Starting phenix.real_space_refine on Sat Mar 23 11:08:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbq_27298/03_2024/8dbq_27298_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbq_27298/03_2024/8dbq_27298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbq_27298/03_2024/8dbq_27298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbq_27298/03_2024/8dbq_27298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbq_27298/03_2024/8dbq_27298_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbq_27298/03_2024/8dbq_27298_updated.pdb" } resolution = 4.0 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= -0.000 sd= 0.003 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 16 5.49 5 Mg 5 5.21 5 S 178 5.16 5 C 23342 2.51 5 N 6275 2.21 5 O 6921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 44": "OD1" <-> "OD2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36737 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "B" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3863 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "E" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "H" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.52, per 1000 atoms: 0.50 Number of scatterers: 36737 At special positions: 0 Unit cell: (180.193, 223.353, 137.033, 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 178 16.00 P 16 15.00 Mg 5 11.99 O 6921 8.00 N 6275 7.00 C 23342 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 - 3.50 Amino acid : False - 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: 14.34 Conformation dependent library (CDL) restraints added in 6.9 seconds 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8756 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 25 sheets defined 56.4% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.17 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.918A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.691A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.871A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 408 removed outlier: 4.032A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 431 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.067A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 5 through 18 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.662A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 251 Proline residue: B 239 - end of helix removed outlier: 3.967A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.643A pdb=" N LEU B 293 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS B 294 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 297 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 340 through 346 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 384 through 390 Processing helix chain 'B' and resid 393 through 407 Processing helix chain 'B' and resid 416 through 431 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 461 through 477 removed outlier: 4.977A pdb=" N GLY B 465 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 470 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 188 removed outlier: 3.524A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.755A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.970A pdb=" N ALA C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.191A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR C 292 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS C 294 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 298 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 410 removed outlier: 4.348A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 430 removed outlier: 3.891A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 478 removed outlier: 4.288A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 168 Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.668A pdb=" N SER D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 213 through 232 removed outlier: 4.162A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 258 Processing helix chain 'D' and resid 271 through 279 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 306 through 313 removed outlier: 3.829A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 351 through 377 Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 384 through 400 Processing helix chain 'D' and resid 407 through 411 removed outlier: 3.910A pdb=" N THR D 411 " --> pdb=" O GLU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 449 through 458 removed outlier: 4.790A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 116 through 118 No H-bonds generated for 'chain 'E' and resid 116 through 118' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 169 removed outlier: 3.791A pdb=" N MET E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU E 169 " --> pdb=" O ASN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 232 removed outlier: 4.611A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 258 removed outlier: 4.193A pdb=" N ALA E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.599A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 306 through 314 removed outlier: 4.157A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N HIS E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 removed outlier: 3.546A pdb=" N LEU E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 369 removed outlier: 7.087A pdb=" N GLN E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N GLU E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS E 353 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 357 " --> pdb=" O HIS E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 377 Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 386 through 399 Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 420 through 432 removed outlier: 4.735A pdb=" N ARG E 425 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 443 Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 155 through 168 removed outlier: 3.630A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 213 through 232 removed outlier: 4.644A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 258 removed outlier: 3.910A pdb=" N LEU F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 271 through 281 removed outlier: 4.421A pdb=" N ARG F 281 " --> pdb=" O VAL F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 306 through 314 removed outlier: 4.249A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 327 Processing helix chain 'F' and resid 346 through 349 No H-bonds generated for 'chain 'F' and resid 346 through 349' Processing helix chain 'F' and resid 351 through 377 removed outlier: 4.001A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 400 Processing helix chain 'F' and resid 407 through 411 Processing helix chain 'F' and resid 420 through 431 Processing helix chain 'F' and resid 440 through 443 Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'G' and resid 3 through 56 removed outlier: 3.735A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 90 through 108 removed outlier: 3.594A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 4.851A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 199 through 201 No H-bonds generated for 'chain 'G' and resid 199 through 201' Processing helix chain 'G' and resid 211 through 282 removed outlier: 3.822A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 102 Processing helix chain 'I' and resid 4 through 41 removed outlier: 3.750A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 removed outlier: 3.622A pdb=" N ILE I 46 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Proline residue: I 47 - end of helix removed outlier: 4.358A pdb=" N ARG I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET I 57 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY I 58 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL I 60 " --> pdb=" O MET I 57 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP I 61 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 41 removed outlier: 4.001A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 76 removed outlier: 3.610A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 4 through 41 removed outlier: 3.695A pdb=" N LEU L 8 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR L 10 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL L 15 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA L 20 " --> pdb=" O MET L 17 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA L 24 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE L 26 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE L 28 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY L 33 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.787A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 4.257A pdb=" N ARG L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA L 62 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.656A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 77 removed outlier: 3.739A pdb=" N THR M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE M 54 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.977A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 removed outlier: 3.613A pdb=" N ILE N 46 " --> pdb=" O PRO N 43 " (cutoff:3.500A) Proline residue: N 47 - end of helix removed outlier: 4.183A pdb=" N ARG N 50 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET N 57 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'O' and resid 5 through 41 removed outlier: 3.507A pdb=" N LEU O 19 " --> pdb=" O MET O 16 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY O 27 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE O 28 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY O 32 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA O 40 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 60 removed outlier: 3.876A pdb=" N ILE O 46 " --> pdb=" O PRO O 43 " (cutoff:3.500A) Proline residue: O 47 - end of helix removed outlier: 4.223A pdb=" N ARG O 50 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE O 53 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL O 56 " --> pdb=" O PHE O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 Processing helix chain 'P' and resid 6 through 41 removed outlier: 3.871A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 76 removed outlier: 4.040A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.851A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.781A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 4.370A pdb=" N ARG Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE Q 54 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET Q 57 " --> pdb=" O PHE Q 54 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.824A pdb=" N ALA Q 67 " --> pdb=" O PRO Q 64 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE Q 76 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.628A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 75 removed outlier: 4.046A pdb=" N ILE R 46 " --> pdb=" O PRO R 43 " (cutoff:3.500A) Proline residue: R 47 - end of helix removed outlier: 4.006A pdb=" N ARG R 50 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP R 61 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE R 63 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'S' and resid 6 through 41 removed outlier: 4.593A pdb=" N TYR S 10 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL S 15 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU S 19 " --> pdb=" O MET S 16 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA S 20 " --> pdb=" O MET S 17 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA S 24 " --> pdb=" O ALA S 21 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE S 26 " --> pdb=" O GLY S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 Proline residue: S 47 - end of helix removed outlier: 3.678A pdb=" N PHE S 54 " --> pdb=" O THR S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 77 Processing helix chain 'W' and resid 7 through 20 Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.628A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.578A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU W 46 " --> pdb=" O GLN W 42 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 63 Processing helix chain 'W' and resid 72 through 82 Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix removed outlier: 4.262A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 131 Processing helix chain 'W' and resid 144 through 146 No H-bonds generated for 'chain 'W' and resid 144 through 146' Processing helix chain 'W' and resid 163 through 173 removed outlier: 4.069A pdb=" N ASP W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL W 173 " --> pdb=" O ARG W 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 22 removed outlier: 3.816A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 135 removed outlier: 3.678A pdb=" N ILE X 40 " --> pdb=" O ARG X 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA X 59 " --> pdb=" O ASP X 55 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 146 through 155 Processing helix chain 'Y' and resid 3 through 24 removed outlier: 3.597A pdb=" N TYR Y 24 " --> pdb=" O ALA Y 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 27 through 37 Processing helix chain 'Y' and resid 40 through 140 removed outlier: 3.947A pdb=" N ALA Y 103 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG Y 138 " --> pdb=" O LYS Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 143 through 155 Processing helix chain 'a' and resid 8 through 15 removed outlier: 3.639A pdb=" N HIS a 14 " --> pdb=" O ASP a 10 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS a 15 " --> pdb=" O TYR a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 66 removed outlier: 3.509A pdb=" N LYS a 66 " --> pdb=" O SER a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 93 removed outlier: 3.606A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP a 92 " --> pdb=" O GLY a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 120 removed outlier: 3.557A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 131 Proline residue: a 127 - end of helix Processing helix chain 'a' and resid 143 through 145 No H-bonds generated for 'chain 'a' and resid 143 through 145' Processing helix chain 'a' and resid 147 through 180 removed outlier: 7.470A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS a 176 " --> pdb=" O GLY a 172 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 228 removed outlier: 3.613A pdb=" N ILE a 189 " --> pdb=" O TRP a 186 " (cutoff:3.500A) Proline residue: a 190 - end of helix removed outlier: 3.701A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY a 197 " --> pdb=" O ILE a 194 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 4.237A pdb=" N LEU a 228 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 3.785A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.875A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.396A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.751A pdb=" N GLY A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 106 through 109 removed outlier: 3.630A pdb=" N ARG A 106 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL A 224 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.514A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.562A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ARG B 93 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR B 91 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= G, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.741A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL B 224 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 327 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.484A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.508A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.431A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ILE C 222 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL C 224 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP C 255 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE C 194 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE C 198 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP C 261 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.676A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.494A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.706A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.587A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 3 through 9 removed outlier: 6.731A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP E 27 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N HIS E 73 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU E 30 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU E 71 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLN E 32 " --> pdb=" O LYS E 69 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N LYS E 69 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.572A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 317 through 320 removed outlier: 8.048A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLY E 149 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL E 296 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 3 through 9 removed outlier: 6.671A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE F 50 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA F 28 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 76 through 78 Processing sheet with id= U, first strand: chain 'F' and resid 317 through 320 removed outlier: 8.392A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL F 296 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 181 through 188 removed outlier: 6.786A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 41 through 45 removed outlier: 3.526A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA H 80 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL H 9 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER H 10 " --> pdb=" O GLN H 14 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLN H 14 " --> pdb=" O SER H 10 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 23 through 26 Processing sheet with id= Y, first strand: chain 'W' and resid 135 through 142 2032 hydrogen bonds defined for protein. 5037 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: 14.24 Time building geometry restraints manager: 15.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6791 1.32 - 1.45: 8377 1.45 - 1.57: 21745 1.57 - 1.69: 25 1.69 - 1.82: 356 Bond restraints: 37294 Sorted by residual: bond pdb=" C PRO E 138 " pdb=" O PRO E 138 " ideal model delta sigma weight residual 1.233 1.202 0.031 1.16e-02 7.43e+03 7.10e+00 bond pdb=" N ARG D 24 " pdb=" CA ARG D 24 " ideal model delta sigma weight residual 1.453 1.487 -0.035 1.31e-02 5.83e+03 7.01e+00 bond pdb=" CA ALA E 137 " pdb=" CB ALA E 137 " ideal model delta sigma weight residual 1.530 1.496 0.034 1.32e-02 5.74e+03 6.52e+00 bond pdb=" N ILE E 130 " pdb=" CA ILE E 130 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.25e-02 6.40e+03 5.95e+00 bond pdb=" N SER E 419 " pdb=" CA SER E 419 " ideal model delta sigma weight residual 1.453 1.482 -0.030 1.31e-02 5.83e+03 5.08e+00 ... (remaining 37289 not shown) Histogram of bond angle deviations from ideal: 98.58 - 107.03: 1085 107.03 - 115.49: 22860 115.49 - 123.94: 25787 123.94 - 132.40: 719 132.40 - 140.85: 34 Bond angle restraints: 50485 Sorted by residual: angle pdb=" C LYS E 131 " pdb=" CA LYS E 131 " pdb=" CB LYS E 131 " ideal model delta sigma weight residual 110.88 100.86 10.02 1.57e+00 4.06e-01 4.07e+01 angle pdb=" C ALA O 62 " pdb=" N ILE O 63 " pdb=" CA ILE O 63 " ideal model delta sigma weight residual 120.24 123.20 -2.96 6.30e-01 2.52e+00 2.21e+01 angle pdb=" N LEU a 125 " pdb=" CA LEU a 125 " pdb=" C LEU a 125 " ideal model delta sigma weight residual 110.97 115.29 -4.32 1.09e+00 8.42e-01 1.57e+01 angle pdb=" CA ILE Q 63 " pdb=" CB ILE Q 63 " pdb=" CG2 ILE Q 63 " ideal model delta sigma weight residual 110.50 116.96 -6.46 1.70e+00 3.46e-01 1.45e+01 angle pdb=" C1' ADP F 500 " pdb=" C2' ADP F 500 " pdb=" C3' ADP F 500 " ideal model delta sigma weight residual 111.00 99.98 11.02 3.00e+00 1.11e-01 1.35e+01 ... (remaining 50480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.68: 22006 30.68 - 61.37: 567 61.37 - 92.05: 89 92.05 - 122.73: 2 122.73 - 153.42: 2 Dihedral angle restraints: 22666 sinusoidal: 8977 harmonic: 13689 Sorted by residual: dihedral pdb=" C5' ADP F 500 " pdb=" O5' ADP F 500 " pdb=" PA ADP F 500 " pdb=" O2A ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 146.59 153.42 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 167.56 132.44 1 2.00e+01 2.50e-03 4.02e+01 dihedral pdb=" O1B ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PB ADP D 500 " pdb=" PA ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 -173.19 113.18 1 2.00e+01 2.50e-03 3.34e+01 ... (remaining 22663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 5799 0.142 - 0.284: 77 0.284 - 0.426: 4 0.426 - 0.567: 0 0.567 - 0.709: 1 Chirality restraints: 5881 Sorted by residual: chirality pdb=" CB ILE Q 63 " pdb=" CA ILE Q 63 " pdb=" CG1 ILE Q 63 " pdb=" CG2 ILE Q 63 " both_signs ideal model delta sigma weight residual False 2.64 1.94 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA THR E 128 " pdb=" N THR E 128 " pdb=" C THR E 128 " pdb=" CB THR E 128 " both_signs ideal model delta sigma weight residual False 2.53 2.88 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA LYS E 131 " pdb=" N LYS E 131 " pdb=" C LYS E 131 " pdb=" CB LYS E 131 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 5878 not shown) Planarity restraints: 6510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 207 " -0.003 2.00e-02 2.50e+03 2.77e-02 1.53e+01 pdb=" CG TYR G 207 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR G 207 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR G 207 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR G 207 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR G 207 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR G 207 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR G 207 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 203 " 0.029 2.00e-02 2.50e+03 2.47e-02 1.52e+01 pdb=" CG TRP G 203 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP G 203 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP G 203 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP G 203 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 203 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP G 203 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 203 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 203 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP G 203 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 195 " 0.008 2.00e-02 2.50e+03 2.43e-02 1.18e+01 pdb=" CG TYR B 195 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR B 195 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR B 195 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 195 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR B 195 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 195 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR B 195 " 0.038 2.00e-02 2.50e+03 ... (remaining 6507 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 48 2.51 - 3.11: 28200 3.11 - 3.70: 54937 3.70 - 4.30: 81617 4.30 - 4.90: 133741 Nonbonded interactions: 298543 Sorted by model distance: nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.911 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 1.945 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.962 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.964 2.170 nonbonded pdb=" O2G ATP E 500 " pdb="MG MG E 501 " model vdw 2.083 2.170 ... (remaining 298538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 408 or resid 410 through 513 or resid 600 throug \ h 601)) selection = (chain 'B' and (resid 2 through 408 or resid 410 through 513 or resid 600 throug \ h 601)) selection = (chain 'C' and (resid 2 through 408 or resid 410 through 513 or resid 600 throug \ h 601)) } ncs_group { reference = (chain 'D' and resid 2 through 459) selection = (chain 'E' and resid 2 through 459) selection = (chain 'F' and resid 2 through 459) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = chain 'Y' } 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: 4.670 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: 0.040 Extract box with map and model: 11.760 Check model and map are aligned: 0.570 Set scattering table: 0.360 Process input model: 94.700 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.005 0.076 37294 Z= 0.302 Angle : 0.889 11.281 50485 Z= 0.492 Chirality : 0.053 0.709 5881 Planarity : 0.010 0.113 6510 Dihedral : 14.273 153.417 13910 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.63 % Favored : 98.35 % Rotamer: Outliers : 1.26 % Allowed : 6.51 % Favored : 92.24 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.03 % 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: -0.19 (0.11), residues: 4775 helix: 0.22 (0.09), residues: 2582 sheet: 0.15 (0.22), residues: 475 loop : -0.52 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP G 203 HIS 0.008 0.002 HIS W 21 PHE 0.026 0.003 PHE a 38 TYR 0.042 0.007 TYR G 207 ARG 0.030 0.004 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 658 time to evaluate : 4.129 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: A 198 ILE cc_start: 0.8937 (mp) cc_final: 0.8537 (mm) REVERT: A 258 ILE cc_start: 0.9124 (tt) cc_final: 0.8805 (tt) REVERT: C 95 LEU cc_start: 0.8904 (tp) cc_final: 0.8615 (tp) REVERT: C 417 THR cc_start: 0.9027 (m) cc_final: 0.8823 (p) REVERT: D 189 PHE cc_start: 0.8829 (t80) cc_final: 0.8383 (t80) REVERT: D 379 MET cc_start: 0.7500 (tpt) cc_final: 0.7082 (tpt) REVERT: D 382 LEU cc_start: 0.8399 (mt) cc_final: 0.7759 (mt) REVERT: D 445 MET cc_start: 0.8770 (mmm) cc_final: 0.8078 (mmm) REVERT: E 136 MET cc_start: 0.9040 (mmm) cc_final: 0.8645 (mmm) REVERT: E 139 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7354 (p90) REVERT: E 209 MET cc_start: 0.8931 (ptp) cc_final: 0.8562 (ptp) REVERT: F 79 VAL cc_start: 0.8351 (m) cc_final: 0.8050 (m) REVERT: F 159 MET cc_start: 0.8607 (mtp) cc_final: 0.8164 (tmm) REVERT: F 254 VAL cc_start: 0.9063 (t) cc_final: 0.8839 (p) REVERT: F 342 ARG cc_start: 0.7921 (mtt-85) cc_final: 0.7718 (tpp-160) REVERT: F 379 MET cc_start: 0.9035 (mtp) cc_final: 0.8431 (tpp) REVERT: F 397 GLN cc_start: 0.8956 (tt0) cc_final: 0.8353 (tm-30) REVERT: G 31 MET cc_start: 0.7653 (ttp) cc_final: 0.6717 (tmm) REVERT: G 32 ARG cc_start: 0.8232 (mmt180) cc_final: 0.8016 (mmt180) REVERT: G 48 MET cc_start: 0.8834 (ttm) cc_final: 0.8493 (ttm) REVERT: G 102 MET cc_start: 0.8749 (ttp) cc_final: 0.7982 (ptm) REVERT: H 8 VAL cc_start: 0.8795 (t) cc_final: 0.7749 (p) REVERT: H 61 PHE cc_start: 0.7931 (m-80) cc_final: 0.7617 (m-10) REVERT: I 16 MET cc_start: 0.7541 (ttm) cc_final: 0.6621 (tpt) REVERT: I 53 PHE cc_start: 0.6100 (t80) cc_final: 0.5582 (t80) REVERT: I 54 PHE cc_start: 0.5537 (m-10) cc_final: 0.5166 (t80) REVERT: J 6 MET cc_start: 0.6977 (mtp) cc_final: 0.6733 (pmm) REVERT: J 15 VAL cc_start: 0.7950 (t) cc_final: 0.7710 (p) REVERT: J 16 MET cc_start: 0.6554 (ttt) cc_final: 0.6152 (tpt) REVERT: J 22 ILE cc_start: 0.6836 (mm) cc_final: 0.6606 (mm) REVERT: L 26 ILE cc_start: 0.8569 (mt) cc_final: 0.8328 (mp) REVERT: L 49 LEU cc_start: 0.8490 (mt) cc_final: 0.8262 (mt) REVERT: L 57 MET cc_start: 0.7724 (tmm) cc_final: 0.6264 (ptm) REVERT: M 53 PHE cc_start: 0.8332 (t80) cc_final: 0.7771 (t80) REVERT: M 65 MET cc_start: 0.6298 (mtp) cc_final: 0.5767 (mmt) REVERT: N 31 LEU cc_start: 0.6701 (tp) cc_final: 0.6214 (mt) REVERT: O 6 MET cc_start: 0.5746 (ttm) cc_final: 0.5371 (pmm) REVERT: P 11 MET cc_start: 0.8422 (tpp) cc_final: 0.8025 (mtp) REVERT: Q 63 ILE cc_start: 0.7590 (tt) cc_final: 0.7163 (tt) REVERT: Q 76 PHE cc_start: 0.6962 (m-80) cc_final: 0.6317 (t80) REVERT: R 6 MET cc_start: 0.5805 (mmt) cc_final: 0.5403 (ttm) REVERT: R 68 VAL cc_start: 0.6051 (t) cc_final: 0.5709 (m) REVERT: S 6 MET cc_start: 0.6404 (mmt) cc_final: 0.6118 (pmm) REVERT: S 75 MET cc_start: 0.5173 (ttt) cc_final: 0.4874 (tpt) REVERT: X 49 ARG cc_start: 0.8437 (mtt180) cc_final: 0.8134 (tpt90) REVERT: X 64 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7793 (mm110) REVERT: Y 62 THR cc_start: 0.5997 (m) cc_final: 0.5746 (p) REVERT: Y 99 THR cc_start: 0.8693 (p) cc_final: 0.8481 (p) REVERT: a 46 MET cc_start: 0.2038 (mmm) cc_final: 0.1712 (mtp) outliers start: 48 outliers final: 9 residues processed: 699 average time/residue: 0.4950 time to fit residues: 549.3983 Evaluate side-chains 374 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 364 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain a residue 193 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 397 optimal weight: 7.9990 chunk 356 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 369 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 224 optimal weight: 2.9990 chunk 274 optimal weight: 10.0000 chunk 427 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 HIS ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 HIS B 294 HIS C 147 GLN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN E 294 GLN E 353 HIS E 437 HIS ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN L 3 ASN M 52 GLN ** O 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 10 GLN ** Y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 37294 Z= 0.300 Angle : 0.714 12.268 50485 Z= 0.372 Chirality : 0.045 0.440 5881 Planarity : 0.006 0.059 6510 Dihedral : 7.414 131.586 5344 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.74 % Favored : 98.24 % Rotamer: Outliers : 2.39 % Allowed : 11.20 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 (0.12), residues: 4775 helix: 0.56 (0.10), residues: 2588 sheet: 0.23 (0.20), residues: 549 loop : -0.43 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 203 HIS 0.013 0.001 HIS X 51 PHE 0.026 0.002 PHE Q 53 TYR 0.017 0.002 TYR C 400 ARG 0.012 0.001 ARG X 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 375 time to evaluate : 4.494 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: A 156 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8242 (mtp) REVERT: B 148 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8453 (t) REVERT: B 245 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8357 (mpp) REVERT: B 414 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8018 (p0) REVERT: D 209 MET cc_start: 0.9030 (mtm) cc_final: 0.8634 (mtm) REVERT: D 379 MET cc_start: 0.7865 (tpt) cc_final: 0.7260 (tpt) REVERT: D 382 LEU cc_start: 0.8581 (mt) cc_final: 0.8053 (mt) REVERT: D 445 MET cc_start: 0.8858 (mmm) cc_final: 0.8124 (mmm) REVERT: F 79 VAL cc_start: 0.8479 (m) cc_final: 0.7807 (m) REVERT: F 159 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8414 (tmm) REVERT: F 342 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.8026 (tpp-160) REVERT: F 379 MET cc_start: 0.9074 (mtp) cc_final: 0.8576 (tpp) REVERT: F 397 GLN cc_start: 0.8946 (tt0) cc_final: 0.8472 (tm-30) REVERT: F 431 MET cc_start: 0.8406 (mtp) cc_final: 0.7293 (ptp) REVERT: G 48 MET cc_start: 0.8831 (ttm) cc_final: 0.8516 (ttm) REVERT: G 102 MET cc_start: 0.8745 (ttp) cc_final: 0.7946 (tmm) REVERT: H 61 PHE cc_start: 0.7881 (m-80) cc_final: 0.7631 (m-10) REVERT: I 10 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7383 (m-80) REVERT: I 16 MET cc_start: 0.7335 (ttm) cc_final: 0.6939 (tpt) REVERT: I 54 PHE cc_start: 0.5808 (m-10) cc_final: 0.5467 (t80) REVERT: I 75 MET cc_start: 0.4009 (mmm) cc_final: 0.3573 (mmm) REVERT: J 16 MET cc_start: 0.6120 (ttt) cc_final: 0.5192 (ttt) REVERT: J 17 MET cc_start: 0.8357 (ptp) cc_final: 0.7836 (mpp) REVERT: L 11 MET cc_start: 0.8180 (mtp) cc_final: 0.6675 (tpt) REVERT: L 16 MET cc_start: 0.4963 (mmm) cc_final: 0.4423 (mmm) REVERT: L 49 LEU cc_start: 0.8600 (mt) cc_final: 0.8239 (tt) REVERT: L 53 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7952 (t80) REVERT: M 65 MET cc_start: 0.6265 (mtp) cc_final: 0.5855 (mmp) REVERT: M 68 VAL cc_start: 0.7066 (t) cc_final: 0.6287 (p) REVERT: N 16 MET cc_start: 0.3140 (tpp) cc_final: 0.2850 (tpp) REVERT: O 6 MET cc_start: 0.6638 (ttm) cc_final: 0.5726 (pmm) REVERT: P 11 MET cc_start: 0.8229 (tpp) cc_final: 0.7901 (mtp) REVERT: P 16 MET cc_start: 0.5445 (mtt) cc_final: 0.4995 (mtt) REVERT: R 6 MET cc_start: 0.5873 (mmt) cc_final: 0.5402 (ttm) REVERT: R 16 MET cc_start: 0.7053 (tpp) cc_final: 0.6498 (tmm) REVERT: S 6 MET cc_start: 0.6481 (mmt) cc_final: 0.6144 (pmm) REVERT: S 57 MET cc_start: 0.8431 (tmt) cc_final: 0.8183 (tpt) REVERT: S 75 MET cc_start: 0.5538 (ttt) cc_final: 0.5067 (tpp) REVERT: W 12 LYS cc_start: 0.9466 (ttmm) cc_final: 0.9186 (ttpp) REVERT: X 49 ARG cc_start: 0.8593 (mtt180) cc_final: 0.8168 (tpt90) REVERT: X 64 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7917 (mm-40) REVERT: X 83 ARG cc_start: 0.8495 (ttp80) cc_final: 0.8260 (ttp-110) REVERT: a 115 MET cc_start: 0.6112 (ttp) cc_final: 0.5666 (ttp) REVERT: a 155 LEU cc_start: 0.7332 (mt) cc_final: 0.7094 (pp) REVERT: a 257 MET cc_start: 0.6866 (tmm) cc_final: 0.6372 (ppp) outliers start: 91 outliers final: 41 residues processed: 436 average time/residue: 0.4822 time to fit residues: 349.3628 Evaluate side-chains 355 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 307 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 53 PHE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 194 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 237 optimal weight: 0.0870 chunk 132 optimal weight: 10.0000 chunk 355 optimal weight: 10.0000 chunk 291 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 428 optimal weight: 20.0000 chunk 462 optimal weight: 3.9990 chunk 381 optimal weight: 8.9990 chunk 424 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 343 optimal weight: 5.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 GLN B 511 GLN C 420 GLN C 511 GLN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 HIS ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 ASN R 52 GLN ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 10 GLN Y 123 GLN ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 132 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 37294 Z= 0.262 Angle : 0.629 9.900 50485 Z= 0.330 Chirality : 0.043 0.243 5881 Planarity : 0.005 0.061 6510 Dihedral : 6.773 113.200 5332 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.09 % Favored : 97.88 % Rotamer: Outliers : 2.31 % Allowed : 13.04 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.49 (0.12), residues: 4775 helix: 0.93 (0.10), residues: 2500 sheet: 0.23 (0.21), residues: 546 loop : -0.40 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 111 HIS 0.007 0.001 HIS F 353 PHE 0.029 0.002 PHE J 54 TYR 0.015 0.001 TYR B 150 ARG 0.009 0.001 ARG H 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 320 time to evaluate : 4.102 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: A 48 MET cc_start: 0.8080 (ptp) cc_final: 0.7784 (ptp) REVERT: B 245 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8449 (mpp) REVERT: B 414 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7964 (p0) REVERT: D 197 ASN cc_start: 0.8363 (m110) cc_final: 0.8031 (t0) REVERT: D 209 MET cc_start: 0.9024 (mtm) cc_final: 0.8646 (mtm) REVERT: D 382 LEU cc_start: 0.8672 (mt) cc_final: 0.8443 (mt) REVERT: D 445 MET cc_start: 0.8876 (mmm) cc_final: 0.8195 (mmm) REVERT: E 139 PHE cc_start: 0.8628 (p90) cc_final: 0.8381 (p90) REVERT: F 56 MET cc_start: 0.9314 (mmm) cc_final: 0.8884 (mmm) REVERT: F 159 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8272 (tmm) REVERT: F 379 MET cc_start: 0.9102 (mtp) cc_final: 0.8445 (tpp) REVERT: F 397 GLN cc_start: 0.8960 (tt0) cc_final: 0.8464 (tm-30) REVERT: F 431 MET cc_start: 0.7842 (mtp) cc_final: 0.7630 (mtm) REVERT: F 445 MET cc_start: 0.6887 (mmp) cc_final: 0.6576 (mmm) REVERT: G 48 MET cc_start: 0.8949 (ttm) cc_final: 0.8466 (ttm) REVERT: G 78 LEU cc_start: 0.9175 (tp) cc_final: 0.8830 (tt) REVERT: G 102 MET cc_start: 0.8717 (ttp) cc_final: 0.7916 (tmm) REVERT: G 125 PHE cc_start: 0.8820 (m-80) cc_final: 0.8580 (m-80) REVERT: G 139 MET cc_start: 0.7231 (mpp) cc_final: 0.6888 (mpp) REVERT: H 61 PHE cc_start: 0.7965 (m-80) cc_final: 0.7732 (m-10) REVERT: I 10 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.7439 (m-80) REVERT: I 22 ILE cc_start: 0.7272 (mp) cc_final: 0.6999 (mt) REVERT: I 45 LEU cc_start: 0.6664 (tp) cc_final: 0.6183 (mm) REVERT: I 53 PHE cc_start: 0.6091 (t80) cc_final: 0.5733 (t80) REVERT: I 54 PHE cc_start: 0.5851 (m-10) cc_final: 0.5565 (t80) REVERT: I 75 MET cc_start: 0.3699 (mmm) cc_final: 0.3414 (mmm) REVERT: J 11 MET cc_start: 0.5627 (mmm) cc_final: 0.4797 (tpp) REVERT: J 16 MET cc_start: 0.5769 (ttt) cc_final: 0.5187 (ttt) REVERT: J 17 MET cc_start: 0.8423 (ptp) cc_final: 0.7760 (mpp) REVERT: L 11 MET cc_start: 0.8240 (mtp) cc_final: 0.6877 (tpt) REVERT: L 49 LEU cc_start: 0.8548 (mt) cc_final: 0.8148 (tt) REVERT: M 35 PHE cc_start: 0.6769 (t80) cc_final: 0.6335 (t80) REVERT: M 55 ILE cc_start: 0.8485 (mm) cc_final: 0.8155 (pt) REVERT: M 65 MET cc_start: 0.6307 (mtp) cc_final: 0.5823 (mmp) REVERT: M 68 VAL cc_start: 0.6767 (t) cc_final: 0.6421 (p) REVERT: N 11 MET cc_start: 0.7320 (mmm) cc_final: 0.7063 (mmm) REVERT: O 6 MET cc_start: 0.6669 (ttm) cc_final: 0.5696 (pmm) REVERT: P 11 MET cc_start: 0.8212 (tpp) cc_final: 0.7835 (mtp) REVERT: R 6 MET cc_start: 0.6207 (mmt) cc_final: 0.5740 (ttm) REVERT: S 17 MET cc_start: 0.8351 (ppp) cc_final: 0.7822 (mpp) REVERT: S 57 MET cc_start: 0.8396 (tmt) cc_final: 0.8169 (tpt) REVERT: S 75 MET cc_start: 0.5746 (ttt) cc_final: 0.5402 (tpp) REVERT: W 12 LYS cc_start: 0.9457 (ttmm) cc_final: 0.9135 (ttpp) REVERT: X 49 ARG cc_start: 0.8603 (mtt180) cc_final: 0.8162 (tpt90) REVERT: Y 98 ARG cc_start: 0.8353 (ptp-110) cc_final: 0.8001 (ptp90) REVERT: a 140 ARG cc_start: 0.6326 (ptm160) cc_final: 0.6077 (tpp-160) REVERT: a 155 LEU cc_start: 0.7504 (mt) cc_final: 0.6946 (tt) outliers start: 88 outliers final: 36 residues processed: 388 average time/residue: 0.4492 time to fit residues: 290.9932 Evaluate side-chains 333 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 293 time to evaluate : 4.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 89 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 423 optimal weight: 9.9990 chunk 322 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 287 optimal weight: 5.9990 chunk 430 optimal weight: 4.9990 chunk 455 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 407 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN G 226 GLN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN O 52 GLN R 5 ASN S 42 GLN W 71 ASN ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 214 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 37294 Z= 0.294 Angle : 0.644 14.818 50485 Z= 0.333 Chirality : 0.043 0.319 5881 Planarity : 0.005 0.064 6510 Dihedral : 6.558 104.621 5331 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 2.99 % Allowed : 13.54 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.51 (0.12), residues: 4775 helix: 0.98 (0.10), residues: 2479 sheet: 0.29 (0.21), residues: 539 loop : -0.44 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP a 111 HIS 0.005 0.001 HIS B 215 PHE 0.038 0.002 PHE Q 53 TYR 0.026 0.001 TYR S 73 ARG 0.012 0.001 ARG F 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 292 time to evaluate : 4.097 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: A 12 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8509 (mp) REVERT: A 48 MET cc_start: 0.8229 (ptp) cc_final: 0.7942 (ptp) REVERT: A 483 MET cc_start: 0.8568 (ppp) cc_final: 0.8359 (ppp) REVERT: B 245 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8218 (mpt) REVERT: C 95 LEU cc_start: 0.9064 (tp) cc_final: 0.8831 (tp) REVERT: C 161 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8388 (mtt90) REVERT: D 209 MET cc_start: 0.8969 (mtm) cc_final: 0.8594 (mtm) REVERT: D 445 MET cc_start: 0.8899 (mmm) cc_final: 0.8239 (mmm) REVERT: F 56 MET cc_start: 0.9305 (mmm) cc_final: 0.8794 (mmm) REVERT: F 159 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8336 (tmm) REVERT: F 366 ARG cc_start: 0.8935 (tpt170) cc_final: 0.8370 (mmm160) REVERT: F 379 MET cc_start: 0.9127 (mtp) cc_final: 0.8359 (tpp) REVERT: F 397 GLN cc_start: 0.8925 (tt0) cc_final: 0.8467 (tm-30) REVERT: F 445 MET cc_start: 0.7011 (mmp) cc_final: 0.6699 (mmm) REVERT: G 48 MET cc_start: 0.8992 (ttm) cc_final: 0.8440 (ttm) REVERT: G 78 LEU cc_start: 0.9132 (tp) cc_final: 0.8820 (tt) REVERT: G 102 MET cc_start: 0.8760 (ttp) cc_final: 0.8038 (tmm) REVERT: H 49 MET cc_start: 0.7693 (tpp) cc_final: 0.7490 (tpp) REVERT: H 81 ASP cc_start: 0.7902 (t70) cc_final: 0.7070 (p0) REVERT: I 10 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: I 54 PHE cc_start: 0.6022 (m-10) cc_final: 0.5541 (t80) REVERT: J 11 MET cc_start: 0.5757 (mmm) cc_final: 0.5177 (tpp) REVERT: J 16 MET cc_start: 0.6551 (ttt) cc_final: 0.6197 (ttm) REVERT: J 17 MET cc_start: 0.8092 (ptp) cc_final: 0.7785 (mtm) REVERT: L 19 LEU cc_start: 0.8258 (tp) cc_final: 0.7996 (mt) REVERT: M 55 ILE cc_start: 0.8613 (mm) cc_final: 0.8379 (pt) REVERT: N 11 MET cc_start: 0.7214 (mmm) cc_final: 0.6950 (mmm) REVERT: O 6 MET cc_start: 0.6767 (ttm) cc_final: 0.6128 (pmm) REVERT: P 11 MET cc_start: 0.8402 (tpp) cc_final: 0.8045 (mtt) REVERT: P 57 MET cc_start: 0.4911 (ppp) cc_final: 0.3913 (ttm) REVERT: R 6 MET cc_start: 0.5972 (mmt) cc_final: 0.5433 (ttm) REVERT: R 16 MET cc_start: 0.6538 (tpp) cc_final: 0.5926 (tmm) REVERT: R 57 MET cc_start: 0.7437 (mmm) cc_final: 0.7173 (mmm) REVERT: S 16 MET cc_start: 0.7984 (tpt) cc_final: 0.7219 (tpp) REVERT: S 17 MET cc_start: 0.8354 (ppp) cc_final: 0.6945 (mpp) REVERT: S 28 ILE cc_start: 0.5861 (pt) cc_final: 0.5267 (pt) REVERT: S 57 MET cc_start: 0.8294 (tmt) cc_final: 0.8040 (tpt) REVERT: S 75 MET cc_start: 0.5734 (ttt) cc_final: 0.5338 (tpp) REVERT: W 12 LYS cc_start: 0.9470 (ttmm) cc_final: 0.9041 (ttpp) REVERT: X 49 ARG cc_start: 0.8642 (mtt180) cc_final: 0.8178 (tpt90) REVERT: a 60 PHE cc_start: 0.7280 (m-80) cc_final: 0.7016 (m-80) REVERT: a 257 MET cc_start: 0.6934 (tmm) cc_final: 0.6665 (tmm) outliers start: 114 outliers final: 61 residues processed: 389 average time/residue: 0.4477 time to fit residues: 292.2880 Evaluate side-chains 340 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 274 time to evaluate : 4.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 74 LYS Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 149 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 379 optimal weight: 6.9990 chunk 258 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 338 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 388 optimal weight: 0.0770 chunk 314 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 232 optimal weight: 3.9990 chunk 408 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN F 343 GLN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37294 Z= 0.194 Angle : 0.591 12.563 50485 Z= 0.302 Chirality : 0.041 0.241 5881 Planarity : 0.004 0.064 6510 Dihedral : 6.290 102.326 5331 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.07 % Allowed : 15.08 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.67 (0.12), residues: 4775 helix: 1.13 (0.10), residues: 2461 sheet: 0.31 (0.21), residues: 532 loop : -0.36 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 111 HIS 0.004 0.001 HIS A 123 PHE 0.034 0.001 PHE J 54 TYR 0.014 0.001 TYR L 73 ARG 0.010 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 297 time to evaluate : 4.181 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: A 156 MET cc_start: 0.9443 (mmt) cc_final: 0.8979 (mmt) REVERT: A 483 MET cc_start: 0.8507 (ppp) cc_final: 0.8304 (ppp) REVERT: B 245 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8290 (mpt) REVERT: C 161 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8372 (mtt90) REVERT: D 209 MET cc_start: 0.8921 (mtm) cc_final: 0.8571 (mtm) REVERT: D 445 MET cc_start: 0.8869 (mmm) cc_final: 0.8180 (mmm) REVERT: F 56 MET cc_start: 0.9339 (mmm) cc_final: 0.8836 (mmm) REVERT: F 159 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8320 (tmm) REVERT: F 366 ARG cc_start: 0.9055 (tpt170) cc_final: 0.8232 (mmm160) REVERT: F 379 MET cc_start: 0.8977 (mtp) cc_final: 0.8173 (tpp) REVERT: F 397 GLN cc_start: 0.8912 (tt0) cc_final: 0.8412 (tm-30) REVERT: F 431 MET cc_start: 0.7843 (mtp) cc_final: 0.7518 (ptp) REVERT: F 445 MET cc_start: 0.6905 (mmp) cc_final: 0.6664 (mmm) REVERT: G 48 MET cc_start: 0.8981 (ttm) cc_final: 0.8440 (ttm) REVERT: G 78 LEU cc_start: 0.9118 (tp) cc_final: 0.8809 (tt) REVERT: G 102 MET cc_start: 0.8756 (ttp) cc_final: 0.8020 (tmm) REVERT: H 49 MET cc_start: 0.7821 (tpp) cc_final: 0.7597 (tpp) REVERT: H 81 ASP cc_start: 0.7799 (t70) cc_final: 0.6995 (p0) REVERT: I 10 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: I 45 LEU cc_start: 0.6704 (tp) cc_final: 0.6039 (mm) REVERT: I 54 PHE cc_start: 0.5884 (m-10) cc_final: 0.5442 (t80) REVERT: I 75 MET cc_start: 0.4256 (mmm) cc_final: 0.3940 (mmm) REVERT: J 11 MET cc_start: 0.6048 (mmm) cc_final: 0.5728 (tpp) REVERT: J 17 MET cc_start: 0.7987 (ptp) cc_final: 0.7716 (ptt) REVERT: L 8 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7830 (mm) REVERT: L 19 LEU cc_start: 0.8199 (tp) cc_final: 0.7799 (mt) REVERT: L 75 MET cc_start: 0.7594 (mmt) cc_final: 0.6883 (tpt) REVERT: M 55 ILE cc_start: 0.8555 (mm) cc_final: 0.8338 (pt) REVERT: M 64 PRO cc_start: 0.7268 (Cg_exo) cc_final: 0.6658 (Cg_endo) REVERT: M 65 MET cc_start: 0.5686 (mtp) cc_final: 0.5246 (mmt) REVERT: N 11 MET cc_start: 0.7189 (mmm) cc_final: 0.6774 (mmm) REVERT: N 16 MET cc_start: 0.3217 (tpp) cc_final: 0.2929 (tpp) REVERT: O 6 MET cc_start: 0.6576 (ttm) cc_final: 0.5995 (pmm) REVERT: P 11 MET cc_start: 0.8398 (tpp) cc_final: 0.8141 (mtt) REVERT: P 57 MET cc_start: 0.4833 (ppp) cc_final: 0.3874 (ttm) REVERT: P 63 ILE cc_start: -0.0210 (OUTLIER) cc_final: -0.0428 (mt) REVERT: R 6 MET cc_start: 0.6006 (mmt) cc_final: 0.5468 (ttm) REVERT: R 16 MET cc_start: 0.6500 (tpp) cc_final: 0.6253 (tmm) REVERT: S 17 MET cc_start: 0.8293 (ppp) cc_final: 0.7118 (ptm) REVERT: S 28 ILE cc_start: 0.6135 (pt) cc_final: 0.5448 (pt) REVERT: S 57 MET cc_start: 0.8182 (tmt) cc_final: 0.7909 (tpt) REVERT: S 75 MET cc_start: 0.5787 (ttt) cc_final: 0.5373 (tpp) REVERT: W 12 LYS cc_start: 0.9437 (ttmm) cc_final: 0.9012 (ttpp) REVERT: X 49 ARG cc_start: 0.8570 (mtt180) cc_final: 0.8088 (tpt90) REVERT: a 46 MET cc_start: 0.3522 (mmt) cc_final: 0.3268 (mmm) REVERT: a 60 PHE cc_start: 0.7250 (m-80) cc_final: 0.7014 (m-80) REVERT: a 93 MET cc_start: 0.8240 (ttt) cc_final: 0.7715 (tmm) REVERT: a 155 LEU cc_start: 0.7843 (mt) cc_final: 0.7440 (tt) REVERT: a 257 MET cc_start: 0.6894 (tmm) cc_final: 0.6565 (tmm) outliers start: 79 outliers final: 53 residues processed: 355 average time/residue: 0.4448 time to fit residues: 268.2516 Evaluate side-chains 338 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 279 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 449 ILE Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 74 LYS Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 209 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 153 optimal weight: 9.9990 chunk 409 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 chunk 267 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 455 optimal weight: 10.0000 chunk 378 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 150 optimal weight: 0.3980 chunk 239 optimal weight: 9.9990 overall best weight: 5.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 GLN C 333 GLN D 7 GLN D 32 GLN G 57 HIS ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 37294 Z= 0.320 Angle : 0.664 10.516 50485 Z= 0.340 Chirality : 0.042 0.233 5881 Planarity : 0.005 0.066 6510 Dihedral : 6.433 103.065 5331 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.04 % Allowed : 14.95 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.49 (0.12), residues: 4775 helix: 1.01 (0.10), residues: 2466 sheet: 0.30 (0.21), residues: 536 loop : -0.52 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a 39 HIS 0.006 0.001 HIS X 51 PHE 0.026 0.002 PHE A 406 TYR 0.022 0.002 TYR B 150 ARG 0.007 0.001 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 280 time to evaluate : 4.173 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: A 12 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8556 (mp) REVERT: A 156 MET cc_start: 0.9448 (mmt) cc_final: 0.8898 (mmt) REVERT: B 245 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8119 (mpt) REVERT: C 161 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8498 (mtt90) REVERT: D 193 MET cc_start: 0.8254 (mmm) cc_final: 0.8033 (mmm) REVERT: D 209 MET cc_start: 0.8951 (mtm) cc_final: 0.8693 (mtm) REVERT: D 445 MET cc_start: 0.8891 (mmm) cc_final: 0.8281 (mmt) REVERT: E 275 MET cc_start: 0.8121 (mmm) cc_final: 0.7888 (tpp) REVERT: F 56 MET cc_start: 0.9332 (mmm) cc_final: 0.9020 (mmm) REVERT: F 159 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8387 (tmm) REVERT: F 215 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8311 (m-40) REVERT: F 366 ARG cc_start: 0.9109 (tpt170) cc_final: 0.8381 (mmm160) REVERT: F 379 MET cc_start: 0.9079 (mtp) cc_final: 0.8086 (tpp) REVERT: F 397 GLN cc_start: 0.8868 (tt0) cc_final: 0.8316 (tm-30) REVERT: F 431 MET cc_start: 0.7909 (mtp) cc_final: 0.7611 (ptp) REVERT: G 48 MET cc_start: 0.9058 (ttm) cc_final: 0.8425 (ttm) REVERT: G 102 MET cc_start: 0.8808 (ttp) cc_final: 0.8135 (tmm) REVERT: G 116 MET cc_start: 0.8836 (mmp) cc_final: 0.8228 (mmp) REVERT: H 23 ILE cc_start: 0.9184 (tt) cc_final: 0.8945 (mp) REVERT: H 49 MET cc_start: 0.7928 (tpp) cc_final: 0.7587 (tpp) REVERT: I 10 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: I 45 LEU cc_start: 0.6902 (tp) cc_final: 0.6315 (mm) REVERT: I 54 PHE cc_start: 0.6271 (m-10) cc_final: 0.5486 (t80) REVERT: I 75 MET cc_start: 0.3984 (mmm) cc_final: 0.3620 (mmm) REVERT: J 16 MET cc_start: 0.5837 (ttt) cc_final: 0.5521 (ttt) REVERT: M 10 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8262 (t80) REVERT: M 55 ILE cc_start: 0.8637 (mm) cc_final: 0.8429 (pt) REVERT: N 11 MET cc_start: 0.7218 (mmm) cc_final: 0.6760 (mmm) REVERT: O 6 MET cc_start: 0.6444 (ttm) cc_final: 0.5866 (pmm) REVERT: O 26 ILE cc_start: 0.7450 (tp) cc_final: 0.7177 (pt) REVERT: P 11 MET cc_start: 0.8298 (tpp) cc_final: 0.7980 (mtt) REVERT: P 57 MET cc_start: 0.4589 (ppp) cc_final: 0.3702 (ttm) REVERT: R 6 MET cc_start: 0.6160 (mmt) cc_final: 0.5620 (ttm) REVERT: R 16 MET cc_start: 0.6503 (tpp) cc_final: 0.6108 (tmm) REVERT: S 17 MET cc_start: 0.8543 (ppp) cc_final: 0.7297 (ptm) REVERT: S 22 ILE cc_start: 0.6350 (mp) cc_final: 0.6079 (mp) REVERT: S 28 ILE cc_start: 0.6327 (pt) cc_final: 0.5712 (pt) REVERT: S 36 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7188 (mt) REVERT: S 57 MET cc_start: 0.8184 (tmt) cc_final: 0.7831 (tpt) REVERT: W 12 LYS cc_start: 0.9465 (ttmm) cc_final: 0.9035 (ttpp) REVERT: X 49 ARG cc_start: 0.8663 (mtt180) cc_final: 0.8203 (mmm160) REVERT: a 60 PHE cc_start: 0.7380 (m-80) cc_final: 0.7144 (m-80) REVERT: a 93 MET cc_start: 0.8327 (ttt) cc_final: 0.8086 (tmm) REVERT: a 155 LEU cc_start: 0.7955 (mt) cc_final: 0.7609 (tt) REVERT: a 257 MET cc_start: 0.7271 (tmm) cc_final: 0.6971 (tmm) outliers start: 116 outliers final: 75 residues processed: 377 average time/residue: 0.4304 time to fit residues: 276.9277 Evaluate side-chains 351 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 268 time to evaluate : 3.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 449 ILE Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 141 ASP Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 74 LYS Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 439 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 259 optimal weight: 3.9990 chunk 332 optimal weight: 3.9990 chunk 257 optimal weight: 0.8980 chunk 383 optimal weight: 8.9990 chunk 254 optimal weight: 10.0000 chunk 453 optimal weight: 0.5980 chunk 284 optimal weight: 1.9990 chunk 276 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 145 ASN ** a 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37294 Z= 0.187 Angle : 0.599 11.766 50485 Z= 0.302 Chirality : 0.041 0.226 5881 Planarity : 0.004 0.064 6510 Dihedral : 6.183 98.352 5331 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.39 % Allowed : 16.13 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 (0.12), residues: 4775 helix: 1.12 (0.10), residues: 2501 sheet: 0.32 (0.22), residues: 531 loop : -0.42 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 111 HIS 0.004 0.001 HIS a 245 PHE 0.040 0.001 PHE J 54 TYR 0.020 0.001 TYR a 94 ARG 0.012 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 283 time to evaluate : 3.852 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: A 12 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8512 (mp) REVERT: A 156 MET cc_start: 0.9448 (mmt) cc_final: 0.8903 (mmt) REVERT: B 110 THR cc_start: 0.9464 (OUTLIER) cc_final: 0.9197 (t) REVERT: B 245 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8196 (mpt) REVERT: D 88 MET cc_start: 0.8457 (mmm) cc_final: 0.8152 (mmm) REVERT: D 209 MET cc_start: 0.8966 (mtm) cc_final: 0.8734 (mtm) REVERT: D 445 MET cc_start: 0.8950 (mmm) cc_final: 0.8374 (mmt) REVERT: F 159 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8327 (tmm) REVERT: F 366 ARG cc_start: 0.9126 (tpt170) cc_final: 0.8401 (mmm160) REVERT: F 379 MET cc_start: 0.8985 (mtp) cc_final: 0.7961 (tpp) REVERT: F 397 GLN cc_start: 0.8879 (tt0) cc_final: 0.8337 (tm-30) REVERT: F 431 MET cc_start: 0.7952 (mtp) cc_final: 0.7653 (ptp) REVERT: F 445 MET cc_start: 0.7430 (mmp) cc_final: 0.7123 (mmm) REVERT: G 48 MET cc_start: 0.9027 (ttm) cc_final: 0.8402 (ttm) REVERT: G 78 LEU cc_start: 0.9158 (tp) cc_final: 0.8749 (tt) REVERT: G 102 MET cc_start: 0.8807 (ttp) cc_final: 0.8144 (tmm) REVERT: G 116 MET cc_start: 0.8796 (mmp) cc_final: 0.8540 (mmp) REVERT: G 125 PHE cc_start: 0.8812 (m-80) cc_final: 0.8526 (m-80) REVERT: H 23 ILE cc_start: 0.9213 (tt) cc_final: 0.8966 (mp) REVERT: I 10 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: I 45 LEU cc_start: 0.6851 (tp) cc_final: 0.6344 (mm) REVERT: I 54 PHE cc_start: 0.6283 (m-10) cc_final: 0.5511 (t80) REVERT: I 75 MET cc_start: 0.4077 (mmm) cc_final: 0.3821 (mmm) REVERT: J 17 MET cc_start: 0.7823 (ptt) cc_final: 0.7154 (ptp) REVERT: L 8 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7841 (mp) REVERT: L 57 MET cc_start: 0.7267 (tmm) cc_final: 0.5904 (ptt) REVERT: L 75 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6465 (tpt) REVERT: M 65 MET cc_start: 0.5252 (mtp) cc_final: 0.4808 (mmp) REVERT: N 11 MET cc_start: 0.7411 (mmm) cc_final: 0.7113 (mmm) REVERT: O 6 MET cc_start: 0.6496 (ttm) cc_final: 0.5978 (pmm) REVERT: P 11 MET cc_start: 0.8276 (tpp) cc_final: 0.7876 (mtp) REVERT: P 57 MET cc_start: 0.4573 (ppp) cc_final: 0.3668 (ttm) REVERT: R 6 MET cc_start: 0.6134 (mmt) cc_final: 0.5597 (ttm) REVERT: R 11 MET cc_start: 0.6480 (ppp) cc_final: 0.4341 (tpt) REVERT: R 16 MET cc_start: 0.6637 (tpp) cc_final: 0.6298 (tmm) REVERT: S 16 MET cc_start: 0.8061 (ttp) cc_final: 0.7714 (tmm) REVERT: S 17 MET cc_start: 0.8535 (ppp) cc_final: 0.7435 (ptm) REVERT: S 28 ILE cc_start: 0.6311 (pt) cc_final: 0.5660 (pt) REVERT: S 57 MET cc_start: 0.8220 (tmt) cc_final: 0.7851 (tpt) REVERT: S 75 MET cc_start: 0.4395 (tpt) cc_final: 0.4045 (tpt) REVERT: W 12 LYS cc_start: 0.9438 (ttmm) cc_final: 0.9009 (ttpp) REVERT: X 49 ARG cc_start: 0.8620 (mtt180) cc_final: 0.8128 (tpt90) REVERT: Y 26 TRP cc_start: 0.5547 (OUTLIER) cc_final: 0.5344 (m-10) REVERT: a 60 PHE cc_start: 0.7375 (m-80) cc_final: 0.7148 (m-80) REVERT: a 93 MET cc_start: 0.8328 (ttt) cc_final: 0.8013 (tmm) REVERT: a 94 TYR cc_start: 0.6045 (t80) cc_final: 0.5326 (t80) REVERT: a 155 LEU cc_start: 0.8138 (mt) cc_final: 0.7875 (tt) REVERT: a 257 MET cc_start: 0.7464 (tmm) cc_final: 0.7205 (tmm) outliers start: 91 outliers final: 58 residues processed: 356 average time/residue: 0.4310 time to fit residues: 261.4348 Evaluate side-chains 333 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 267 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 449 ILE Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 26 TRP Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 74 LYS Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 280 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 271 optimal weight: 0.8980 chunk 136 optimal weight: 0.3980 chunk 89 optimal weight: 10.0000 chunk 87 optimal weight: 0.0170 chunk 288 optimal weight: 3.9990 chunk 309 optimal weight: 0.0050 chunk 224 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 356 optimal weight: 9.9990 overall best weight: 1.0634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 GLN G 142 ASN ** O 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 37294 Z= 0.158 Angle : 0.599 11.375 50485 Z= 0.298 Chirality : 0.041 0.273 5881 Planarity : 0.004 0.063 6510 Dihedral : 5.913 92.282 5330 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.81 % Allowed : 16.97 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.74 (0.12), residues: 4775 helix: 1.20 (0.10), residues: 2499 sheet: 0.37 (0.22), residues: 542 loop : -0.41 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 107 HIS 0.005 0.001 HIS a 245 PHE 0.022 0.001 PHE M 35 TYR 0.018 0.001 TYR a 94 ARG 0.009 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 291 time to evaluate : 4.254 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: A 12 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8524 (mp) REVERT: A 156 MET cc_start: 0.9440 (mmt) cc_final: 0.8928 (mmt) REVERT: D 209 MET cc_start: 0.8898 (mtm) cc_final: 0.8645 (mtm) REVERT: D 445 MET cc_start: 0.8949 (mmm) cc_final: 0.8248 (mmm) REVERT: F 159 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8318 (tmm) REVERT: F 275 MET cc_start: 0.8437 (ptm) cc_final: 0.8208 (ptm) REVERT: F 366 ARG cc_start: 0.9118 (tpt170) cc_final: 0.8401 (mmm160) REVERT: F 379 MET cc_start: 0.8875 (mtp) cc_final: 0.7977 (tpp) REVERT: F 397 GLN cc_start: 0.8874 (tt0) cc_final: 0.8240 (tm-30) REVERT: F 411 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8741 (p) REVERT: F 431 MET cc_start: 0.7901 (mtp) cc_final: 0.7615 (ptp) REVERT: G 48 MET cc_start: 0.8956 (ttm) cc_final: 0.8244 (ttm) REVERT: G 78 LEU cc_start: 0.9153 (tp) cc_final: 0.8744 (tt) REVERT: G 102 MET cc_start: 0.8710 (ttp) cc_final: 0.8055 (tmm) REVERT: G 116 MET cc_start: 0.8800 (mmp) cc_final: 0.8538 (mmp) REVERT: G 125 PHE cc_start: 0.8778 (m-80) cc_final: 0.8505 (m-80) REVERT: H 49 MET cc_start: 0.7697 (tpp) cc_final: 0.7340 (tpp) REVERT: I 45 LEU cc_start: 0.6872 (tp) cc_final: 0.6353 (mm) REVERT: I 54 PHE cc_start: 0.6278 (m-10) cc_final: 0.5569 (t80) REVERT: J 16 MET cc_start: 0.5396 (ttt) cc_final: 0.5045 (ttt) REVERT: J 17 MET cc_start: 0.7598 (ptt) cc_final: 0.6834 (ptp) REVERT: L 8 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7961 (mp) REVERT: L 16 MET cc_start: 0.2762 (mmm) cc_final: 0.2231 (mmm) REVERT: L 57 MET cc_start: 0.7272 (tmm) cc_final: 0.5962 (ptt) REVERT: L 75 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6417 (tpt) REVERT: M 65 MET cc_start: 0.5222 (mtp) cc_final: 0.4863 (mmp) REVERT: N 11 MET cc_start: 0.7525 (mmm) cc_final: 0.7163 (mmm) REVERT: O 6 MET cc_start: 0.6424 (ttm) cc_final: 0.5996 (pmm) REVERT: P 11 MET cc_start: 0.8306 (tpp) cc_final: 0.7896 (mtp) REVERT: P 57 MET cc_start: 0.4574 (ppp) cc_final: 0.3630 (ttm) REVERT: R 6 MET cc_start: 0.6317 (mmt) cc_final: 0.5767 (ttm) REVERT: R 11 MET cc_start: 0.6318 (ppp) cc_final: 0.4285 (tpt) REVERT: R 16 MET cc_start: 0.6658 (tpp) cc_final: 0.6399 (tmm) REVERT: S 17 MET cc_start: 0.8646 (ppp) cc_final: 0.7801 (ptm) REVERT: S 57 MET cc_start: 0.8269 (tmt) cc_final: 0.7874 (tpt) REVERT: S 75 MET cc_start: 0.4396 (tpt) cc_final: 0.4103 (tpt) REVERT: W 12 LYS cc_start: 0.9428 (ttmm) cc_final: 0.9082 (ttpp) REVERT: W 147 MET cc_start: 0.8698 (mtm) cc_final: 0.8392 (mpp) REVERT: X 49 ARG cc_start: 0.8631 (mtt180) cc_final: 0.8154 (tpt90) REVERT: a 46 MET cc_start: 0.3840 (mmt) cc_final: 0.3554 (mmm) REVERT: a 93 MET cc_start: 0.8316 (ttt) cc_final: 0.8009 (tmm) REVERT: a 94 TYR cc_start: 0.5969 (t80) cc_final: 0.5404 (t80) REVERT: a 201 LEU cc_start: 0.7679 (tp) cc_final: 0.7464 (pp) REVERT: a 257 MET cc_start: 0.7498 (tmm) cc_final: 0.7219 (tmm) outliers start: 69 outliers final: 50 residues processed: 346 average time/residue: 0.4347 time to fit residues: 255.9999 Evaluate side-chains 327 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 272 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 449 ILE Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain a residue 74 LYS Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 412 optimal weight: 7.9990 chunk 434 optimal weight: 5.9990 chunk 396 optimal weight: 6.9990 chunk 423 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 332 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 382 optimal weight: 5.9990 chunk 400 optimal weight: 8.9990 chunk 421 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 37294 Z= 0.316 Angle : 0.683 12.187 50485 Z= 0.344 Chirality : 0.042 0.278 5881 Planarity : 0.005 0.062 6510 Dihedral : 6.141 95.121 5330 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.12 % Allowed : 16.82 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.61 (0.12), residues: 4775 helix: 1.14 (0.11), residues: 2469 sheet: 0.45 (0.22), residues: 513 loop : -0.55 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 111 HIS 0.007 0.001 HIS X 51 PHE 0.038 0.002 PHE J 54 TYR 0.037 0.002 TYR I 10 ARG 0.009 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 267 time to evaluate : 4.112 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: A 12 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8692 (mp) REVERT: A 156 MET cc_start: 0.9454 (mmt) cc_final: 0.8881 (mmt) REVERT: B 110 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9235 (t) REVERT: D 209 MET cc_start: 0.8924 (mtm) cc_final: 0.8691 (mtm) REVERT: D 445 MET cc_start: 0.8915 (mmm) cc_final: 0.8282 (mmt) REVERT: F 159 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8397 (tmm) REVERT: F 275 MET cc_start: 0.8524 (ptm) cc_final: 0.8269 (ptm) REVERT: F 366 ARG cc_start: 0.9151 (tpt170) cc_final: 0.8462 (mmm160) REVERT: F 379 MET cc_start: 0.9035 (mtp) cc_final: 0.8072 (tpp) REVERT: F 397 GLN cc_start: 0.8831 (tt0) cc_final: 0.8237 (tm-30) REVERT: F 431 MET cc_start: 0.8007 (mtp) cc_final: 0.7726 (ptp) REVERT: G 48 MET cc_start: 0.9002 (ttm) cc_final: 0.8290 (ttm) REVERT: G 102 MET cc_start: 0.8730 (ttp) cc_final: 0.8117 (tmm) REVERT: H 49 MET cc_start: 0.7931 (tpp) cc_final: 0.7545 (tpp) REVERT: I 45 LEU cc_start: 0.6953 (tp) cc_final: 0.6472 (mm) REVERT: I 54 PHE cc_start: 0.6289 (m-10) cc_final: 0.5508 (t80) REVERT: J 17 MET cc_start: 0.7421 (ptt) cc_final: 0.6697 (ptp) REVERT: L 8 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7975 (mp) REVERT: L 16 MET cc_start: 0.3157 (mmm) cc_final: 0.2951 (mmm) REVERT: L 57 MET cc_start: 0.7366 (tmm) cc_final: 0.5955 (ptt) REVERT: M 65 MET cc_start: 0.5353 (mtp) cc_final: 0.4958 (mmp) REVERT: N 11 MET cc_start: 0.7536 (mmm) cc_final: 0.7194 (mmm) REVERT: P 11 MET cc_start: 0.8306 (tpp) cc_final: 0.7925 (mtt) REVERT: P 57 MET cc_start: 0.4540 (ppp) cc_final: 0.3446 (ttm) REVERT: R 6 MET cc_start: 0.6339 (mmt) cc_final: 0.5850 (ttm) REVERT: R 16 MET cc_start: 0.6346 (tpp) cc_final: 0.5949 (tmm) REVERT: S 17 MET cc_start: 0.8495 (ppp) cc_final: 0.7787 (ptm) REVERT: W 12 LYS cc_start: 0.9471 (ttmm) cc_final: 0.9094 (ttpp) REVERT: X 49 ARG cc_start: 0.8616 (mtt180) cc_final: 0.8161 (mmm160) REVERT: a 46 MET cc_start: 0.4160 (mmt) cc_final: 0.3872 (mmm) REVERT: a 93 MET cc_start: 0.8539 (ttt) cc_final: 0.7296 (mmm) REVERT: a 201 LEU cc_start: 0.7690 (tp) cc_final: 0.7489 (pp) REVERT: a 257 MET cc_start: 0.7599 (tmm) cc_final: 0.7217 (tmm) outliers start: 81 outliers final: 61 residues processed: 333 average time/residue: 0.4383 time to fit residues: 249.1163 Evaluate side-chains 328 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 263 time to evaluate : 4.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 449 ILE Chi-restraints excluded: chain G residue 176 ASN Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 141 ASP Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 74 LYS Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 277 optimal weight: 7.9990 chunk 447 optimal weight: 0.0570 chunk 273 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 469 optimal weight: 20.0000 chunk 431 optimal weight: 8.9990 chunk 373 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 288 optimal weight: 4.9990 chunk 229 optimal weight: 0.7980 overall best weight: 2.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37294 Z= 0.208 Angle : 0.637 12.493 50485 Z= 0.316 Chirality : 0.041 0.212 5881 Planarity : 0.004 0.062 6510 Dihedral : 6.001 92.154 5330 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.73 % Allowed : 17.50 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.71 (0.12), residues: 4775 helix: 1.20 (0.11), residues: 2494 sheet: 0.50 (0.23), residues: 503 loop : -0.50 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP a 111 HIS 0.004 0.001 HIS B 479 PHE 0.019 0.001 PHE M 35 TYR 0.015 0.001 TYR F 444 ARG 0.008 0.000 ARG H 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 269 time to evaluate : 3.962 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: A 156 MET cc_start: 0.9440 (mmt) cc_final: 0.8915 (mmt) REVERT: B 110 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9234 (t) REVERT: D 193 MET cc_start: 0.8205 (mmm) cc_final: 0.7878 (mmm) REVERT: D 209 MET cc_start: 0.8874 (mtm) cc_final: 0.8609 (mtm) REVERT: D 445 MET cc_start: 0.8925 (mmm) cc_final: 0.8293 (mmt) REVERT: F 159 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8350 (tmm) REVERT: F 275 MET cc_start: 0.8439 (ptm) cc_final: 0.8201 (ptm) REVERT: F 366 ARG cc_start: 0.9157 (tpt170) cc_final: 0.8562 (mmm160) REVERT: F 379 MET cc_start: 0.8919 (mtp) cc_final: 0.7864 (tpp) REVERT: F 397 GLN cc_start: 0.8836 (tt0) cc_final: 0.8217 (tm-30) REVERT: F 431 MET cc_start: 0.7994 (mtp) cc_final: 0.7735 (ptp) REVERT: G 48 MET cc_start: 0.8964 (ttm) cc_final: 0.8282 (ttm) REVERT: G 102 MET cc_start: 0.8718 (ttp) cc_final: 0.8005 (tmm) REVERT: H 49 MET cc_start: 0.7999 (tpp) cc_final: 0.7586 (tpp) REVERT: I 45 LEU cc_start: 0.6706 (tp) cc_final: 0.6325 (mm) REVERT: I 54 PHE cc_start: 0.6282 (m-10) cc_final: 0.5483 (t80) REVERT: J 17 MET cc_start: 0.7492 (ptt) cc_final: 0.6586 (ptp) REVERT: L 8 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7909 (mp) REVERT: L 57 MET cc_start: 0.7363 (tmm) cc_final: 0.6062 (ptt) REVERT: M 65 MET cc_start: 0.5131 (mtp) cc_final: 0.4682 (mmp) REVERT: N 11 MET cc_start: 0.7425 (mmm) cc_final: 0.7070 (mmm) REVERT: O 6 MET cc_start: 0.5821 (ttp) cc_final: 0.5234 (pmm) REVERT: P 11 MET cc_start: 0.8320 (tpp) cc_final: 0.7904 (mtt) REVERT: P 57 MET cc_start: 0.4655 (ppp) cc_final: 0.3581 (ttm) REVERT: R 6 MET cc_start: 0.6417 (mmt) cc_final: 0.5890 (ttm) REVERT: R 11 MET cc_start: 0.6519 (ppp) cc_final: 0.4671 (tpt) REVERT: R 16 MET cc_start: 0.6569 (tpp) cc_final: 0.6121 (tmm) REVERT: R 57 MET cc_start: 0.7366 (mmm) cc_final: 0.7121 (mmm) REVERT: S 16 MET cc_start: 0.7248 (ppp) cc_final: 0.6584 (ppp) REVERT: S 17 MET cc_start: 0.8386 (ppp) cc_final: 0.7956 (ptm) REVERT: S 57 MET cc_start: 0.7652 (tmm) cc_final: 0.6545 (tpt) REVERT: W 12 LYS cc_start: 0.9441 (ttmm) cc_final: 0.9114 (ttpp) REVERT: X 49 ARG cc_start: 0.8620 (mtt180) cc_final: 0.8181 (mmm160) REVERT: Y 22 MET cc_start: 0.1538 (tpt) cc_final: 0.1191 (tmm) REVERT: a 46 MET cc_start: 0.4055 (mmt) cc_final: 0.3768 (mmm) REVERT: a 93 MET cc_start: 0.8651 (ttt) cc_final: 0.7649 (mmt) REVERT: a 257 MET cc_start: 0.7651 (tmm) cc_final: 0.7263 (tmm) outliers start: 66 outliers final: 55 residues processed: 325 average time/residue: 0.4377 time to fit residues: 243.2218 Evaluate side-chains 321 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 263 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 449 ILE Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 14 PHE Chi-restraints excluded: chain X residue 141 ASP Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 74 LYS Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 296 optimal weight: 2.9990 chunk 398 optimal weight: 4.9990 chunk 114 optimal weight: 0.3980 chunk 344 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 374 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 384 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS a 17 ASN ** a 116 ASN ** 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 = 0.3500 r_free = 0.3500 target = 0.057652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.041808 restraints weight = 249704.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.042790 restraints weight = 142055.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.042832 restraints weight = 81517.518| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37294 Z= 0.165 Angle : 0.621 12.327 50485 Z= 0.307 Chirality : 0.041 0.177 5881 Planarity : 0.004 0.060 6510 Dihedral : 5.793 87.899 5330 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.63 % Allowed : 17.44 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.79 (0.12), residues: 4775 helix: 1.24 (0.10), residues: 2536 sheet: 0.50 (0.22), residues: 526 loop : -0.46 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 111 HIS 0.005 0.000 HIS B 479 PHE 0.042 0.001 PHE J 54 TYR 0.013 0.001 TYR F 435 ARG 0.008 0.000 ARG H 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6941.94 seconds wall clock time: 126 minutes 22.61 seconds (7582.61 seconds total)