Starting phenix.real_space_refine on Thu Jun 19 21:15:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9avj_43903/06_2025/9avj_43903.cif Found real_map, /net/cci-nas-00/data/ceres_data/9avj_43903/06_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_43903/06_2025/9avj_43903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9avj_43903/06_2025/9avj_43903.map" model { file = "/net/cci-nas-00/data/ceres_data/9avj_43903/06_2025/9avj_43903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9avj_43903/06_2025/9avj_43903.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 72 5.16 5 C 14601 2.51 5 N 4058 2.21 5 O 4437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23188 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3598 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Chain breaks: 1 Chain: "B" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3542 Classifications: {'peptide': 462} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 439} Chain breaks: 1 Chain: "C" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3534 Classifications: {'peptide': 461} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 439} Chain breaks: 2 Chain: "D" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3611 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "E" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3589 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 441} Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3614 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Chain: "G" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1540 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.58, per 1000 atoms: 0.54 Number of scatterers: 23188 At special positions: 0 Unit cell: (137.054, 126.208, 127.194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 15 15.00 Mg 5 11.99 O 4437 8.00 N 4058 7.00 C 14601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.86 Conformation dependent library (CDL) restraints added in 3.1 seconds 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5448 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 24 sheets defined 46.7% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 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: 7.62 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.30: 3989 1.30 - 1.62: 19416 1.62 - 1.94: 159 1.94 - 2.26: 0 2.26 - 2.58: 1 Bond restraints: 23565 Sorted by residual: bond pdb=" CB PRO F 117 " pdb=" CG PRO F 117 " ideal model delta sigma weight residual 1.492 2.579 -1.087 5.00e-02 4.00e+02 4.73e+02 bond pdb=" CG PRO F 117 " pdb=" CD PRO F 117 " ideal model delta sigma weight residual 1.503 0.986 0.517 3.40e-02 8.65e+02 2.31e+02 bond pdb=" O3A ANP F 500 " pdb=" PB ANP F 500 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP A 600 " pdb=" PB ANP A 600 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP D 500 " pdb=" PB ANP D 500 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 ... (remaining 23560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.34: 31929 19.34 - 38.68: 2 38.68 - 58.02: 0 58.02 - 77.37: 0 77.37 - 96.71: 1 Bond angle restraints: 31932 Sorted by residual: angle pdb=" CB PRO F 117 " pdb=" CG PRO F 117 " pdb=" CD PRO F 117 " ideal model delta sigma weight residual 106.10 9.39 96.71 3.20e+00 9.77e-02 9.13e+02 angle pdb=" N PRO F 117 " pdb=" CA PRO F 117 " pdb=" CB PRO F 117 " ideal model delta sigma weight residual 103.35 86.44 16.91 8.70e-01 1.32e+00 3.78e+02 angle pdb=" CA PRO F 117 " pdb=" N PRO F 117 " pdb=" CD PRO F 117 " ideal model delta sigma weight residual 112.00 85.51 26.49 1.40e+00 5.10e-01 3.58e+02 angle pdb=" CA PRO F 117 " pdb=" CB PRO F 117 " pdb=" CG PRO F 117 " ideal model delta sigma weight residual 104.50 75.98 28.52 1.90e+00 2.77e-01 2.25e+02 angle pdb=" CA PRO A 449 " pdb=" N PRO A 449 " pdb=" CD PRO A 449 " ideal model delta sigma weight residual 112.00 93.92 18.08 1.40e+00 5.10e-01 1.67e+02 ... (remaining 31927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.33: 13536 26.33 - 52.66: 760 52.66 - 78.99: 81 78.99 - 105.32: 26 105.32 - 131.65: 2 Dihedral angle restraints: 14405 sinusoidal: 5896 harmonic: 8509 Sorted by residual: dihedral pdb=" N PRO F 117 " pdb=" C PRO F 117 " pdb=" CA PRO F 117 " pdb=" CB PRO F 117 " ideal model delta harmonic sigma weight residual 115.10 97.65 17.45 0 2.50e+00 1.60e-01 4.87e+01 dihedral pdb=" CA PRO F 117 " pdb=" CB PRO F 117 " pdb=" CG PRO F 117 " pdb=" CD PRO F 117 " ideal model delta sinusoidal sigma weight residual 38.00 169.65 -131.65 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" CA ILE G 178 " pdb=" C ILE G 178 " pdb=" N GLN G 179 " pdb=" CA GLN G 179 " ideal model delta harmonic sigma weight residual 180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 14402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3013 0.062 - 0.124: 589 0.124 - 0.186: 61 0.186 - 0.247: 4 0.247 - 0.309: 9 Chirality restraints: 3676 Sorted by residual: chirality pdb=" CB ILE B 184 " pdb=" CA ILE B 184 " pdb=" CG1 ILE B 184 " pdb=" CG2 ILE B 184 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3' ANP D 500 " pdb=" C2' ANP D 500 " pdb=" C4' ANP D 500 " pdb=" O3' ANP D 500 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C3' ANP C 600 " pdb=" C2' ANP C 600 " pdb=" C4' ANP C 600 " pdb=" O3' ANP C 600 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 3673 not shown) Planarity restraints: 4160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 85 " -0.117 5.00e-02 4.00e+02 1.63e-01 4.23e+01 pdb=" N PRO F 86 " 0.281 5.00e-02 4.00e+02 pdb=" CA PRO F 86 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO F 86 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 280 " -0.111 5.00e-02 4.00e+02 1.60e-01 4.10e+01 pdb=" N PRO A 281 " 0.277 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 448 " -0.110 5.00e-02 4.00e+02 1.51e-01 3.65e+01 pdb=" N PRO F 449 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO F 449 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO F 449 " -0.079 5.00e-02 4.00e+02 ... (remaining 4157 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 114 2.51 - 3.11: 17128 3.11 - 3.71: 34233 3.71 - 4.30: 46914 4.30 - 4.90: 78236 Nonbonded interactions: 176625 Sorted by model distance: nonbonded pdb=" O2B ANP F 500 " pdb="MG MG F 501 " model vdw 1.914 2.170 nonbonded pdb=" O1G ANP D 500 " pdb="MG MG D 501 " model vdw 1.928 2.170 nonbonded pdb=" O2B ANP D 500 " pdb="MG MG D 501 " model vdw 1.939 2.170 nonbonded pdb=" O2B ANP C 600 " pdb="MG MG C 601 " model vdw 1.972 2.170 nonbonded pdb=" O1G ANP B 600 " pdb="MG MG B 601 " model vdw 1.975 2.170 ... (remaining 176620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 396 or resid 404 through 444 or resid 450 throu \ gh 495 or resid 600 through 601)) selection = (chain 'B' and (resid 28 through 444 or resid 450 through 495 or resid 600 throu \ gh 601)) selection = (chain 'C' and (resid 28 through 396 or resid 404 through 495 or resid 600 throu \ gh 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 189 or resid 191 through 466)) selection = (chain 'E' and (resid 2 through 189 or resid 191 through 466)) selection = (chain 'F' and (resid 2 through 189 or resid 191 through 466)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 49.250 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 2956 helix: -0.38 (0.15), residues: 1070 sheet: 0.46 (0.23), residues: 455 loop : -0.43 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS F 363 PHE 0.047 0.003 PHE D 255 TYR 0.032 0.002 TYR G 90 ARG 0.014 0.001 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.18137 ( 898) hydrogen bonds : angle 6.97303 ( 2559) covalent geometry : bond 0.00974 (23565) covalent geometry : angle 1.08360 (31932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 687 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ILE cc_start: 0.5764 (pt) cc_final: 0.5519 (pt) REVERT: B 463 PHE cc_start: 0.7128 (t80) cc_final: 0.6807 (t80) REVERT: C 46 ASN cc_start: 0.7052 (m-40) cc_final: 0.6494 (m-40) REVERT: D 128 LEU cc_start: 0.7006 (mt) cc_final: 0.6104 (mt) REVERT: D 400 VAL cc_start: 0.7444 (t) cc_final: 0.7055 (p) outliers start: 9 outliers final: 2 residues processed: 695 average time/residue: 0.3703 time to fit residues: 395.6025 Evaluate side-chains 458 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 456 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain D residue 30 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 3.9990 chunk 223 optimal weight: 0.0070 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 overall best weight: 2.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 333 ASN A 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 466 GLN B 469 GLN B 483 ASN C 143 HIS C 185 ASN C 422 GLN C 474 HIS D 174 ASN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.116530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.098473 restraints weight = 72630.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.100961 restraints weight = 43663.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.102660 restraints weight = 30268.888| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 23565 Z= 0.168 Angle : 0.726 14.060 31932 Z= 0.373 Chirality : 0.048 0.194 3676 Planarity : 0.006 0.101 4160 Dihedral : 7.628 104.927 3411 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.33 % Allowed : 19.98 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 2956 helix: 0.01 (0.15), residues: 1086 sheet: 0.70 (0.24), residues: 436 loop : -0.52 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 425 PHE 0.020 0.002 PHE A 494 TYR 0.020 0.002 TYR E 148 ARG 0.007 0.001 ARG G 263 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 898) hydrogen bonds : angle 5.35708 ( 2559) covalent geometry : bond 0.00396 (23565) covalent geometry : angle 0.72630 (31932) *********************** 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 591 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 485 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.7341 (mtp) cc_final: 0.7111 (mtm) REVERT: A 491 ILE cc_start: 0.8662 (mt) cc_final: 0.8393 (tt) REVERT: B 48 MET cc_start: 0.8278 (ptp) cc_final: 0.7958 (ptp) REVERT: B 62 MET cc_start: 0.4065 (ppp) cc_final: 0.3587 (ppp) REVERT: B 284 GLU cc_start: 0.8727 (mp0) cc_final: 0.8204 (mp0) REVERT: B 299 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7174 (mm-30) REVERT: B 483 ASN cc_start: 0.9116 (t0) cc_final: 0.8803 (t0) REVERT: B 491 ILE cc_start: 0.9507 (mm) cc_final: 0.9299 (tt) REVERT: C 245 MET cc_start: 0.7768 (mtt) cc_final: 0.7500 (mmt) REVERT: C 273 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9501 (pp) REVERT: C 391 GLU cc_start: 0.9287 (tp30) cc_final: 0.9049 (mm-30) REVERT: D 52 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6241 (tp) REVERT: D 202 MET cc_start: 0.8781 (tpp) cc_final: 0.8292 (mmm) REVERT: D 213 MET cc_start: 0.7142 (mmm) cc_final: 0.6824 (mmm) REVERT: D 226 MET cc_start: 0.8112 (mtt) cc_final: 0.7812 (mmm) REVERT: D 253 ASN cc_start: 0.7350 (m110) cc_final: 0.7073 (m-40) REVERT: D 400 VAL cc_start: 0.8454 (t) cc_final: 0.8159 (p) REVERT: E 218 MET cc_start: 0.9145 (mtp) cc_final: 0.8502 (mmm) REVERT: E 354 LEU cc_start: 0.8174 (tp) cc_final: 0.7753 (tt) REVERT: E 364 TYR cc_start: 0.8713 (t80) cc_final: 0.8398 (t80) REVERT: F 23 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.7682 (tp) REVERT: F 54 LEU cc_start: 0.9065 (mm) cc_final: 0.8775 (mm) REVERT: F 218 MET cc_start: 0.8005 (mtm) cc_final: 0.7428 (mtm) REVERT: F 219 ASN cc_start: 0.7818 (p0) cc_final: 0.6124 (p0) REVERT: F 220 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8134 (mt-10) REVERT: F 361 GLU cc_start: 0.8709 (mp0) cc_final: 0.7543 (tm-30) REVERT: F 389 MET cc_start: 0.7926 (ppp) cc_final: 0.7412 (ppp) REVERT: G 225 TYR cc_start: 0.9332 (t80) cc_final: 0.9087 (t80) REVERT: G 243 MET cc_start: 0.8753 (mmm) cc_final: 0.8512 (mmm) REVERT: G 265 ARG cc_start: 0.8739 (mtm110) cc_final: 0.8212 (mtm110) outliers start: 106 outliers final: 52 residues processed: 557 average time/residue: 0.3515 time to fit residues: 302.8499 Evaluate side-chains 472 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 417 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 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 5 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.114964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.096803 restraints weight = 72232.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.099300 restraints weight = 43395.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.101026 restraints weight = 30282.119| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23565 Z= 0.142 Angle : 0.682 13.267 31932 Z= 0.342 Chirality : 0.047 0.235 3676 Planarity : 0.005 0.073 4160 Dihedral : 7.238 102.958 3411 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.21 % Allowed : 21.16 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 2956 helix: 0.15 (0.15), residues: 1093 sheet: 0.70 (0.24), residues: 429 loop : -0.49 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 363 PHE 0.028 0.002 PHE A 318 TYR 0.025 0.001 TYR G 90 ARG 0.009 0.001 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 898) hydrogen bonds : angle 5.19216 ( 2559) covalent geometry : bond 0.00330 (23565) covalent geometry : angle 0.68189 (31932) *********************** 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 546 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 443 time to evaluate : 2.494 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: 0.8855 (mtp) cc_final: 0.8312 (mpp) REVERT: A 191 MET cc_start: 0.7835 (tpt) cc_final: 0.7296 (tpp) REVERT: A 245 MET cc_start: 0.7413 (mtp) cc_final: 0.7209 (mtm) REVERT: A 418 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8047 (tp30) REVERT: A 457 GLU cc_start: 0.8255 (pt0) cc_final: 0.8052 (pt0) REVERT: B 48 MET cc_start: 0.8321 (ptp) cc_final: 0.7954 (ptp) REVERT: B 60 MET cc_start: 0.8529 (mmm) cc_final: 0.8239 (mmm) REVERT: B 62 MET cc_start: 0.4343 (ppp) cc_final: 0.3805 (ppp) REVERT: B 137 MET cc_start: 0.6507 (mmt) cc_final: 0.5528 (mmp) REVERT: B 284 GLU cc_start: 0.8842 (mp0) cc_final: 0.8300 (mp0) REVERT: B 345 GLN cc_start: 0.6692 (mm-40) cc_final: 0.6481 (mm-40) REVERT: B 375 MET cc_start: 0.8009 (tmm) cc_final: 0.7740 (tmm) REVERT: C 101 GLU cc_start: 0.8916 (mp0) cc_final: 0.8715 (mp0) REVERT: C 270 TYR cc_start: 0.8503 (t80) cc_final: 0.8075 (t80) REVERT: C 283 ARG cc_start: 0.7694 (ttp80) cc_final: 0.7493 (ttp80) REVERT: C 391 GLU cc_start: 0.9313 (tp30) cc_final: 0.9060 (mm-30) REVERT: D 52 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6565 (tp) REVERT: D 213 MET cc_start: 0.7190 (mmm) cc_final: 0.6912 (mmm) REVERT: D 218 MET cc_start: 0.8249 (mtm) cc_final: 0.7812 (mtm) REVERT: D 226 MET cc_start: 0.8184 (mtt) cc_final: 0.7795 (mmm) REVERT: D 253 ASN cc_start: 0.7534 (m110) cc_final: 0.7154 (m110) REVERT: D 400 VAL cc_start: 0.8431 (t) cc_final: 0.8174 (p) REVERT: E 15 ASP cc_start: 0.7671 (m-30) cc_final: 0.7451 (m-30) REVERT: E 201 GLU cc_start: 0.9075 (tp30) cc_final: 0.8555 (tp30) REVERT: E 218 MET cc_start: 0.9028 (mtp) cc_final: 0.8673 (mmm) REVERT: E 338 MET cc_start: 0.8133 (tmm) cc_final: 0.7859 (ppp) REVERT: E 364 TYR cc_start: 0.8647 (t80) cc_final: 0.8343 (t80) REVERT: F 28 ASN cc_start: 0.3602 (OUTLIER) cc_final: 0.2796 (m110) REVERT: F 263 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7309 (mt-10) REVERT: G 21 LYS cc_start: 0.9378 (tptp) cc_final: 0.9011 (tptp) REVERT: G 25 MET cc_start: 0.9109 (ppp) cc_final: 0.8904 (ppp) REVERT: G 95 LEU cc_start: 0.8838 (pp) cc_final: 0.8492 (mt) REVERT: G 243 MET cc_start: 0.8786 (mmm) cc_final: 0.8537 (mmm) outliers start: 103 outliers final: 70 residues processed: 517 average time/residue: 0.3355 time to fit residues: 269.7467 Evaluate side-chains 477 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 405 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 342 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 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 121 VAL Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain 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 129 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 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 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 22 HIS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 139 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 14 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 135 optimal weight: 0.0770 chunk 69 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 5 optimal weight: 0.2980 chunk 258 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 176 optimal weight: 30.0000 chunk 107 optimal weight: 6.9990 overall best weight: 4.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN B 294 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN D 324 HIS ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 200 HIS F 28 ASN ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.111593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.093933 restraints weight = 75435.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.096316 restraints weight = 45522.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097949 restraints weight = 31624.188| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 23565 Z= 0.206 Angle : 0.712 12.613 31932 Z= 0.362 Chirality : 0.047 0.190 3676 Planarity : 0.005 0.068 4160 Dihedral : 7.199 97.782 3411 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 5.15 % Allowed : 21.81 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 2956 helix: 0.09 (0.15), residues: 1098 sheet: 0.64 (0.24), residues: 431 loop : -0.57 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 363 PHE 0.051 0.002 PHE G 41 TYR 0.024 0.002 TYR F 27 ARG 0.008 0.001 ARG B 271 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 898) hydrogen bonds : angle 5.19884 ( 2559) covalent geometry : bond 0.00469 (23565) covalent geometry : angle 0.71237 (31932) *********************** 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 546 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 420 time to evaluate : 2.543 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: 0.8777 (mtp) cc_final: 0.8541 (mtm) REVERT: A 245 MET cc_start: 0.7528 (mtp) cc_final: 0.7301 (mtm) REVERT: A 277 LEU cc_start: 0.8504 (mt) cc_final: 0.8214 (mt) REVERT: A 457 GLU cc_start: 0.8254 (pt0) cc_final: 0.7989 (pt0) REVERT: B 48 MET cc_start: 0.8276 (ptp) cc_final: 0.8039 (ptp) REVERT: B 51 GLU cc_start: 0.5676 (OUTLIER) cc_final: 0.5315 (tt0) REVERT: B 60 MET cc_start: 0.8487 (mmm) cc_final: 0.8212 (mmm) REVERT: B 62 MET cc_start: 0.5134 (ppp) cc_final: 0.4647 (ppp) REVERT: B 137 MET cc_start: 0.6480 (mmt) cc_final: 0.5571 (mmp) REVERT: B 284 GLU cc_start: 0.9028 (mp0) cc_final: 0.8312 (mp0) REVERT: C 137 MET cc_start: 0.5500 (mpp) cc_final: 0.4980 (mpp) REVERT: C 272 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8311 (mt-10) REVERT: C 283 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7716 (ttp80) REVERT: C 386 LEU cc_start: 0.8687 (tp) cc_final: 0.8468 (tt) REVERT: C 391 GLU cc_start: 0.9339 (tp30) cc_final: 0.9087 (mm-30) REVERT: C 456 PHE cc_start: 0.9207 (t80) cc_final: 0.8806 (m-80) REVERT: D 218 MET cc_start: 0.7925 (mtm) cc_final: 0.7712 (mtm) REVERT: D 226 MET cc_start: 0.8342 (mtt) cc_final: 0.7947 (mmm) REVERT: D 253 ASN cc_start: 0.7634 (m110) cc_final: 0.7223 (m-40) REVERT: E 201 GLU cc_start: 0.9078 (tp30) cc_final: 0.8650 (tp30) REVERT: E 213 MET cc_start: 0.7248 (mtm) cc_final: 0.6857 (mtp) REVERT: E 364 TYR cc_start: 0.8736 (t80) cc_final: 0.8437 (t80) REVERT: F 226 MET cc_start: 0.7566 (mtt) cc_final: 0.7332 (mtp) REVERT: F 389 MET cc_start: 0.7864 (ppp) cc_final: 0.7327 (ppp) REVERT: G 9 ARG cc_start: 0.9207 (mtp180) cc_final: 0.8870 (mtp180) REVERT: G 18 GLN cc_start: 0.9420 (mt0) cc_final: 0.9209 (mp10) REVERT: G 21 LYS cc_start: 0.9352 (tptp) cc_final: 0.9136 (tptp) REVERT: G 243 MET cc_start: 0.8847 (mmm) cc_final: 0.8519 (mmt) REVERT: G 265 ARG cc_start: 0.8792 (mtp180) cc_final: 0.8443 (mtm180) outliers start: 126 outliers final: 92 residues processed: 508 average time/residue: 0.3360 time to fit residues: 268.4848 Evaluate side-chains 488 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 394 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 342 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 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 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 346 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 40 SER 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 18 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 140 optimal weight: 0.0970 chunk 96 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 263 optimal weight: 2.9990 chunk 165 optimal weight: 0.0670 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN D 365 GLN F 53 HIS ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN ** G 103 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 = 0.3973 r_free = 0.3973 target = 0.116073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.096823 restraints weight = 74725.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.099460 restraints weight = 43874.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.101353 restraints weight = 29696.368| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4108 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= 0.122 Angle : 0.645 12.400 31932 Z= 0.327 Chirality : 0.046 0.252 3676 Planarity : 0.005 0.060 4160 Dihedral : 6.941 94.457 3411 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.88 % Allowed : 24.18 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 2956 helix: 0.21 (0.15), residues: 1103 sheet: 0.78 (0.25), residues: 414 loop : -0.49 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 324 PHE 0.051 0.002 PHE G 41 TYR 0.029 0.001 TYR G 90 ARG 0.008 0.000 ARG D 435 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 898) hydrogen bonds : angle 4.99843 ( 2559) covalent geometry : bond 0.00279 (23565) covalent geometry : angle 0.64502 (31932) *********************** 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 524 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 429 time to evaluate : 2.624 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 201 LYS cc_start: 0.7252 (ptmt) cc_final: 0.6663 (pttm) REVERT: A 245 MET cc_start: 0.7420 (mtp) cc_final: 0.7200 (mtm) REVERT: B 48 MET cc_start: 0.8348 (ptp) cc_final: 0.8087 (ptp) REVERT: B 51 GLU cc_start: 0.5193 (OUTLIER) cc_final: 0.4507 (tt0) REVERT: B 60 MET cc_start: 0.8505 (mmm) cc_final: 0.8203 (mmm) REVERT: B 62 MET cc_start: 0.4983 (ppp) cc_final: 0.3989 (ppp) REVERT: B 137 MET cc_start: 0.6624 (mmt) cc_final: 0.5811 (mmp) REVERT: B 284 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: C 101 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8845 (mm-30) REVERT: C 137 MET cc_start: 0.5924 (mpp) cc_final: 0.5444 (mpp) REVERT: C 272 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: C 283 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7498 (ttp80) REVERT: C 372 ILE cc_start: 0.9341 (mm) cc_final: 0.9070 (tp) REVERT: C 391 GLU cc_start: 0.9352 (tp30) cc_final: 0.9066 (mm-30) REVERT: C 456 PHE cc_start: 0.9214 (t80) cc_final: 0.8832 (m-80) REVERT: D 52 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6904 (tp) REVERT: D 226 MET cc_start: 0.8146 (mtt) cc_final: 0.7828 (mmm) REVERT: D 253 ASN cc_start: 0.7669 (m110) cc_final: 0.7260 (m110) REVERT: D 432 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7249 (tp30) REVERT: D 435 ARG cc_start: 0.7422 (ttp80) cc_final: 0.6966 (ttp80) REVERT: E 218 MET cc_start: 0.8932 (mtp) cc_final: 0.8603 (mmm) REVERT: E 235 MET cc_start: 0.7031 (mmt) cc_final: 0.6826 (mmt) REVERT: E 338 MET cc_start: 0.8207 (ppp) cc_final: 0.7772 (ppp) REVERT: F 8 GLN cc_start: 0.8088 (tt0) cc_final: 0.7315 (tm-30) REVERT: F 148 TYR cc_start: 0.7833 (m-80) cc_final: 0.7158 (m-80) REVERT: F 226 MET cc_start: 0.7574 (mtt) cc_final: 0.7343 (mtp) REVERT: F 389 MET cc_start: 0.7719 (ppp) cc_final: 0.7147 (ppp) REVERT: G 9 ARG cc_start: 0.9260 (mtp180) cc_final: 0.8904 (mtp180) REVERT: G 21 LYS cc_start: 0.9380 (tptp) cc_final: 0.9154 (tptp) REVERT: G 243 MET cc_start: 0.8919 (mmm) cc_final: 0.8568 (mmt) REVERT: G 248 ASP cc_start: 0.9307 (OUTLIER) cc_final: 0.8931 (p0) REVERT: G 265 ARG cc_start: 0.8834 (mtp180) cc_final: 0.8469 (mtm180) outliers start: 95 outliers final: 66 residues processed: 496 average time/residue: 0.3302 time to fit residues: 257.1736 Evaluate side-chains 465 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 394 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 293 LEU 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 382 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 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 386 LEU 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 129 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 327 SER 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 103 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 397 LYS 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 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 172 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 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 95 LEU Chi-restraints excluded: chain G residue 248 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 289 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 194 optimal weight: 0.9990 chunk 211 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN F 8 GLN ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** 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 = 0.3791 r_free = 0.3791 target = 0.108453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090688 restraints weight = 77550.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.093129 restraints weight = 45988.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.094761 restraints weight = 31471.721| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 23565 Z= 0.252 Angle : 0.763 11.837 31932 Z= 0.388 Chirality : 0.048 0.199 3676 Planarity : 0.005 0.067 4160 Dihedral : 7.270 91.871 3411 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.80 % Allowed : 22.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 2956 helix: -0.04 (0.15), residues: 1109 sheet: 0.34 (0.25), residues: 417 loop : -0.74 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS A 474 PHE 0.040 0.002 PHE A 318 TYR 0.020 0.002 TYR B 220 ARG 0.009 0.001 ARG E 115 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 898) hydrogen bonds : angle 5.38682 ( 2559) covalent geometry : bond 0.00573 (23565) covalent geometry : angle 0.76321 (31932) *********************** 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 544 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 402 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.5743 (OUTLIER) cc_final: 0.5404 (mt) REVERT: A 137 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7928 (mmm) REVERT: A 165 GLU cc_start: 0.8029 (tp30) cc_final: 0.7649 (tp30) REVERT: A 245 MET cc_start: 0.7607 (mtp) cc_final: 0.7370 (mtm) REVERT: A 462 LEU cc_start: 0.9774 (mm) cc_final: 0.9454 (pp) REVERT: B 48 MET cc_start: 0.8345 (ptp) cc_final: 0.8057 (ptp) REVERT: B 51 GLU cc_start: 0.5855 (OUTLIER) cc_final: 0.5526 (tt0) REVERT: B 60 MET cc_start: 0.8379 (mmm) cc_final: 0.8061 (mmm) REVERT: B 62 MET cc_start: 0.5465 (ppp) cc_final: 0.5157 (ppp) REVERT: B 202 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: B 284 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8285 (mp0) REVERT: C 101 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8812 (mm-30) REVERT: C 137 MET cc_start: 0.6258 (mpp) cc_final: 0.5722 (mpp) REVERT: C 283 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7766 (ttp80) REVERT: C 322 GLN cc_start: 0.7507 (mm-40) cc_final: 0.6896 (mm-40) REVERT: C 391 GLU cc_start: 0.9354 (tp30) cc_final: 0.8956 (tt0) REVERT: C 456 PHE cc_start: 0.9252 (t80) cc_final: 0.8821 (m-80) REVERT: D 226 MET cc_start: 0.8366 (mtt) cc_final: 0.8135 (mmm) REVERT: D 253 ASN cc_start: 0.7834 (m110) cc_final: 0.7510 (m-40) REVERT: D 315 ASP cc_start: 0.7639 (t0) cc_final: 0.7378 (t0) REVERT: D 432 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7752 (tp30) REVERT: E 213 MET cc_start: 0.7070 (mtm) cc_final: 0.6701 (mtp) REVERT: E 218 MET cc_start: 0.9000 (mtp) cc_final: 0.8671 (mmm) REVERT: E 237 GLU cc_start: 0.8270 (tt0) cc_final: 0.7491 (tp30) REVERT: E 455 LEU cc_start: 0.9534 (tp) cc_final: 0.9246 (pp) REVERT: F 226 MET cc_start: 0.7908 (mtt) cc_final: 0.7697 (mtp) REVERT: F 389 MET cc_start: 0.7799 (ppp) cc_final: 0.7270 (ppp) REVERT: G 7 LYS cc_start: 0.9509 (tptp) cc_final: 0.9295 (tptt) REVERT: G 9 ARG cc_start: 0.9099 (mtp180) cc_final: 0.8778 (mtp180) REVERT: G 21 LYS cc_start: 0.9324 (tptp) cc_final: 0.9110 (tptp) REVERT: G 243 MET cc_start: 0.8916 (mmm) cc_final: 0.8695 (mmm) outliers start: 142 outliers final: 108 residues processed: 500 average time/residue: 0.3317 time to fit residues: 260.9014 Evaluate side-chains 478 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 365 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 248 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 217 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 255 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS D 253 ASN ** E 119 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.109865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.091828 restraints weight = 76631.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.094333 restraints weight = 45061.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.096017 restraints weight = 30906.423| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23565 Z= 0.155 Angle : 0.702 12.578 31932 Z= 0.353 Chirality : 0.047 0.234 3676 Planarity : 0.005 0.085 4160 Dihedral : 7.105 93.128 3411 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.29 % Allowed : 25.29 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 2956 helix: 0.12 (0.15), residues: 1109 sheet: 0.65 (0.25), residues: 395 loop : -0.66 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 34 PHE 0.037 0.002 PHE A 318 TYR 0.027 0.001 TYR D 377 ARG 0.017 0.001 ARG G 4 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 898) hydrogen bonds : angle 5.17890 ( 2559) covalent geometry : bond 0.00359 (23565) covalent geometry : angle 0.70205 (31932) *********************** 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 505 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 400 time to evaluate : 2.727 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 76 LEU cc_start: 0.5671 (OUTLIER) cc_final: 0.5324 (mt) REVERT: A 137 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7866 (mmm) REVERT: A 165 GLU cc_start: 0.7922 (tp30) cc_final: 0.7525 (tp30) REVERT: A 191 MET cc_start: 0.7544 (tpt) cc_final: 0.6835 (mmm) REVERT: A 201 LYS cc_start: 0.7395 (ptmt) cc_final: 0.6817 (pttm) REVERT: A 245 MET cc_start: 0.7531 (mtp) cc_final: 0.7299 (mtm) REVERT: A 462 LEU cc_start: 0.9779 (mm) cc_final: 0.9486 (pp) REVERT: B 48 MET cc_start: 0.8306 (ptp) cc_final: 0.8031 (ptp) REVERT: B 51 GLU cc_start: 0.5283 (OUTLIER) cc_final: 0.4636 (tt0) REVERT: B 60 MET cc_start: 0.8498 (mmm) cc_final: 0.8114 (mmm) REVERT: B 62 MET cc_start: 0.5315 (ppp) cc_final: 0.4465 (ppp) REVERT: B 137 MET cc_start: 0.6359 (mmt) cc_final: 0.5654 (mtm) REVERT: B 202 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: B 284 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: B 363 VAL cc_start: 0.8874 (t) cc_final: 0.8640 (p) REVERT: B 462 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9038 (pp) REVERT: C 101 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8787 (mm-30) REVERT: C 137 MET cc_start: 0.6141 (mpp) cc_final: 0.5684 (mpp) REVERT: C 322 GLN cc_start: 0.7474 (mm-40) cc_final: 0.6876 (mm-40) REVERT: C 391 GLU cc_start: 0.9262 (tp30) cc_final: 0.8956 (tt0) REVERT: C 456 PHE cc_start: 0.9245 (t80) cc_final: 0.8802 (m-80) REVERT: D 52 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6967 (tp) REVERT: D 226 MET cc_start: 0.8298 (mtt) cc_final: 0.7890 (mmm) REVERT: D 253 ASN cc_start: 0.7736 (m-40) cc_final: 0.7384 (m-40) REVERT: D 432 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7753 (tp30) REVERT: E 64 MET cc_start: 0.5096 (mmp) cc_final: 0.4117 (mmm) REVERT: E 218 MET cc_start: 0.8912 (mtp) cc_final: 0.8542 (mmm) REVERT: E 237 GLU cc_start: 0.8201 (tt0) cc_final: 0.7455 (tp30) REVERT: E 455 LEU cc_start: 0.9524 (tp) cc_final: 0.9263 (pp) REVERT: F 389 MET cc_start: 0.7776 (ppp) cc_final: 0.7221 (ppp) REVERT: G 21 LYS cc_start: 0.9343 (tptp) cc_final: 0.9131 (tptp) REVERT: G 243 MET cc_start: 0.8949 (mmm) cc_final: 0.8729 (mmm) REVERT: G 252 GLU cc_start: 0.8953 (mp0) cc_final: 0.8656 (pm20) REVERT: G 265 ARG cc_start: 0.8673 (mtm180) cc_final: 0.8228 (mtm180) outliers start: 105 outliers final: 78 residues processed: 477 average time/residue: 0.3246 time to fit residues: 244.9574 Evaluate side-chains 464 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 379 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain 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 202 GLU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 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 76 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 152 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 chunk 270 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN A 469 GLN ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN D 243 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.107063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.089636 restraints weight = 78930.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.092002 restraints weight = 46373.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.093619 restraints weight = 31739.193| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 23565 Z= 0.249 Angle : 0.789 16.256 31932 Z= 0.398 Chirality : 0.049 0.536 3676 Planarity : 0.005 0.065 4160 Dihedral : 7.392 91.555 3411 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.02 % Allowed : 25.61 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 2956 helix: -0.06 (0.15), residues: 1108 sheet: 0.26 (0.25), residues: 400 loop : -0.86 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS D 53 PHE 0.037 0.002 PHE A 318 TYR 0.022 0.002 TYR B 220 ARG 0.019 0.001 ARG G 4 Details of bonding type rmsd hydrogen bonds : bond 0.04781 ( 898) hydrogen bonds : angle 5.44547 ( 2559) covalent geometry : bond 0.00564 (23565) covalent geometry : angle 0.78929 (31932) *********************** 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 505 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 382 time to evaluate : 2.662 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 76 LEU cc_start: 0.5693 (OUTLIER) cc_final: 0.5329 (mt) REVERT: A 137 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7863 (mmm) REVERT: A 165 GLU cc_start: 0.7977 (tp30) cc_final: 0.7572 (tp30) REVERT: A 245 MET cc_start: 0.7641 (mtp) cc_final: 0.7404 (mtm) REVERT: B 48 MET cc_start: 0.8288 (ptp) cc_final: 0.8027 (ptp) REVERT: B 51 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.5324 (tt0) REVERT: B 60 MET cc_start: 0.8315 (mmm) cc_final: 0.8047 (mmm) REVERT: B 62 MET cc_start: 0.5718 (ppp) cc_final: 0.4816 (ppp) REVERT: B 137 MET cc_start: 0.6143 (mmt) cc_final: 0.5557 (mtm) REVERT: B 202 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: B 245 MET cc_start: 0.7221 (mpp) cc_final: 0.6729 (mmt) REVERT: B 284 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: C 391 GLU cc_start: 0.9256 (tp30) cc_final: 0.8983 (tt0) REVERT: D 52 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6905 (tp) REVERT: D 226 MET cc_start: 0.8310 (mtt) cc_final: 0.7963 (mmm) REVERT: D 253 ASN cc_start: 0.7773 (m-40) cc_final: 0.7417 (m110) REVERT: D 315 ASP cc_start: 0.7778 (t0) cc_final: 0.7543 (t0) REVERT: D 338 MET cc_start: 0.8226 (ptp) cc_final: 0.7934 (ptp) REVERT: D 432 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7947 (tp30) REVERT: E 237 GLU cc_start: 0.8357 (tt0) cc_final: 0.7615 (tp30) REVERT: E 364 TYR cc_start: 0.8714 (t80) cc_final: 0.8389 (t80) REVERT: F 253 ASN cc_start: 0.6580 (t0) cc_final: 0.6337 (t0) REVERT: F 389 MET cc_start: 0.7810 (ppp) cc_final: 0.7275 (ppp) REVERT: G 7 LYS cc_start: 0.9512 (tptp) cc_final: 0.9291 (tptt) REVERT: G 21 LYS cc_start: 0.9326 (tptp) cc_final: 0.9107 (tptp) REVERT: G 243 MET cc_start: 0.9007 (mmm) cc_final: 0.8774 (mmm) REVERT: G 266 GLN cc_start: 0.9167 (mp10) cc_final: 0.8940 (mp10) outliers start: 123 outliers final: 105 residues processed: 471 average time/residue: 0.3623 time to fit residues: 271.1414 Evaluate side-chains 473 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 362 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 6 ILE 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 166 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 254 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 262 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 45 optimal weight: 0.0040 chunk 3 optimal weight: 6.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 HIS ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS D 278 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 = 0.3891 r_free = 0.3891 target = 0.111659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.093666 restraints weight = 78178.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.096165 restraints weight = 45278.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.097867 restraints weight = 30821.195| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23565 Z= 0.173 Angle : 0.750 18.125 31932 Z= 0.372 Chirality : 0.048 0.506 3676 Planarity : 0.005 0.083 4160 Dihedral : 7.256 92.911 3411 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.13 % Allowed : 26.67 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 2956 helix: 0.04 (0.15), residues: 1110 sheet: 0.41 (0.25), residues: 405 loop : -0.79 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 53 PHE 0.033 0.002 PHE A 318 TYR 0.016 0.001 TYR B 220 ARG 0.020 0.001 ARG G 4 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 898) hydrogen bonds : angle 5.29362 ( 2559) covalent geometry : bond 0.00404 (23565) covalent geometry : angle 0.74960 (31932) *********************** 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 488 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 387 time to evaluate : 2.541 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: A 76 LEU cc_start: 0.5692 (OUTLIER) cc_final: 0.5327 (mt) REVERT: A 137 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7846 (mmm) REVERT: A 165 GLU cc_start: 0.7953 (tp30) cc_final: 0.7561 (tp30) REVERT: A 191 MET cc_start: 0.7581 (tpt) cc_final: 0.6897 (mmm) REVERT: A 201 LYS cc_start: 0.7381 (ptmt) cc_final: 0.6687 (pttm) REVERT: A 245 MET cc_start: 0.7593 (mtp) cc_final: 0.7325 (mtm) REVERT: A 486 ASP cc_start: 0.8954 (t0) cc_final: 0.8708 (p0) REVERT: B 48 MET cc_start: 0.8264 (ptp) cc_final: 0.8014 (ptp) REVERT: B 51 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.4990 (tt0) REVERT: B 60 MET cc_start: 0.8189 (mmm) cc_final: 0.7919 (mmm) REVERT: B 62 MET cc_start: 0.5892 (ppp) cc_final: 0.4984 (ppp) REVERT: B 137 MET cc_start: 0.6004 (mmt) cc_final: 0.5411 (mtm) REVERT: B 202 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: B 245 MET cc_start: 0.7181 (mpp) cc_final: 0.6667 (mmt) REVERT: B 283 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7836 (ttm-80) REVERT: B 284 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: B 343 PHE cc_start: 0.8576 (t80) cc_final: 0.8290 (t80) REVERT: B 462 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9048 (pp) REVERT: C 202 GLU cc_start: 0.8554 (tp30) cc_final: 0.8116 (mm-30) REVERT: C 203 SER cc_start: 0.8869 (p) cc_final: 0.8597 (t) REVERT: C 391 GLU cc_start: 0.9238 (tp30) cc_final: 0.9019 (tt0) REVERT: D 52 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7224 (tp) REVERT: D 226 MET cc_start: 0.8120 (mtt) cc_final: 0.7872 (mmm) REVERT: D 253 ASN cc_start: 0.7733 (m-40) cc_final: 0.7381 (m110) REVERT: D 284 GLU cc_start: 0.8226 (tt0) cc_final: 0.7750 (tt0) REVERT: D 432 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7959 (tp30) REVERT: E 226 MET cc_start: 0.8883 (ttm) cc_final: 0.8362 (tmm) REVERT: E 237 GLU cc_start: 0.8418 (tt0) cc_final: 0.7754 (tp30) REVERT: E 455 LEU cc_start: 0.9476 (tp) cc_final: 0.9221 (pp) REVERT: F 226 MET cc_start: 0.7485 (mmt) cc_final: 0.6597 (mmt) REVERT: F 253 ASN cc_start: 0.6563 (t0) cc_final: 0.6346 (t0) REVERT: F 389 MET cc_start: 0.7851 (ppp) cc_final: 0.7319 (ppp) REVERT: G 21 LYS cc_start: 0.9344 (tptp) cc_final: 0.9098 (tptp) REVERT: G 243 MET cc_start: 0.9077 (mmm) cc_final: 0.8820 (mmm) REVERT: G 265 ARG cc_start: 0.8716 (mtm180) cc_final: 0.8472 (mtm180) outliers start: 101 outliers final: 85 residues processed: 455 average time/residue: 0.3783 time to fit residues: 273.0564 Evaluate side-chains 462 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 370 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain 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 202 GLU Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 48 MET 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 224 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 137 THR 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 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 2 optimal weight: 9.9990 chunk 160 optimal weight: 0.8980 chunk 191 optimal weight: 0.0370 chunk 248 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 281 optimal weight: 20.0000 chunk 184 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 276 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 overall best weight: 3.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 ASN D 53 HIS ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.111931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093773 restraints weight = 78165.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.096398 restraints weight = 43933.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.098174 restraints weight = 29415.710| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23565 Z= 0.169 Angle : 0.751 18.085 31932 Z= 0.372 Chirality : 0.048 0.499 3676 Planarity : 0.005 0.093 4160 Dihedral : 7.180 91.440 3411 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.17 % Allowed : 27.04 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 2956 helix: 0.13 (0.15), residues: 1102 sheet: 0.45 (0.25), residues: 408 loop : -0.79 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS D 53 PHE 0.034 0.002 PHE B 460 TYR 0.020 0.001 TYR B 438 ARG 0.017 0.001 ARG G 4 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 898) hydrogen bonds : angle 5.28212 ( 2559) covalent geometry : bond 0.00394 (23565) covalent geometry : angle 0.75082 (31932) ********************** 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 476 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 374 time to evaluate : 3.079 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: A 36 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.5954 (t0) REVERT: A 76 LEU cc_start: 0.5779 (OUTLIER) cc_final: 0.5391 (mt) REVERT: A 137 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7859 (mmm) REVERT: A 165 GLU cc_start: 0.7884 (tp30) cc_final: 0.7494 (tp30) REVERT: A 191 MET cc_start: 0.7629 (tpt) cc_final: 0.6955 (mmm) REVERT: A 245 MET cc_start: 0.7583 (mtp) cc_final: 0.7315 (mtm) REVERT: A 462 LEU cc_start: 0.9726 (mm) cc_final: 0.9414 (pp) REVERT: B 48 MET cc_start: 0.8286 (ptp) cc_final: 0.8033 (ptp) REVERT: B 51 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.4955 (tt0) REVERT: B 60 MET cc_start: 0.8209 (mmm) cc_final: 0.7941 (mmm) REVERT: B 62 MET cc_start: 0.5755 (ppp) cc_final: 0.4888 (ppp) REVERT: B 137 MET cc_start: 0.6042 (mmt) cc_final: 0.5411 (mtm) REVERT: B 202 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: B 245 MET cc_start: 0.7238 (mpp) cc_final: 0.6719 (mmt) REVERT: B 283 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7821 (ttm-80) REVERT: B 284 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: B 343 PHE cc_start: 0.8581 (t80) cc_final: 0.8217 (t80) REVERT: B 363 VAL cc_start: 0.8893 (t) cc_final: 0.8639 (p) REVERT: B 462 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9073 (pp) REVERT: C 137 MET cc_start: 0.6317 (mpp) cc_final: 0.5783 (mpp) REVERT: C 203 SER cc_start: 0.8874 (p) cc_final: 0.8615 (t) REVERT: C 391 GLU cc_start: 0.9249 (tp30) cc_final: 0.9012 (tt0) REVERT: D 52 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7154 (tp) REVERT: D 64 MET cc_start: 0.6653 (pmm) cc_final: 0.6354 (pmm) REVERT: D 226 MET cc_start: 0.8143 (mtt) cc_final: 0.7860 (mmm) REVERT: D 253 ASN cc_start: 0.7692 (m-40) cc_final: 0.7348 (m110) REVERT: D 432 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7970 (tp30) REVERT: E 226 MET cc_start: 0.8842 (ttm) cc_final: 0.8287 (tmm) REVERT: E 237 GLU cc_start: 0.8394 (tt0) cc_final: 0.7771 (tp30) REVERT: E 364 TYR cc_start: 0.8724 (t80) cc_final: 0.8412 (t80) REVERT: E 455 LEU cc_start: 0.9489 (tp) cc_final: 0.9213 (pp) REVERT: F 202 MET cc_start: 0.9061 (mmm) cc_final: 0.8826 (mmt) REVERT: F 226 MET cc_start: 0.7598 (mmt) cc_final: 0.6739 (mmt) REVERT: F 253 ASN cc_start: 0.6611 (t0) cc_final: 0.6397 (t0) REVERT: F 389 MET cc_start: 0.7693 (ppp) cc_final: 0.7153 (ppp) REVERT: G 21 LYS cc_start: 0.9339 (tptp) cc_final: 0.9136 (tptp) REVERT: G 243 MET cc_start: 0.9062 (mmm) cc_final: 0.8811 (mmm) outliers start: 102 outliers final: 90 residues processed: 446 average time/residue: 0.3166 time to fit residues: 225.1936 Evaluate side-chains 466 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 368 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 95 MET 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 198 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 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 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 273 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 205 optimal weight: 0.0980 chunk 186 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 289 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 HIS ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 ASN ** 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 = 0.3964 r_free = 0.3964 target = 0.114125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.095347 restraints weight = 77930.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.098011 restraints weight = 44471.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.099841 restraints weight = 29929.146| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.5404 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= 0.139 Angle : 0.737 18.485 31932 Z= 0.362 Chirality : 0.048 0.511 3676 Planarity : 0.005 0.084 4160 Dihedral : 7.022 91.232 3411 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.00 % Allowed : 27.17 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 2956 helix: 0.15 (0.15), residues: 1117 sheet: 0.53 (0.25), residues: 410 loop : -0.71 (0.17), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS D 53 PHE 0.031 0.002 PHE B 291 TYR 0.013 0.001 TYR A 251 ARG 0.016 0.000 ARG G 4 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 898) hydrogen bonds : angle 5.21276 ( 2559) covalent geometry : bond 0.00325 (23565) covalent geometry : angle 0.73703 (31932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8277.71 seconds wall clock time: 145 minutes 27.44 seconds (8727.44 seconds total)