mt) REVERT: A 137 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7833 (mmm) REVERT: A 165 GLU cc_start: 0.7840 (tp30) cc_final: 0.7498 (tp30) REVERT: A 181 ASP cc_start: 0.9034 (m-30) cc_final: 0.8489 (m-30) REVERT: A 191 MET cc_start: 0.7800 (tpt) cc_final: 0.7412 (tpt) REVERT: A 462 LEU cc_start: 0.9764 (mm) cc_final: 0.9469 (pp) REVERT: B 48 MET cc_start: 0.8214 (ptp) cc_final: 0.7995 (ptp) REVERT: B 51 GLU cc_start: 0.5692 (OUTLIER) cc_final: 0.5110 (tt0) REVERT: B 62 MET cc_start: 0.5604 (ppp) cc_final: 0.4680 (ppp) REVERT: B 137 MET cc_start: 0.6172 (mmt) cc_final: 0.5375 (mtm) REVERT: B 245 MET cc_start: 0.7367 (mpp) cc_final: 0.6789 (mmm) REVERT: B 284 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: B 299 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 272 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8315 (mt-10) REVERT: C 322 GLN cc_start: 0.7607 (mm-40) cc_final: 0.6959 (mm-40) REVERT: C 456 PHE cc_start: 0.9249 (t80) cc_final: 0.8802 (m-80) REVERT: D 52 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6992 (tp) REVERT: D 202 MET cc_start: 0.8943 (tpp) cc_final: 0.8601 (mmm) REVERT: D 207 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8234 (t) REVERT: D 218 MET cc_start: 0.8396 (ptp) cc_final: 0.8078 (ptp) REVERT: D 226 MET cc_start: 0.8369 (ttm) cc_final: 0.7386 (tpp) REVERT: D 253 ASN cc_start: 0.7866 (m110) cc_final: 0.7577 (m-40) REVERT: D 256 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8844 (tpp80) REVERT: D 432 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7991 (tp30) REVERT: E 15 ASP cc_start: 0.7716 (m-30) cc_final: 0.7515 (m-30) REVERT: E 237 GLU cc_start: 0.8099 (tt0) cc_final: 0.7383 (tp30) REVERT: E 338 MET cc_start: 0.8508 (pmm) cc_final: 0.8081 (ppp) REVERT: E 455 LEU cc_start: 0.9440 (tp) cc_final: 0.9184 (pp) REVERT: F 8 GLN cc_start: 0.7895 (mp10) cc_final: 0.7481 (mp10) REVERT: F 226 MET cc_start: 0.7580 (mmt) cc_final: 0.7274 (mmt) REVERT: F 300 ILE cc_start: 0.8121 (mt) cc_final: 0.7919 (mm) REVERT: F 389 MET cc_start: 0.7839 (ppp) cc_final: 0.7262 (ppp) REVERT: G 5 ASP cc_start: 0.9349 (t0) cc_final: 0.8636 (t0) REVERT: G 9 ARG cc_start: 0.9162 (ptm160) cc_final: 0.8709 (ptt180) REVERT: G 243 MET cc_start: 0.9052 (mmm) cc_final: 0.8739 (mmm) REVERT: G 266 GLN cc_start: 0.9179 (mp10) cc_final: 0.8965 (mp10) outliers start: 109 outliers final: 87 residues processed: 457 average time/residue: 0.1536 time to fit residues: 112.0886 Evaluate side-chains 466 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 371 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE 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 473 GLU 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 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 247 GLU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 364 SER 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 95 MET Chi-restraints excluded: chain C residue 109 ASN 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 243 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 339 ASP 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 C residue 461 TYR 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 207 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 256 ARG 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 E residue 46 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 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 46 LEU 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 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 333 ARG 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 248 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 10.0000 chunk 193 optimal weight: 0.0870 chunk 287 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 256 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.110898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.092865 restraints weight = 75671.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.095282 restraints weight = 45062.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.096950 restraints weight = 31028.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.098065 restraints weight = 23644.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.098958 restraints weight = 19357.596| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23565 Z= 0.155 Angle : 0.719 12.431 31932 Z= 0.358 Chirality : 0.047 0.301 3676 Planarity : 0.005 0.095 4160 Dihedral : 6.842 90.330 3411 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.80 % Allowed : 26.10 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.15), residues: 2956 helix: 0.23 (0.15), residues: 1106 sheet: 0.61 (0.25), residues: 404 loop : -0.57 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 4 TYR 0.016 0.001 TYR C 248 PHE 0.031 0.002 PHE B 291 HIS 0.005 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00361 (23565) covalent geometry : angle 0.71894 (31932) hydrogen bonds : bond 0.04047 ( 898) hydrogen bonds : angle 5.13851 ( 2559) ********************** 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 474 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 381 time to evaluate : 0.979 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 48 MET cc_start: 0.8113 (mtp) cc_final: 0.7890 (mpp) REVERT: A 76 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5347 (mt) REVERT: A 137 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7759 (mmm) REVERT: A 165 GLU cc_start: 0.7845 (tp30) cc_final: 0.7507 (tp30) REVERT: A 181 ASP cc_start: 0.8958 (m-30) cc_final: 0.8443 (m-30) REVERT: A 191 MET cc_start: 0.7838 (tpt) cc_final: 0.7442 (tpt) REVERT: A 462 LEU cc_start: 0.9759 (mm) cc_final: 0.9455 (pp) REVERT: B 48 MET cc_start: 0.8228 (ptp) cc_final: 0.7997 (ptp) REVERT: B 51 GLU cc_start: 0.5431 (OUTLIER) cc_final: 0.4816 (tt0) REVERT: B 62 MET cc_start: 0.5382 (ppp) cc_final: 0.4597 (ppp) REVERT: B 137 MET cc_start: 0.5948 (mmt) cc_final: 0.5462 (mtm) REVERT: B 245 MET cc_start: 0.7384 (mpp) cc_final: 0.6852 (mmt) REVERT: B 284 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: B 299 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7947 (mm-30) REVERT: C 137 MET cc_start: 0.5554 (mpp) cc_final: 0.5211 (mpp) REVERT: C 272 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8080 (mm-30) REVERT: C 322 GLN cc_start: 0.7561 (mm-40) cc_final: 0.6921 (mm-40) REVERT: C 456 PHE cc_start: 0.9244 (t80) cc_final: 0.8792 (m-80) REVERT: D 52 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7004 (tp) REVERT: D 202 MET cc_start: 0.8926 (tpp) cc_final: 0.8583 (mmm) REVERT: D 207 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8146 (t) REVERT: D 218 MET cc_start: 0.8378 (ptp) cc_final: 0.8035 (ptp) REVERT: D 226 MET cc_start: 0.8180 (ttm) cc_final: 0.7284 (tpp) REVERT: D 253 ASN cc_start: 0.7908 (m110) cc_final: 0.7603 (m-40) REVERT: D 256 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8828 (tpp80) REVERT: D 432 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7873 (tp30) REVERT: E 15 ASP cc_start: 0.7735 (m-30) cc_final: 0.7530 (m-30) REVERT: E 64 MET cc_start: 0.4082 (mmp) cc_final: 0.3628 (mmm) REVERT: E 237 GLU cc_start: 0.8139 (tt0) cc_final: 0.7351 (tp30) REVERT: E 338 MET cc_start: 0.8483 (pmm) cc_final: 0.6579 (tmm) REVERT: E 364 TYR cc_start: 0.8569 (t80) cc_final: 0.8249 (t80) REVERT: E 455 LEU cc_start: 0.9448 (tp) cc_final: 0.9188 (pp) REVERT: F 8 GLN cc_start: 0.7760 (mp10) cc_final: 0.7507 (mp10) REVERT: F 64 MET cc_start: 0.8314 (mmm) cc_final: 0.7122 (mmm) REVERT: F 106 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8328 (mp0) REVERT: F 389 MET cc_start: 0.7797 (ppp) cc_final: 0.7229 (ppp) REVERT: G 5 ASP cc_start: 0.9297 (t0) cc_final: 0.8608 (t0) REVERT: G 9 ARG cc_start: 0.9113 (ptm160) cc_final: 0.8696 (ptt180) REVERT: G 130 MET cc_start: 0.7005 (mmp) cc_final: 0.6396 (tpt) REVERT: G 243 MET cc_start: 0.8993 (mmm) cc_final: 0.8696 (mmm) REVERT: G 265 ARG cc_start: 0.8819 (mtp-110) cc_final: 0.8428 (mtm180) outliers start: 93 outliers final: 82 residues processed: 448 average time/residue: 0.1572 time to fit residues: 113.3152 Evaluate side-chains 459 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 369 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 255 HIS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 51 GLU 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 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 347 ASP Chi-restraints excluded: chain B residue 364 SER 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 95 MET Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 150 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 243 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 298 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 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 461 TYR 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 142 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 256 ARG 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 E residue 46 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 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 46 LEU 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 254 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 333 ARG 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 456 VAL Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 139 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 258 optimal weight: 8.9990 chunk 189 optimal weight: 0.8980 chunk 83 optimal weight: 0.3980 chunk 249 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 270 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 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 = 0.3866 r_free = 0.3866 target = 0.113228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.094883 restraints weight = 73428.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.097382 restraints weight = 43163.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.099116 restraints weight = 29701.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100278 restraints weight = 22602.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.101195 restraints weight = 18497.760| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23565 Z= 0.120 Angle : 0.704 13.410 31932 Z= 0.348 Chirality : 0.047 0.291 3676 Planarity : 0.005 0.077 4160 Dihedral : 6.548 88.447 3411 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.86 % Allowed : 27.00 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.16), residues: 2956 helix: 0.46 (0.16), residues: 1093 sheet: 0.68 (0.25), residues: 420 loop : -0.45 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 4 TYR 0.017 0.001 TYR C 248 PHE 0.030 0.001 PHE B 291 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00273 (23565) covalent geometry : angle 0.70408 (31932) hydrogen bonds : bond 0.03688 ( 898) hydrogen bonds : angle 4.98000 ( 2559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3996.46 seconds wall clock time: 69 minutes 42.20 seconds (4182.20 seconds total)