Starting phenix.real_space_refine on Fri Feb 23 04:52:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbw_27311/02_2024/8dbw_27311_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbw_27311/02_2024/8dbw_27311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbw_27311/02_2024/8dbw_27311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbw_27311/02_2024/8dbw_27311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbw_27311/02_2024/8dbw_27311_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbw_27311/02_2024/8dbw_27311_updated.pdb" } resolution = 4.1 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 23389 2.51 5 N 6292 2.21 5 O 6955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36835 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3852 Classifications: {'peptide': 510} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Chain: "B" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3810 Classifications: {'peptide': 505} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 486} Chain: "C" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3845 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3534 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "E" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3534 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "F" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3521 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "G" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2187 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain: "H" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1022 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "I" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} 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: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "W" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1318 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1179 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 150} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "Y" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1172 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Modifications used: {'COO': 1} 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: 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} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" 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} Time building chain proxies: 18.19, per 1000 atoms: 0.49 Number of scatterers: 36835 At special positions: 0 Unit cell: (178.035, 220.116, 135.954, 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 6955 8.00 N 6292 7.00 C 23389 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: 13.57 Conformation dependent library (CDL) restraints added in 7.1 seconds 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8790 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 178 helices and 24 sheets defined 55.4% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.60 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 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.760A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.570A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.112A 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 288 through 300 removed outlier: 3.657A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS A 294 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 299 " --> 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 362 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 406 removed outlier: 4.556A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 455 through 458 removed outlier: 4.367A pdb=" N ASP A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.144A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 11 through 17 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 187 removed outlier: 4.128A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.823A 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 290 through 300 removed outlier: 3.625A pdb=" N ARG B 296 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 381 removed outlier: 3.566A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 381' Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 391 through 409 removed outlier: 3.903A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N PHE B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 430 Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 462 through 478 removed outlier: 4.323A pdb=" N GLY B 465 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.905A pdb=" N ALA B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' 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 151 through 156 Processing helix chain 'C' and resid 175 through 189 removed outlier: 4.457A pdb=" N ASP C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 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 251 Proline residue: C 239 - end of helix removed outlier: 3.883A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 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 290 through 300 removed outlier: 3.981A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'C' and resid 357 through 360 No H-bonds generated for 'chain 'C' and resid 357 through 360' Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 416 through 430 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 464 through 477 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 494 through 509 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 169 removed outlier: 3.841A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU D 169 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 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: 5.221A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 258 removed outlier: 3.785A pdb=" N VAL D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 279 removed outlier: 3.638A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) 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 314 removed outlier: 4.036A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 351 through 377 removed outlier: 3.603A pdb=" N GLU D 369 " --> pdb=" O GLN D 365 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 370 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) 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 399 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 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 168 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: 4.727A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 Processing helix chain 'E' and resid 271 through 279 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 312 Processing helix chain 'E' and resid 323 through 327 Processing helix chain 'E' and resid 346 through 349 No H-bonds generated for 'chain 'E' and resid 346 through 349' Processing helix chain 'E' and resid 351 through 376 removed outlier: 3.862A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) 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 384 through 399 Processing helix chain 'E' and resid 406 through 411 Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 440 through 443 Processing helix chain 'E' and resid 449 through 458 removed outlier: 3.695A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' 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 166 Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 213 through 233 removed outlier: 4.223A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 255 Processing helix chain 'F' and resid 271 through 280 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 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 312 through 314 No H-bonds generated for 'chain 'F' and resid 312 through 314' 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: 4.078A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 381 No H-bonds generated for 'chain 'F' and resid 379 through 381' Processing helix chain 'F' and resid 384 through 399 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 removed outlier: 3.539A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 57 Proline residue: G 43 - end of helix removed outlier: 4.050A pdb=" N HIS G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 4.534A 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 205 through 207 No H-bonds generated for 'chain 'G' and resid 205 through 207' Processing helix chain 'G' and resid 211 through 283 removed outlier: 3.512A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 107 removed outlier: 3.659A pdb=" N SER H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 135 removed outlier: 4.221A pdb=" N GLN H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS H 135 " --> pdb=" O ILE H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 41 removed outlier: 3.764A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 removed outlier: 3.621A pdb=" N ILE I 46 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Proline residue: I 47 - end of helix removed outlier: 4.510A pdb=" N ARG I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET I 57 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY I 58 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.564A pdb=" N PHE I 76 " --> pdb=" O TYR I 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 41 removed outlier: 4.098A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 76 removed outlier: 3.716A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 4.976A 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: 3.749A pdb=" N LEU L 8 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR L 10 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL L 15 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA L 20 " --> pdb=" O MET L 17 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA L 24 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE L 26 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY L 27 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY L 33 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.799A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 4.274A pdb=" N ARG L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY L 58 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 3.529A pdb=" N LEU L 70 " --> pdb=" O ALA L 67 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET L 75 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.654A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 Proline residue: M 47 - end of helix removed outlier: 3.826A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.575A pdb=" N PHE M 76 " --> pdb=" O TYR M 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.166A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 removed outlier: 3.844A pdb=" N ILE N 46 " --> pdb=" O PRO N 43 " (cutoff:3.500A) Proline residue: N 47 - end of helix removed outlier: 4.289A pdb=" N ARG N 50 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN N 52 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix removed outlier: 3.508A pdb=" N PHE N 76 " --> pdb=" O TYR N 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 41 removed outlier: 3.623A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 60 removed outlier: 3.880A pdb=" N ILE O 46 " --> pdb=" O PRO O 43 " (cutoff:3.500A) Proline residue: O 47 - end of helix removed outlier: 4.253A pdb=" N ARG O 50 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE O 53 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL O 56 " --> pdb=" O PHE O 53 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY O 58 " --> pdb=" O ILE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 Processing helix chain 'P' and resid 6 through 41 removed outlier: 3.638A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 76 removed outlier: 3.849A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.841A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.779A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 4.461A pdb=" N ARG Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE Q 54 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.721A pdb=" N PHE Q 76 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.736A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 76 removed outlier: 3.678A pdb=" N ILE R 46 " --> pdb=" O PRO R 43 " (cutoff:3.500A) Proline residue: R 47 - end of helix removed outlier: 3.575A pdb=" N VAL R 56 " --> pdb=" O PHE R 53 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP R 61 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE R 63 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 4.033A pdb=" N PHE R 76 " --> pdb=" O TYR R 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 41 removed outlier: 4.836A pdb=" N TYR S 10 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA S 24 " --> pdb=" O ALA S 21 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE S 28 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY S 32 " --> pdb=" O GLY S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 Proline residue: S 47 - end of helix Processing helix chain 'S' and resid 62 through 77 Processing helix chain 'W' and resid 4 through 20 Proline residue: W 9 - end of helix removed outlier: 3.652A pdb=" N GLU W 20 " --> pdb=" O ASP W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 38 removed outlier: 3.753A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 Processing helix chain 'W' and resid 53 through 63 removed outlier: 3.966A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 82 removed outlier: 3.793A pdb=" N ARG W 77 " --> pdb=" O GLN W 73 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN W 82 " --> pdb=" O VAL W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix 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 Processing helix chain 'X' and resid 6 through 23 Processing helix chain 'X' and resid 27 through 29 No H-bonds generated for 'chain 'X' and resid 27 through 29' Processing helix chain 'X' and resid 31 through 136 removed outlier: 3.608A pdb=" N ILE X 40 " --> pdb=" O ARG X 36 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE X 75 " --> pdb=" O GLU X 71 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 152 removed outlier: 4.400A pdb=" N VAL X 149 " --> pdb=" O SER X 146 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP X 150 " --> pdb=" O ASP X 147 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 24 Processing helix chain 'Y' and resid 29 through 137 removed outlier: 4.103A pdb=" N ALA Y 32 " --> pdb=" O LEU Y 29 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP Y 88 " --> pdb=" O GLN Y 85 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU Y 89 " --> pdb=" O ILE Y 86 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU Y 120 " --> pdb=" O ARG Y 117 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 152 Processing helix chain 'a' and resid 8 through 15 Processing helix chain 'a' and resid 44 through 64 Processing helix chain 'a' and resid 74 through 92 removed outlier: 4.090A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 120 removed outlier: 4.201A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 132 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 166 removed outlier: 3.532A pdb=" N TYR a 164 " --> pdb=" O LEU a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 171 No H-bonds generated for 'chain 'a' and resid 168 through 171' Processing helix chain 'a' and resid 173 through 179 Processing helix chain 'a' and resid 187 through 228 removed outlier: 3.832A pdb=" N VAL a 191 " --> pdb=" O ALA a 187 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.715A pdb=" N LEU a 207 " --> pdb=" O LYS a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 4.396A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.942A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 4.158A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU A 66 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N HIS A 42 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.467A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 323 through 328 removed outlier: 6.505A pdb=" N LYS A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ILE A 259 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 194 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.268A pdb=" N ASN B 27 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET B 76 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA B 61 " --> pdb=" O MET B 76 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 Processing sheet with id= G, first strand: chain 'B' and resid 352 through 355 removed outlier: 7.802A pdb=" N ILE B 353 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLU B 165 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA B 326 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE B 167 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLY B 169 " --> pdb=" O PRO B 328 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE B 330 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 260 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE B 259 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 194 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASP B 261 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 196 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.804A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET C 76 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA C 61 " --> pdb=" O MET C 76 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 96 through 99 Processing sheet with id= J, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.365A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL C 224 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU C 327 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.388A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 3 through 9 removed outlier: 6.576A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA D 28 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.245A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.056A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 3 through 9 removed outlier: 6.711A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.502A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 317 through 319 removed outlier: 8.337A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 4 through 9 removed outlier: 6.471A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA F 28 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 76 through 78 Processing sheet with id= T, first strand: chain 'F' and resid 317 through 320 removed outlier: 7.705A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL F 296 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 181 through 186 removed outlier: 3.643A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 43 through 45 removed outlier: 3.627A pdb=" N THR H 43 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA H 80 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL H 9 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 22 through 25 removed outlier: 3.593A pdb=" N GLN H 24 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR H 82 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'W' and resid 139 through 142 removed outlier: 4.200A pdb=" N MET W 157 " --> pdb=" O ALA W 154 " (cutoff:3.500A) 2027 hydrogen bonds defined for protein. 5007 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: 13.82 Time building geometry restraints manager: 14.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8630 1.33 - 1.45: 6796 1.45 - 1.57: 21583 1.57 - 1.69: 27 1.69 - 1.81: 356 Bond restraints: 37392 Sorted by residual: bond pdb=" N ALA H 39 " pdb=" CA ALA H 39 " ideal model delta sigma weight residual 1.455 1.495 -0.040 9.60e-03 1.09e+04 1.78e+01 bond pdb=" N GLN H 72 " pdb=" CA GLN H 72 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.27e+01 bond pdb=" N LEU H 42 " pdb=" CA LEU H 42 " ideal model delta sigma weight residual 1.455 1.497 -0.042 1.25e-02 6.40e+03 1.15e+01 bond pdb=" N TRP G 203 " pdb=" CA TRP G 203 " ideal model delta sigma weight residual 1.455 1.497 -0.041 1.23e-02 6.61e+03 1.14e+01 bond pdb=" N TYR H 35 " pdb=" CA TYR H 35 " ideal model delta sigma weight residual 1.455 1.485 -0.030 9.60e-03 1.09e+04 9.79e+00 ... (remaining 37387 not shown) Histogram of bond angle deviations from ideal: 98.64 - 107.50: 1242 107.50 - 116.35: 23971 116.35 - 125.21: 25038 125.21 - 134.07: 369 134.07 - 142.92: 17 Bond angle restraints: 50637 Sorted by residual: angle pdb=" N ALA H 39 " pdb=" CA ALA H 39 " pdb=" C ALA H 39 " ideal model delta sigma weight residual 108.25 116.59 -8.34 1.16e+00 7.43e-01 5.17e+01 angle pdb=" N PRO H 73 " pdb=" CA PRO H 73 " pdb=" C PRO H 73 " ideal model delta sigma weight residual 111.41 120.14 -8.73 1.50e+00 4.44e-01 3.39e+01 angle pdb=" N LEU H 42 " pdb=" CA LEU H 42 " pdb=" C LEU H 42 " ideal model delta sigma weight residual 108.99 117.67 -8.68 1.57e+00 4.06e-01 3.06e+01 angle pdb=" C LEU Q 45 " pdb=" N ILE Q 46 " pdb=" CA ILE Q 46 " ideal model delta sigma weight residual 120.24 123.66 -3.42 6.30e-01 2.52e+00 2.95e+01 angle pdb=" C PRO H 40 " pdb=" CA PRO H 40 " pdb=" CB PRO H 40 " ideal model delta sigma weight residual 111.56 102.80 8.76 1.65e+00 3.67e-01 2.82e+01 ... (remaining 50632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.26: 21914 29.26 - 58.51: 713 58.51 - 87.77: 87 87.77 - 117.02: 7 117.02 - 146.28: 3 Dihedral angle restraints: 22724 sinusoidal: 8981 harmonic: 13743 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 86.28 -146.28 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 70.25 -130.26 1 2.00e+01 2.50e-03 3.95e+01 dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 63.42 -123.42 1 2.00e+01 2.50e-03 3.72e+01 ... (remaining 22721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 5373 0.087 - 0.173: 508 0.173 - 0.260: 14 0.260 - 0.347: 4 0.347 - 0.433: 2 Chirality restraints: 5901 Sorted by residual: chirality pdb=" CA HIS H 38 " pdb=" N HIS H 38 " pdb=" C HIS H 38 " pdb=" CB HIS H 38 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CB THR H 43 " pdb=" CA THR H 43 " pdb=" OG1 THR H 43 " pdb=" CG2 THR H 43 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA PRO H 73 " pdb=" N PRO H 73 " pdb=" C PRO H 73 " pdb=" CB PRO H 73 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 5898 not shown) Planarity restraints: 6546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 474 " -0.005 2.00e-02 2.50e+03 3.46e-02 2.39e+01 pdb=" CG TYR B 474 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR B 474 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR B 474 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 474 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR B 474 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 474 " 0.049 2.00e-02 2.50e+03 pdb=" OH TYR B 474 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP G 203 " 0.023 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C TRP G 203 " -0.081 2.00e-02 2.50e+03 pdb=" O TRP G 203 " 0.030 2.00e-02 2.50e+03 pdb=" N ASP G 204 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS a 167 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C LYS a 167 " -0.079 2.00e-02 2.50e+03 pdb=" O LYS a 167 " 0.030 2.00e-02 2.50e+03 pdb=" N MET a 168 " 0.026 2.00e-02 2.50e+03 ... (remaining 6543 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 166 2.60 - 3.18: 33029 3.18 - 3.75: 56839 3.75 - 4.33: 79734 4.33 - 4.90: 130034 Nonbonded interactions: 299802 Sorted by model distance: nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 2.029 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.081 2.170 nonbonded pdb=" O2A ATP A 600 " pdb="MG MG A 601 " model vdw 2.107 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 2.111 2.170 nonbonded pdb=" OG1 THR F 156 " pdb="MG MG F 501 " model vdw 2.125 2.170 ... (remaining 299797 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 7 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB )) or resid 420 through 511 or resid 600 through 601)) selection = (chain 'B' and (resid 7 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB )) or resid 420 through 511 or resid 600 through 601)) selection = (chain 'C' and (resid 7 through 511 or resid 600 through 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' and (resid 1 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 57 or (resid 58 through 59 and (nam \ e N or name CA or name C or name O or name CB )) or resid 60 through 62 or (resi \ d 63 and (name N or name CA or name C or name O or name CB )) or resid 64 throug \ h 65 or (resid 66 through 70 and (name N or name CA or name C or name O or name \ CB )) or resid 71 through 72 or (resid 73 and (name N or name CA or name C or na \ me O or name CB )) or resid 74 through 76 or (resid 77 and (name N or name CA or \ name C or name O or name CB )) or resid 78 through 153)) selection = (chain 'Y' and (resid 1 through 90 or (resid 91 through 92 and (name N or name C \ A or name C or name O or name CB )) or resid 93 through 153)) } 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 11.180 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 94.820 Find NCS groups from input model: 2.970 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.004 0.089 37392 Z= 0.283 Angle : 0.809 12.359 50637 Z= 0.441 Chirality : 0.050 0.433 5901 Planarity : 0.010 0.120 6546 Dihedral : 14.491 146.278 13934 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.23 % Favored : 97.70 % Rotamer: Outliers : 1.10 % Allowed : 6.87 % Favored : 92.03 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.91 % 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: -0.09 (0.11), residues: 4793 helix: 0.69 (0.10), residues: 2631 sheet: -0.05 (0.23), residues: 497 loop : -1.18 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP G 203 HIS 0.018 0.002 HIS G 54 PHE 0.028 0.002 PHE O 54 TYR 0.053 0.006 TYR B 474 ARG 0.029 0.004 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 633 time to evaluate : 3.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8280 (mtp) cc_final: 0.7759 (mtp) REVERT: A 69 ASP cc_start: 0.7133 (m-30) cc_final: 0.6609 (t0) REVERT: A 148 THR cc_start: 0.8912 (m) cc_final: 0.8677 (p) REVERT: A 156 MET cc_start: 0.8985 (mtm) cc_final: 0.8655 (mtp) REVERT: A 448 LEU cc_start: 0.9441 (mt) cc_final: 0.9033 (tp) REVERT: A 468 GLU cc_start: 0.9135 (tt0) cc_final: 0.8866 (tm-30) REVERT: B 468 GLU cc_start: 0.8799 (tt0) cc_final: 0.8103 (tm-30) REVERT: C 430 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9350 (tp) REVERT: D 205 VAL cc_start: 0.8740 (t) cc_final: 0.8400 (p) REVERT: D 263 SER cc_start: 0.9376 (t) cc_final: 0.9156 (m) REVERT: D 445 MET cc_start: 0.8274 (mmt) cc_final: 0.7897 (tpp) REVERT: E 160 MET cc_start: 0.9217 (mtm) cc_final: 0.8978 (mtp) REVERT: F 209 MET cc_start: 0.8747 (ptp) cc_final: 0.8288 (ptp) REVERT: F 318 THR cc_start: 0.9189 (p) cc_final: 0.8895 (t) REVERT: F 381 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7193 (tm-30) REVERT: F 445 MET cc_start: 0.7979 (mmt) cc_final: 0.7705 (tmm) REVERT: G 79 VAL cc_start: 0.8954 (t) cc_final: 0.8617 (t) REVERT: G 86 LEU cc_start: 0.8873 (mt) cc_final: 0.8421 (mm) REVERT: G 139 MET cc_start: 0.8274 (mmm) cc_final: 0.7282 (tpt) REVERT: G 194 ASP cc_start: 0.8083 (p0) cc_final: 0.7813 (m-30) REVERT: G 224 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8600 (pt0) REVERT: H 15 MET cc_start: 0.6065 (tpp) cc_final: 0.4837 (tpp) REVERT: H 76 VAL cc_start: -0.1406 (OUTLIER) cc_final: -0.1846 (p) REVERT: J 11 MET cc_start: 0.8223 (tpp) cc_final: 0.7952 (mtp) REVERT: L 75 MET cc_start: 0.6204 (ttt) cc_final: 0.5939 (ttt) REVERT: L 78 VAL cc_start: 0.4000 (t) cc_final: 0.3696 (t) REVERT: M 11 MET cc_start: 0.7893 (tpt) cc_final: 0.6578 (mmm) REVERT: M 60 VAL cc_start: 0.5298 (t) cc_final: 0.5019 (t) REVERT: M 68 VAL cc_start: 0.8825 (t) cc_final: 0.8371 (t) REVERT: O 9 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6451 (mm) REVERT: O 11 MET cc_start: 0.8086 (tpt) cc_final: 0.7542 (mtt) REVERT: P 6 MET cc_start: 0.6847 (mmt) cc_final: 0.6610 (mmt) REVERT: Q 57 MET cc_start: 0.5430 (tmm) cc_final: 0.5210 (tmm) REVERT: Q 65 MET cc_start: 0.4304 (mtt) cc_final: 0.3290 (tpt) REVERT: R 11 MET cc_start: 0.5855 (tpt) cc_final: 0.5399 (mtm) REVERT: S 49 LEU cc_start: 0.8677 (mt) cc_final: 0.8233 (tp) REVERT: S 75 MET cc_start: 0.4214 (ttt) cc_final: 0.3804 (ttt) REVERT: W 119 GLN cc_start: 0.9300 (tm-30) cc_final: 0.9025 (mp10) REVERT: X 141 ASP cc_start: 0.8264 (m-30) cc_final: 0.7831 (p0) REVERT: Y 22 MET cc_start: 0.5065 (mmp) cc_final: 0.4454 (mmm) REVERT: Y 150 ASP cc_start: 0.9158 (m-30) cc_final: 0.8407 (p0) REVERT: Y 151 LYS cc_start: 0.8963 (tttt) cc_final: 0.8691 (ptpp) REVERT: a 47 MET cc_start: 0.6970 (tmt) cc_final: 0.6496 (ptt) REVERT: a 97 LYS cc_start: 0.7710 (mttt) cc_final: 0.7344 (pttt) REVERT: a 252 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8061 (mm-40) outliers start: 42 outliers final: 11 residues processed: 668 average time/residue: 0.5143 time to fit residues: 546.1197 Evaluate side-chains 351 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 337 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 7.9990 chunk 358 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 241 optimal weight: 0.0170 chunk 191 optimal weight: 8.9990 chunk 370 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 429 optimal weight: 8.9990 overall best weight: 6.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 ASN B 511 GLN C 185 ASN D 73 HIS E 170 HIS F 43 GLN G 91 ASN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS I 52 GLN L 3 ASN P 52 GLN Q 42 GLN S 52 GLN W 42 GLN ** X 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 17 ASN a 33 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.163 37392 Z= 0.397 Angle : 0.766 17.893 50637 Z= 0.401 Chirality : 0.046 0.321 5901 Planarity : 0.006 0.067 6546 Dihedral : 8.283 137.495 5367 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.82 % Favored : 97.16 % Rotamer: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.09 (0.12), residues: 4793 helix: 0.66 (0.10), residues: 2593 sheet: -0.16 (0.22), residues: 558 loop : -1.08 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP G 203 HIS 0.008 0.002 HIS a 14 PHE 0.034 0.003 PHE a 163 TYR 0.034 0.002 TYR C 474 ARG 0.011 0.001 ARG L 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 381 time to evaluate : 4.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7407 (m-30) cc_final: 0.6707 (t0) REVERT: A 386 MET cc_start: 0.9145 (tpp) cc_final: 0.8893 (tpp) REVERT: A 448 LEU cc_start: 0.9573 (mt) cc_final: 0.9328 (mt) REVERT: A 468 GLU cc_start: 0.9268 (tt0) cc_final: 0.8675 (tm-30) REVERT: B 52 MET cc_start: 0.7087 (mtm) cc_final: 0.6858 (mtm) REVERT: B 156 MET cc_start: 0.9392 (mmm) cc_final: 0.8795 (mmm) REVERT: B 504 LEU cc_start: 0.9317 (mm) cc_final: 0.9013 (mt) REVERT: C 76 MET cc_start: 0.8345 (mpp) cc_final: 0.7882 (mtm) REVERT: C 86 MET cc_start: 0.9068 (mtt) cc_final: 0.8863 (mtm) REVERT: D 56 MET cc_start: 0.8791 (tpp) cc_final: 0.8549 (mmm) REVERT: D 275 MET cc_start: 0.8571 (tpp) cc_final: 0.8317 (tpt) REVERT: D 368 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8528 (tp40) REVERT: D 397 GLN cc_start: 0.9189 (tt0) cc_final: 0.8542 (tm-30) REVERT: D 445 MET cc_start: 0.8598 (mmt) cc_final: 0.8397 (mmm) REVERT: F 56 MET cc_start: 0.9203 (mmm) cc_final: 0.8951 (mmm) REVERT: F 209 MET cc_start: 0.8739 (ptp) cc_final: 0.8322 (ptp) REVERT: F 318 THR cc_start: 0.9468 (p) cc_final: 0.9230 (t) REVERT: F 445 MET cc_start: 0.8055 (mmt) cc_final: 0.7616 (tmm) REVERT: G 86 LEU cc_start: 0.9099 (mt) cc_final: 0.8835 (mm) REVERT: G 102 MET cc_start: 0.8629 (tmm) cc_final: 0.8408 (tmm) REVERT: G 187 LEU cc_start: 0.9045 (tp) cc_final: 0.8770 (tp) REVERT: G 194 ASP cc_start: 0.8275 (p0) cc_final: 0.8000 (m-30) REVERT: H 49 MET cc_start: 0.2009 (ppp) cc_final: 0.1499 (ppp) REVERT: H 127 GLN cc_start: 0.6817 (mp10) cc_final: 0.6160 (tt0) REVERT: J 11 MET cc_start: 0.8371 (tpp) cc_final: 0.8056 (mtp) REVERT: L 17 MET cc_start: 0.7257 (mtm) cc_final: 0.7054 (mpp) REVERT: L 75 MET cc_start: 0.6269 (ttt) cc_final: 0.6035 (ttt) REVERT: M 11 MET cc_start: 0.8146 (tpt) cc_final: 0.6764 (mmm) REVERT: O 11 MET cc_start: 0.7984 (tpt) cc_final: 0.7390 (mmt) REVERT: O 35 PHE cc_start: 0.7480 (t80) cc_final: 0.7016 (t80) REVERT: P 15 VAL cc_start: 0.7334 (t) cc_final: 0.7125 (p) REVERT: S 17 MET cc_start: 0.4809 (ttt) cc_final: 0.4235 (tpt) REVERT: S 49 LEU cc_start: 0.9030 (mt) cc_final: 0.8649 (tp) REVERT: W 43 MET cc_start: 0.9120 (tpp) cc_final: 0.8773 (tpp) REVERT: X 22 MET cc_start: 0.4369 (ptp) cc_final: 0.4147 (ptp) REVERT: X 141 ASP cc_start: 0.8508 (m-30) cc_final: 0.7817 (t0) REVERT: Y 22 MET cc_start: 0.5366 (mmp) cc_final: 0.4538 (ttt) REVERT: Y 98 ARG cc_start: 0.8874 (mtp180) cc_final: 0.8605 (mmm-85) REVERT: a 6 MET cc_start: -0.0326 (ttt) cc_final: -0.0533 (ttt) REVERT: a 47 MET cc_start: 0.7034 (tmm) cc_final: 0.6685 (ptt) REVERT: a 93 MET cc_start: 0.7039 (ttt) cc_final: 0.6793 (mmp) REVERT: a 97 LYS cc_start: 0.7532 (mttt) cc_final: 0.7179 (pttt) REVERT: a 252 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8438 (mm-40) outliers start: 4 outliers final: 0 residues processed: 384 average time/residue: 0.5038 time to fit residues: 323.3570 Evaluate side-chains 290 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 4.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 357 optimal weight: 8.9990 chunk 292 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 430 optimal weight: 8.9990 chunk 464 optimal weight: 1.9990 chunk 383 optimal weight: 8.9990 chunk 426 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 345 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN B 215 HIS B 361 ASN B 435 GLN C 185 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN E 208 GLN ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 GLN Q 52 GLN R 5 ASN ** X 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN a 33 GLN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37392 Z= 0.289 Angle : 0.656 11.364 50637 Z= 0.343 Chirality : 0.044 0.225 5901 Planarity : 0.005 0.107 6546 Dihedral : 7.817 147.137 5367 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.09 % Favored : 96.89 % Rotamer: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 0.01 (0.12), residues: 4793 helix: 0.77 (0.10), residues: 2582 sheet: -0.04 (0.22), residues: 533 loop : -1.09 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 26 HIS 0.014 0.002 HIS G 54 PHE 0.034 0.002 PHE a 85 TYR 0.017 0.002 TYR O 10 ARG 0.011 0.001 ARG X 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 358 time to evaluate : 4.499 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: A 386 MET cc_start: 0.9130 (tpp) cc_final: 0.8487 (tpp) REVERT: A 448 LEU cc_start: 0.9559 (mt) cc_final: 0.9256 (mt) REVERT: A 468 GLU cc_start: 0.9077 (tt0) cc_final: 0.8742 (tm-30) REVERT: B 52 MET cc_start: 0.7206 (mtm) cc_final: 0.6831 (mtm) REVERT: B 412 ASP cc_start: 0.7796 (m-30) cc_final: 0.7353 (t70) REVERT: B 468 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8621 (tm-30) REVERT: B 504 LEU cc_start: 0.9447 (mm) cc_final: 0.9082 (mt) REVERT: C 76 MET cc_start: 0.8393 (mpp) cc_final: 0.7802 (mtm) REVERT: C 86 MET cc_start: 0.9086 (mtt) cc_final: 0.8868 (mtm) REVERT: D 209 MET cc_start: 0.8969 (mtp) cc_final: 0.8681 (mtp) REVERT: D 368 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8653 (tp40) REVERT: D 397 GLN cc_start: 0.9203 (tt0) cc_final: 0.8548 (tm-30) REVERT: D 445 MET cc_start: 0.8641 (mmt) cc_final: 0.8203 (tpp) REVERT: E 88 MET cc_start: 0.8476 (mpp) cc_final: 0.8263 (mpp) REVERT: E 193 MET cc_start: 0.8284 (mtm) cc_final: 0.7971 (mpp) REVERT: E 209 MET cc_start: 0.8582 (mtm) cc_final: 0.8381 (mtm) REVERT: F 56 MET cc_start: 0.9117 (mmm) cc_final: 0.8792 (mmm) REVERT: F 136 MET cc_start: 0.9274 (mmp) cc_final: 0.8487 (mmp) REVERT: F 209 MET cc_start: 0.8624 (ptp) cc_final: 0.8236 (ptp) REVERT: F 445 MET cc_start: 0.8063 (mmt) cc_final: 0.7652 (tmm) REVERT: G 48 MET cc_start: 0.9023 (ttm) cc_final: 0.8808 (ttm) REVERT: G 102 MET cc_start: 0.8691 (tmm) cc_final: 0.8426 (tmm) REVERT: G 187 LEU cc_start: 0.9128 (tp) cc_final: 0.8901 (tp) REVERT: G 194 ASP cc_start: 0.8210 (p0) cc_final: 0.7984 (m-30) REVERT: H 15 MET cc_start: 0.6302 (tpp) cc_final: 0.5845 (tpp) REVERT: H 49 MET cc_start: 0.3186 (ppp) cc_final: 0.2854 (ppp) REVERT: H 127 GLN cc_start: 0.6674 (mp10) cc_final: 0.6251 (tt0) REVERT: J 11 MET cc_start: 0.8485 (tpp) cc_final: 0.8098 (mtp) REVERT: L 75 MET cc_start: 0.6911 (ttt) cc_final: 0.6639 (ttt) REVERT: O 11 MET cc_start: 0.7590 (tpt) cc_final: 0.7130 (mtp) REVERT: O 16 MET cc_start: 0.6944 (ppp) cc_final: 0.6216 (ppp) REVERT: O 35 PHE cc_start: 0.7281 (t80) cc_final: 0.6872 (t80) REVERT: O 65 MET cc_start: 0.1543 (ptt) cc_final: 0.0805 (ptt) REVERT: P 17 MET cc_start: 0.5494 (ttp) cc_final: 0.5218 (tmm) REVERT: P 30 ILE cc_start: 0.7047 (tt) cc_final: 0.6762 (pt) REVERT: Q 53 PHE cc_start: 0.7403 (t80) cc_final: 0.6860 (t80) REVERT: Q 54 PHE cc_start: 0.7898 (m-80) cc_final: 0.6695 (t80) REVERT: R 11 MET cc_start: 0.5919 (mtm) cc_final: 0.5327 (mpp) REVERT: R 17 MET cc_start: 0.8008 (mtt) cc_final: 0.7387 (ptt) REVERT: S 17 MET cc_start: 0.4296 (ttt) cc_final: 0.4058 (tpt) REVERT: S 49 LEU cc_start: 0.9091 (mt) cc_final: 0.8691 (tp) REVERT: W 43 MET cc_start: 0.9196 (tpp) cc_final: 0.8831 (tpp) REVERT: X 22 MET cc_start: 0.4589 (ptp) cc_final: 0.4285 (ptp) REVERT: X 117 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.7695 (tmm160) REVERT: X 141 ASP cc_start: 0.8539 (m-30) cc_final: 0.7930 (t0) REVERT: Y 22 MET cc_start: 0.5447 (mmp) cc_final: 0.4591 (ttt) REVERT: Y 97 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8734 (tm-30) REVERT: Y 98 ARG cc_start: 0.8893 (mtp180) cc_final: 0.8456 (mmm-85) REVERT: Y 150 ASP cc_start: 0.9258 (m-30) cc_final: 0.8982 (m-30) REVERT: a 6 MET cc_start: -0.0383 (ttt) cc_final: -0.1304 (ttt) REVERT: a 47 MET cc_start: 0.6966 (tmm) cc_final: 0.6651 (ptt) REVERT: a 97 LYS cc_start: 0.7444 (mttt) cc_final: 0.6951 (pttt) outliers start: 2 outliers final: 0 residues processed: 360 average time/residue: 0.4738 time to fit residues: 289.0870 Evaluate side-chains 286 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 425 optimal weight: 4.9990 chunk 323 optimal weight: 20.0000 chunk 223 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 205 optimal weight: 8.9990 chunk 288 optimal weight: 10.0000 chunk 431 optimal weight: 40.0000 chunk 457 optimal weight: 5.9990 chunk 225 optimal weight: 8.9990 chunk 409 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 511 GLN C 185 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 37392 Z= 0.270 Angle : 0.631 15.485 50637 Z= 0.325 Chirality : 0.043 0.313 5901 Planarity : 0.005 0.073 6546 Dihedral : 7.521 145.368 5367 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.43 % Rotamer: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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 (0.12), residues: 4793 helix: 0.88 (0.10), residues: 2584 sheet: -0.06 (0.22), residues: 547 loop : -0.89 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 26 HIS 0.008 0.001 HIS H 38 PHE 0.037 0.002 PHE R 53 TYR 0.019 0.001 TYR I 10 ARG 0.017 0.000 ARG R 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 342 time to evaluate : 3.820 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: 0.8513 (mtp) cc_final: 0.8307 (mtp) REVERT: A 386 MET cc_start: 0.9214 (tpp) cc_final: 0.8677 (tpp) REVERT: A 448 LEU cc_start: 0.9577 (mt) cc_final: 0.9312 (mt) REVERT: A 468 GLU cc_start: 0.9099 (tt0) cc_final: 0.8722 (tm-30) REVERT: B 48 MET cc_start: 0.7827 (ptp) cc_final: 0.7050 (ptp) REVERT: B 52 MET cc_start: 0.7194 (mtm) cc_final: 0.6810 (mtm) REVERT: B 412 ASP cc_start: 0.7692 (m-30) cc_final: 0.7329 (t70) REVERT: B 468 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8702 (tm-30) REVERT: C 76 MET cc_start: 0.8464 (mpp) cc_final: 0.7875 (mtm) REVERT: C 86 MET cc_start: 0.9122 (mtt) cc_final: 0.8895 (mtm) REVERT: D 160 MET cc_start: 0.8374 (tpt) cc_final: 0.8141 (tpp) REVERT: D 209 MET cc_start: 0.8963 (mtp) cc_final: 0.8699 (mtp) REVERT: D 368 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8732 (tp40) REVERT: D 397 GLN cc_start: 0.9166 (tt0) cc_final: 0.8595 (tm-30) REVERT: E 209 MET cc_start: 0.8570 (mtm) cc_final: 0.8299 (mtm) REVERT: E 445 MET cc_start: 0.8746 (mmm) cc_final: 0.8470 (mmm) REVERT: F 56 MET cc_start: 0.9106 (mmm) cc_final: 0.8780 (mmm) REVERT: F 136 MET cc_start: 0.9250 (mmp) cc_final: 0.8380 (mmp) REVERT: F 209 MET cc_start: 0.8568 (ptp) cc_final: 0.8182 (ptp) REVERT: F 445 MET cc_start: 0.8159 (mmt) cc_final: 0.7622 (tmm) REVERT: G 23 MET cc_start: 0.8545 (ttm) cc_final: 0.8245 (ttm) REVERT: G 102 MET cc_start: 0.8658 (tmm) cc_final: 0.8396 (tmm) REVERT: G 187 LEU cc_start: 0.9115 (tp) cc_final: 0.8877 (tp) REVERT: G 243 MET cc_start: 0.9003 (mmm) cc_final: 0.8679 (mmm) REVERT: H 15 MET cc_start: 0.6435 (tpp) cc_final: 0.5853 (tpp) REVERT: H 49 MET cc_start: 0.3303 (ppp) cc_final: 0.3070 (ppp) REVERT: J 11 MET cc_start: 0.8428 (tpp) cc_final: 0.8121 (mtp) REVERT: M 54 PHE cc_start: 0.6678 (m-80) cc_final: 0.6295 (t80) REVERT: O 11 MET cc_start: 0.7616 (tpt) cc_final: 0.7051 (mtp) REVERT: O 16 MET cc_start: 0.7573 (ppp) cc_final: 0.7338 (tmm) REVERT: O 35 PHE cc_start: 0.7385 (t80) cc_final: 0.6918 (t80) REVERT: P 30 ILE cc_start: 0.7038 (tt) cc_final: 0.6756 (pt) REVERT: Q 53 PHE cc_start: 0.7902 (t80) cc_final: 0.7651 (t80) REVERT: R 17 MET cc_start: 0.8099 (mtt) cc_final: 0.7524 (ptt) REVERT: S 17 MET cc_start: 0.4840 (ttt) cc_final: 0.4466 (tpt) REVERT: S 35 PHE cc_start: 0.7224 (t80) cc_final: 0.6944 (t80) REVERT: W 43 MET cc_start: 0.9131 (tpp) cc_final: 0.8743 (tpp) REVERT: X 22 MET cc_start: 0.4861 (ptp) cc_final: 0.4592 (ptp) REVERT: X 141 ASP cc_start: 0.8467 (m-30) cc_final: 0.7957 (t0) REVERT: Y 22 MET cc_start: 0.5118 (mmp) cc_final: 0.4338 (ttt) REVERT: Y 98 ARG cc_start: 0.8879 (mtp180) cc_final: 0.8501 (mmm-85) REVERT: Y 150 ASP cc_start: 0.9262 (m-30) cc_final: 0.9015 (m-30) REVERT: a 6 MET cc_start: -0.0478 (ttt) cc_final: -0.0746 (ttt) REVERT: a 47 MET cc_start: 0.6938 (tmm) cc_final: 0.6608 (ptt) REVERT: a 97 LYS cc_start: 0.7360 (mttt) cc_final: 0.6791 (pttt) REVERT: a 216 TYR cc_start: 0.8424 (t80) cc_final: 0.7925 (t80) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.4626 time to fit residues: 267.7096 Evaluate side-chains 280 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 4.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 340 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 390 optimal weight: 10.0000 chunk 316 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 233 optimal weight: 0.9980 chunk 410 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN B 361 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN F 19 GLN G 35 GLN G 200 HIS H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37392 Z= 0.199 Angle : 0.586 9.918 50637 Z= 0.303 Chirality : 0.041 0.219 5901 Planarity : 0.005 0.069 6546 Dihedral : 7.181 129.591 5367 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.11 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 0.29 (0.12), residues: 4793 helix: 0.99 (0.10), residues: 2567 sheet: -0.02 (0.22), residues: 537 loop : -0.89 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 27 HIS 0.006 0.001 HIS H 38 PHE 0.033 0.002 PHE a 60 TYR 0.016 0.001 TYR a 216 ARG 0.013 0.000 ARG R 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 4.629 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: A 386 MET cc_start: 0.9120 (tpp) cc_final: 0.8889 (tpp) REVERT: A 448 LEU cc_start: 0.9563 (mt) cc_final: 0.9289 (mt) REVERT: B 48 MET cc_start: 0.7768 (ptp) cc_final: 0.7160 (ptp) REVERT: B 412 ASP cc_start: 0.7454 (m-30) cc_final: 0.7158 (t70) REVERT: B 468 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8671 (tm-30) REVERT: C 76 MET cc_start: 0.8512 (mpp) cc_final: 0.7911 (mtm) REVERT: C 86 MET cc_start: 0.9113 (mtt) cc_final: 0.8895 (mtm) REVERT: C 393 ILE cc_start: 0.8918 (pt) cc_final: 0.8638 (tp) REVERT: D 209 MET cc_start: 0.8971 (mtp) cc_final: 0.8735 (mtp) REVERT: D 368 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8775 (tp40) REVERT: D 397 GLN cc_start: 0.9151 (tt0) cc_final: 0.8598 (tm-30) REVERT: D 445 MET cc_start: 0.8692 (mmm) cc_final: 0.7927 (tpp) REVERT: E 209 MET cc_start: 0.8523 (mtm) cc_final: 0.8193 (mtm) REVERT: F 56 MET cc_start: 0.9100 (mmm) cc_final: 0.8760 (mmt) REVERT: F 130 ILE cc_start: 0.9692 (mt) cc_final: 0.9389 (mt) REVERT: F 136 MET cc_start: 0.9229 (mmp) cc_final: 0.8335 (mmp) REVERT: F 209 MET cc_start: 0.8480 (ptp) cc_final: 0.8150 (ptp) REVERT: F 445 MET cc_start: 0.8181 (mmt) cc_final: 0.7610 (tmm) REVERT: G 23 MET cc_start: 0.8586 (ttm) cc_final: 0.8285 (ttm) REVERT: G 102 MET cc_start: 0.8635 (tmm) cc_final: 0.8394 (tmm) REVERT: G 178 MET cc_start: 0.8709 (pmm) cc_final: 0.8328 (pmm) REVERT: G 187 LEU cc_start: 0.9115 (tp) cc_final: 0.8887 (tp) REVERT: H 15 MET cc_start: 0.6575 (tpp) cc_final: 0.5900 (tpp) REVERT: H 49 MET cc_start: 0.3608 (ppp) cc_final: 0.3377 (ppp) REVERT: J 11 MET cc_start: 0.8383 (tpp) cc_final: 0.8085 (mtp) REVERT: M 54 PHE cc_start: 0.6761 (m-80) cc_final: 0.6370 (t80) REVERT: O 11 MET cc_start: 0.7516 (tpt) cc_final: 0.6847 (mtp) REVERT: O 35 PHE cc_start: 0.7223 (t80) cc_final: 0.6295 (t80) REVERT: O 53 PHE cc_start: 0.7913 (t80) cc_final: 0.7324 (t80) REVERT: P 30 ILE cc_start: 0.6981 (tt) cc_final: 0.6721 (pt) REVERT: S 17 MET cc_start: 0.5257 (ttt) cc_final: 0.4783 (tpt) REVERT: W 43 MET cc_start: 0.9102 (tpp) cc_final: 0.8717 (tpp) REVERT: X 22 MET cc_start: 0.5083 (ptp) cc_final: 0.4817 (ptm) REVERT: X 117 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7691 (tmm160) REVERT: X 141 ASP cc_start: 0.8484 (m-30) cc_final: 0.8097 (t0) REVERT: Y 22 MET cc_start: 0.5094 (mmp) cc_final: 0.4316 (ttt) REVERT: Y 98 ARG cc_start: 0.8825 (mtp180) cc_final: 0.8524 (mmm-85) REVERT: Y 150 ASP cc_start: 0.9275 (m-30) cc_final: 0.9013 (m-30) REVERT: a 6 MET cc_start: -0.0520 (ttt) cc_final: -0.0768 (ttt) REVERT: a 47 MET cc_start: 0.6930 (tmm) cc_final: 0.6637 (ptt) REVERT: a 97 LYS cc_start: 0.7349 (mttt) cc_final: 0.6704 (pttt) REVERT: a 216 TYR cc_start: 0.8510 (t80) cc_final: 0.8250 (t80) REVERT: a 248 ILE cc_start: 0.7991 (mt) cc_final: 0.7621 (mt) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.4816 time to fit residues: 275.7421 Evaluate side-chains 274 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 4.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 10.0000 chunk 411 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 112 optimal weight: 0.0470 chunk 457 optimal weight: 5.9990 chunk 379 optimal weight: 9.9990 chunk 211 optimal weight: 0.0370 chunk 38 optimal weight: 0.0060 chunk 151 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 overall best weight: 1.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN C 185 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN G 200 HIS H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN a 33 GLN a 214 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37392 Z= 0.166 Angle : 0.569 9.160 50637 Z= 0.295 Chirality : 0.041 0.237 5901 Planarity : 0.004 0.046 6546 Dihedral : 6.875 122.287 5367 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.12), residues: 4793 helix: 1.06 (0.10), residues: 2605 sheet: 0.04 (0.22), residues: 535 loop : -0.80 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP W 27 HIS 0.008 0.001 HIS G 54 PHE 0.023 0.001 PHE R 35 TYR 0.016 0.001 TYR G 205 ARG 0.008 0.000 ARG a 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 4.431 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: 0.8447 (mtp) cc_final: 0.8167 (mtp) REVERT: A 386 MET cc_start: 0.9066 (tpp) cc_final: 0.8518 (tpp) REVERT: A 448 LEU cc_start: 0.9551 (mt) cc_final: 0.9294 (mt) REVERT: A 468 GLU cc_start: 0.9045 (tt0) cc_final: 0.8743 (tm-30) REVERT: B 48 MET cc_start: 0.7762 (ptp) cc_final: 0.7164 (ptp) REVERT: B 52 MET cc_start: 0.7364 (mtm) cc_final: 0.7092 (mtm) REVERT: B 412 ASP cc_start: 0.7302 (m-30) cc_final: 0.7038 (t70) REVERT: B 468 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8658 (tm-30) REVERT: C 76 MET cc_start: 0.8487 (mpp) cc_final: 0.7866 (mtm) REVERT: C 86 MET cc_start: 0.9045 (mtt) cc_final: 0.8834 (mtm) REVERT: C 393 ILE cc_start: 0.8917 (pt) cc_final: 0.8630 (tp) REVERT: D 209 MET cc_start: 0.8927 (mtp) cc_final: 0.8697 (mtp) REVERT: D 368 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8825 (tp40) REVERT: D 397 GLN cc_start: 0.9100 (tt0) cc_final: 0.8594 (tm-30) REVERT: D 445 MET cc_start: 0.8670 (mmm) cc_final: 0.7935 (tpp) REVERT: E 209 MET cc_start: 0.8494 (mtm) cc_final: 0.8148 (mtm) REVERT: E 275 MET cc_start: 0.9454 (tpp) cc_final: 0.9129 (tpp) REVERT: F 56 MET cc_start: 0.9099 (mmm) cc_final: 0.8872 (mmm) REVERT: F 136 MET cc_start: 0.9225 (mmp) cc_final: 0.8237 (mmp) REVERT: F 209 MET cc_start: 0.8310 (ptp) cc_final: 0.8056 (ptp) REVERT: F 294 GLN cc_start: 0.9032 (mt0) cc_final: 0.8801 (mp10) REVERT: F 445 MET cc_start: 0.8236 (mmt) cc_final: 0.7632 (tmm) REVERT: G 23 MET cc_start: 0.8597 (ttm) cc_final: 0.8304 (ttm) REVERT: G 102 MET cc_start: 0.8609 (tmm) cc_final: 0.8374 (tmm) REVERT: G 178 MET cc_start: 0.8688 (pmm) cc_final: 0.8350 (pmm) REVERT: G 187 LEU cc_start: 0.9097 (tp) cc_final: 0.8894 (tp) REVERT: H 15 MET cc_start: 0.6242 (tpp) cc_final: 0.5691 (tpp) REVERT: H 23 ILE cc_start: 0.7620 (pt) cc_final: 0.7099 (mm) REVERT: H 49 MET cc_start: 0.3825 (ppp) cc_final: 0.3597 (ppp) REVERT: J 11 MET cc_start: 0.8420 (tpp) cc_final: 0.8044 (mmm) REVERT: L 6 MET cc_start: 0.3518 (tmm) cc_final: 0.3276 (tmm) REVERT: L 17 MET cc_start: 0.5719 (mpp) cc_final: 0.5414 (mpp) REVERT: L 75 MET cc_start: 0.6437 (ttt) cc_final: 0.6001 (mmt) REVERT: M 54 PHE cc_start: 0.6832 (m-80) cc_final: 0.6449 (t80) REVERT: O 11 MET cc_start: 0.7369 (tpt) cc_final: 0.6813 (mtp) REVERT: O 16 MET cc_start: 0.7281 (tmm) cc_final: 0.6209 (ppp) REVERT: O 35 PHE cc_start: 0.7118 (t80) cc_final: 0.6210 (t80) REVERT: O 53 PHE cc_start: 0.7878 (t80) cc_final: 0.7248 (t80) REVERT: P 30 ILE cc_start: 0.6913 (tt) cc_final: 0.6638 (pt) REVERT: Q 53 PHE cc_start: 0.7686 (t80) cc_final: 0.7473 (t80) REVERT: Q 60 VAL cc_start: 0.3872 (t) cc_final: 0.2898 (t) REVERT: R 16 MET cc_start: 0.5275 (ttt) cc_final: 0.4936 (ttm) REVERT: R 17 MET cc_start: 0.7781 (mtt) cc_final: 0.7201 (tpt) REVERT: S 17 MET cc_start: 0.5317 (ttt) cc_final: 0.4669 (tpt) REVERT: X 22 MET cc_start: 0.5134 (ptp) cc_final: 0.4852 (ptm) REVERT: X 117 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7645 (tmm160) REVERT: X 141 ASP cc_start: 0.8451 (m-30) cc_final: 0.8092 (t0) REVERT: Y 22 MET cc_start: 0.4939 (mmp) cc_final: 0.4185 (ttt) REVERT: Y 98 ARG cc_start: 0.8829 (mtp180) cc_final: 0.8541 (mmm-85) REVERT: Y 150 ASP cc_start: 0.9280 (m-30) cc_final: 0.9019 (m-30) REVERT: a 6 MET cc_start: -0.0548 (ttt) cc_final: -0.0800 (ttt) REVERT: a 47 MET cc_start: 0.6911 (tmm) cc_final: 0.6564 (ptt) REVERT: a 97 LYS cc_start: 0.7389 (mttt) cc_final: 0.6608 (ttpt) REVERT: a 216 TYR cc_start: 0.8558 (t80) cc_final: 0.8183 (t80) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.4868 time to fit residues: 272.5311 Evaluate side-chains 269 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 334 optimal weight: 0.9990 chunk 258 optimal weight: 10.0000 chunk 385 optimal weight: 5.9990 chunk 255 optimal weight: 0.0770 chunk 455 optimal weight: 20.0000 chunk 285 optimal weight: 7.9990 chunk 277 optimal weight: 0.1980 chunk 210 optimal weight: 7.9990 overall best weight: 2.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN G 200 HIS H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN a 214 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37392 Z= 0.177 Angle : 0.567 11.282 50637 Z= 0.293 Chirality : 0.041 0.189 5901 Planarity : 0.004 0.052 6546 Dihedral : 6.672 117.778 5367 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.05 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.12), residues: 4793 helix: 1.09 (0.10), residues: 2600 sheet: -0.04 (0.22), residues: 533 loop : -0.77 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP W 27 HIS 0.004 0.001 HIS H 5 PHE 0.025 0.001 PHE R 35 TYR 0.016 0.001 TYR a 216 ARG 0.007 0.000 ARG a 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 4.667 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 48 MET cc_start: 0.8447 (mpp) cc_final: 0.8206 (mmt) REVERT: A 156 MET cc_start: 0.8439 (mtp) cc_final: 0.8147 (mtp) REVERT: A 245 MET cc_start: 0.8484 (mpp) cc_final: 0.8182 (mpp) REVERT: A 386 MET cc_start: 0.9079 (tpp) cc_final: 0.8543 (tpp) REVERT: A 448 LEU cc_start: 0.9555 (mt) cc_final: 0.9276 (mt) REVERT: A 468 GLU cc_start: 0.9073 (tt0) cc_final: 0.8800 (tm-30) REVERT: B 48 MET cc_start: 0.7891 (ptp) cc_final: 0.7293 (ptp) REVERT: B 52 MET cc_start: 0.7285 (mtm) cc_final: 0.6992 (mtm) REVERT: B 412 ASP cc_start: 0.7406 (m-30) cc_final: 0.7082 (t70) REVERT: B 439 MET cc_start: 0.9154 (mmm) cc_final: 0.8937 (mmm) REVERT: B 468 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8670 (tm-30) REVERT: C 76 MET cc_start: 0.8461 (mpp) cc_final: 0.7865 (mtm) REVERT: C 393 ILE cc_start: 0.8906 (pt) cc_final: 0.8610 (tp) REVERT: D 209 MET cc_start: 0.8946 (mtp) cc_final: 0.8724 (mtp) REVERT: D 368 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8857 (tp40) REVERT: D 397 GLN cc_start: 0.9095 (tt0) cc_final: 0.8609 (tm-30) REVERT: E 193 MET cc_start: 0.8411 (mpp) cc_final: 0.8181 (mpp) REVERT: E 209 MET cc_start: 0.8524 (mtm) cc_final: 0.8115 (mtm) REVERT: F 56 MET cc_start: 0.9082 (mmm) cc_final: 0.8870 (mmm) REVERT: F 136 MET cc_start: 0.9218 (mmp) cc_final: 0.8243 (mmp) REVERT: F 294 GLN cc_start: 0.9015 (mt0) cc_final: 0.8797 (mp10) REVERT: F 445 MET cc_start: 0.8269 (mmt) cc_final: 0.7638 (tmm) REVERT: G 102 MET cc_start: 0.8578 (tmm) cc_final: 0.8362 (tmm) REVERT: G 178 MET cc_start: 0.8666 (pmm) cc_final: 0.8351 (pmm) REVERT: G 243 MET cc_start: 0.8872 (mmm) cc_final: 0.8542 (mmm) REVERT: H 15 MET cc_start: 0.6434 (tpp) cc_final: 0.5869 (tpp) REVERT: J 11 MET cc_start: 0.8334 (tpp) cc_final: 0.8055 (mtp) REVERT: L 6 MET cc_start: 0.3490 (tmm) cc_final: 0.3261 (tmm) REVERT: L 17 MET cc_start: 0.5854 (mpp) cc_final: 0.5590 (mpp) REVERT: L 68 VAL cc_start: 0.6239 (t) cc_final: 0.5972 (t) REVERT: L 75 MET cc_start: 0.6611 (ttt) cc_final: 0.6268 (mmt) REVERT: M 54 PHE cc_start: 0.6852 (m-80) cc_final: 0.6453 (t80) REVERT: O 11 MET cc_start: 0.7395 (tpt) cc_final: 0.6718 (mtp) REVERT: O 16 MET cc_start: 0.7098 (tmm) cc_final: 0.6326 (ppp) REVERT: O 35 PHE cc_start: 0.6975 (t80) cc_final: 0.6054 (t80) REVERT: O 53 PHE cc_start: 0.7923 (t80) cc_final: 0.7326 (t80) REVERT: P 30 ILE cc_start: 0.6735 (tt) cc_final: 0.6443 (pt) REVERT: Q 35 PHE cc_start: 0.6661 (t80) cc_final: 0.6368 (t80) REVERT: R 16 MET cc_start: 0.5323 (ttt) cc_final: 0.5007 (ttm) REVERT: R 17 MET cc_start: 0.7848 (mtt) cc_final: 0.7251 (tpt) REVERT: S 17 MET cc_start: 0.5433 (ttt) cc_final: 0.4814 (tpt) REVERT: X 22 MET cc_start: 0.5107 (ptp) cc_final: 0.4828 (ptm) REVERT: X 117 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7674 (tmm160) REVERT: X 141 ASP cc_start: 0.8433 (m-30) cc_final: 0.8093 (t0) REVERT: Y 22 MET cc_start: 0.4949 (mmp) cc_final: 0.4194 (ttt) REVERT: Y 98 ARG cc_start: 0.8836 (mtp180) cc_final: 0.8569 (mmm-85) REVERT: Y 150 ASP cc_start: 0.9305 (m-30) cc_final: 0.9050 (m-30) REVERT: a 6 MET cc_start: -0.0600 (ttt) cc_final: -0.0830 (ttt) REVERT: a 47 MET cc_start: 0.6938 (tmm) cc_final: 0.6592 (ptt) REVERT: a 97 LYS cc_start: 0.7292 (mttt) cc_final: 0.6515 (ttpt) REVERT: a 216 TYR cc_start: 0.8489 (t80) cc_final: 0.8279 (t80) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.4763 time to fit residues: 265.7211 Evaluate side-chains 274 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 272 optimal weight: 10.0000 chunk 137 optimal weight: 0.0270 chunk 89 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 289 optimal weight: 0.8980 chunk 310 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 358 optimal weight: 0.0570 overall best weight: 1.1758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 425 GLN C 185 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN G 200 HIS H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 82 ASN X 85 GLN a 33 GLN a 214 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 37392 Z= 0.157 Angle : 0.558 13.043 50637 Z= 0.286 Chirality : 0.041 0.186 5901 Planarity : 0.004 0.066 6546 Dihedral : 6.498 118.020 5367 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.86 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 0.55 (0.12), residues: 4793 helix: 1.18 (0.10), residues: 2597 sheet: 0.03 (0.22), residues: 545 loop : -0.74 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 107 HIS 0.005 0.001 HIS D 170 PHE 0.014 0.001 PHE Q 53 TYR 0.023 0.001 TYR R 10 ARG 0.007 0.000 ARG Y 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 4.096 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 48 MET cc_start: 0.8445 (mpp) cc_final: 0.8204 (mmt) REVERT: A 156 MET cc_start: 0.8429 (mtp) cc_final: 0.8147 (mtp) REVERT: A 386 MET cc_start: 0.9047 (tpp) cc_final: 0.8562 (tpp) REVERT: A 448 LEU cc_start: 0.9562 (mt) cc_final: 0.9294 (mt) REVERT: A 468 GLU cc_start: 0.9050 (tt0) cc_final: 0.8799 (tm-30) REVERT: B 48 MET cc_start: 0.7775 (ptp) cc_final: 0.7313 (ptp) REVERT: B 52 MET cc_start: 0.7233 (mtm) cc_final: 0.6955 (mtm) REVERT: B 412 ASP cc_start: 0.7524 (m-30) cc_final: 0.7146 (t70) REVERT: B 439 MET cc_start: 0.9147 (mmm) cc_final: 0.8925 (mmm) REVERT: C 76 MET cc_start: 0.8461 (mpp) cc_final: 0.7642 (mtm) REVERT: D 379 MET cc_start: 0.7862 (tmm) cc_final: 0.7498 (tmm) REVERT: D 397 GLN cc_start: 0.9066 (tt0) cc_final: 0.8603 (tm-30) REVERT: E 193 MET cc_start: 0.8437 (mpp) cc_final: 0.8182 (mpp) REVERT: E 275 MET cc_start: 0.9474 (tpp) cc_final: 0.9130 (tpp) REVERT: F 56 MET cc_start: 0.9097 (mmm) cc_final: 0.8866 (mmm) REVERT: F 136 MET cc_start: 0.9190 (mmp) cc_final: 0.8224 (mmp) REVERT: F 209 MET cc_start: 0.7970 (ptp) cc_final: 0.7761 (ptp) REVERT: F 445 MET cc_start: 0.8230 (mmt) cc_final: 0.7585 (tmm) REVERT: G 31 MET cc_start: 0.9124 (tmm) cc_final: 0.8801 (tmm) REVERT: G 48 MET cc_start: 0.9229 (ttm) cc_final: 0.8707 (mtp) REVERT: G 102 MET cc_start: 0.8550 (tmm) cc_final: 0.8342 (tmm) REVERT: G 178 MET cc_start: 0.8634 (pmm) cc_final: 0.8323 (pmm) REVERT: G 187 LEU cc_start: 0.9089 (tp) cc_final: 0.8878 (tp) REVERT: G 246 MET cc_start: 0.8967 (mmp) cc_final: 0.8694 (mmp) REVERT: H 15 MET cc_start: 0.6423 (tpp) cc_final: 0.5845 (tpp) REVERT: H 23 ILE cc_start: 0.7257 (tt) cc_final: 0.6651 (mm) REVERT: H 25 VAL cc_start: 0.8922 (t) cc_final: 0.8621 (t) REVERT: J 11 MET cc_start: 0.8304 (tpp) cc_final: 0.8016 (mtp) REVERT: L 6 MET cc_start: 0.3702 (tmm) cc_final: 0.3468 (tmm) REVERT: L 75 MET cc_start: 0.6542 (ttt) cc_final: 0.6160 (mmt) REVERT: M 54 PHE cc_start: 0.6847 (m-80) cc_final: 0.6449 (t80) REVERT: O 11 MET cc_start: 0.7369 (tpt) cc_final: 0.6707 (mtp) REVERT: O 16 MET cc_start: 0.7050 (tmm) cc_final: 0.6424 (ppp) REVERT: O 35 PHE cc_start: 0.7107 (t80) cc_final: 0.6166 (t80) REVERT: O 53 PHE cc_start: 0.8014 (t80) cc_final: 0.7529 (t80) REVERT: P 11 MET cc_start: 0.6673 (mpp) cc_final: 0.6319 (mpp) REVERT: P 30 ILE cc_start: 0.6755 (tt) cc_final: 0.6467 (pt) REVERT: Q 11 MET cc_start: 0.7621 (ppp) cc_final: 0.7356 (ppp) REVERT: Q 60 VAL cc_start: 0.3922 (t) cc_final: 0.2891 (t) REVERT: R 16 MET cc_start: 0.5237 (ttt) cc_final: 0.4933 (ttm) REVERT: R 17 MET cc_start: 0.7853 (mtt) cc_final: 0.7304 (tpt) REVERT: S 17 MET cc_start: 0.5302 (ttt) cc_final: 0.4661 (tpt) REVERT: X 22 MET cc_start: 0.5120 (ptp) cc_final: 0.4826 (ptm) REVERT: X 117 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7698 (tmm160) REVERT: X 141 ASP cc_start: 0.8413 (m-30) cc_final: 0.8070 (t0) REVERT: Y 22 MET cc_start: 0.4701 (mmp) cc_final: 0.3927 (ttt) REVERT: Y 98 ARG cc_start: 0.8839 (mtp180) cc_final: 0.8589 (mmm-85) REVERT: Y 150 ASP cc_start: 0.9333 (m-30) cc_final: 0.9087 (m-30) REVERT: a 6 MET cc_start: -0.0703 (ttt) cc_final: -0.0941 (ttt) REVERT: a 47 MET cc_start: 0.6820 (tmm) cc_final: 0.6466 (ptt) REVERT: a 97 LYS cc_start: 0.7355 (mttt) cc_final: 0.6583 (ttpt) REVERT: a 157 VAL cc_start: 0.8488 (t) cc_final: 0.8213 (p) REVERT: a 216 TYR cc_start: 0.8412 (t80) cc_final: 0.8165 (t80) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.4602 time to fit residues: 261.8255 Evaluate side-chains 277 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 4.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 414 optimal weight: 30.0000 chunk 436 optimal weight: 0.8980 chunk 398 optimal weight: 8.9990 chunk 424 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 333 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 383 optimal weight: 0.0670 chunk 401 optimal weight: 1.9990 chunk 423 optimal weight: 6.9990 overall best weight: 3.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN C 185 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN a 214 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37392 Z= 0.220 Angle : 0.592 10.947 50637 Z= 0.305 Chirality : 0.042 0.436 5901 Planarity : 0.004 0.047 6546 Dihedral : 6.517 118.677 5367 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.42 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 4793 helix: 1.11 (0.10), residues: 2608 sheet: 0.13 (0.22), residues: 544 loop : -0.74 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 107 HIS 0.006 0.001 HIS D 170 PHE 0.027 0.002 PHE a 163 TYR 0.019 0.001 TYR R 10 ARG 0.009 0.000 ARG X 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 4.349 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 48 MET cc_start: 0.8518 (mpp) cc_final: 0.8266 (mmt) REVERT: A 245 MET cc_start: 0.8486 (mpp) cc_final: 0.8272 (mpp) REVERT: A 386 MET cc_start: 0.9115 (tpp) cc_final: 0.8592 (tpp) REVERT: A 448 LEU cc_start: 0.9573 (mt) cc_final: 0.9292 (mt) REVERT: A 468 GLU cc_start: 0.9074 (tt0) cc_final: 0.8796 (tm-30) REVERT: B 48 MET cc_start: 0.7895 (ptp) cc_final: 0.7388 (ptp) REVERT: B 52 MET cc_start: 0.7126 (mtm) cc_final: 0.6917 (mtm) REVERT: B 412 ASP cc_start: 0.7542 (m-30) cc_final: 0.7179 (t70) REVERT: B 439 MET cc_start: 0.9152 (mmm) cc_final: 0.8927 (mmm) REVERT: C 76 MET cc_start: 0.8450 (mpp) cc_final: 0.7763 (mtm) REVERT: D 209 MET cc_start: 0.8614 (mtp) cc_final: 0.8413 (mtt) REVERT: D 397 GLN cc_start: 0.9130 (tt0) cc_final: 0.8679 (tm-30) REVERT: D 445 MET cc_start: 0.8850 (mmm) cc_final: 0.8099 (mmm) REVERT: E 275 MET cc_start: 0.9488 (tpp) cc_final: 0.9054 (tpp) REVERT: F 56 MET cc_start: 0.9053 (mmm) cc_final: 0.8846 (mmm) REVERT: F 136 MET cc_start: 0.9208 (mmp) cc_final: 0.8251 (mmp) REVERT: F 209 MET cc_start: 0.8086 (ptp) cc_final: 0.7782 (ptp) REVERT: F 445 MET cc_start: 0.8232 (mmt) cc_final: 0.7546 (tmm) REVERT: G 178 MET cc_start: 0.8662 (pmm) cc_final: 0.8388 (pmm) REVERT: H 15 MET cc_start: 0.6723 (tpp) cc_final: 0.6255 (tpp) REVERT: J 11 MET cc_start: 0.8327 (tpp) cc_final: 0.8009 (mtp) REVERT: J 35 PHE cc_start: 0.6906 (t80) cc_final: 0.6696 (t80) REVERT: L 6 MET cc_start: 0.3874 (tmm) cc_final: 0.3638 (tmm) REVERT: L 75 MET cc_start: 0.6577 (ttt) cc_final: 0.6191 (mmt) REVERT: M 54 PHE cc_start: 0.6879 (m-80) cc_final: 0.6443 (t80) REVERT: O 11 MET cc_start: 0.7410 (tpt) cc_final: 0.6692 (mtp) REVERT: O 35 PHE cc_start: 0.7075 (t80) cc_final: 0.6111 (t80) REVERT: O 53 PHE cc_start: 0.8076 (t80) cc_final: 0.7581 (t80) REVERT: P 11 MET cc_start: 0.6571 (mpp) cc_final: 0.6196 (mpp) REVERT: P 30 ILE cc_start: 0.6774 (tt) cc_final: 0.6487 (pt) REVERT: Q 11 MET cc_start: 0.7584 (ppp) cc_final: 0.7307 (ppp) REVERT: R 16 MET cc_start: 0.5287 (ttt) cc_final: 0.4968 (ttm) REVERT: R 17 MET cc_start: 0.7792 (mtt) cc_final: 0.7395 (tpt) REVERT: R 75 MET cc_start: 0.3645 (ttt) cc_final: 0.3320 (tmm) REVERT: S 17 MET cc_start: 0.5172 (ttt) cc_final: 0.4631 (tpt) REVERT: X 22 MET cc_start: 0.5070 (ptp) cc_final: 0.4781 (ptm) REVERT: X 117 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7730 (tmm160) REVERT: X 141 ASP cc_start: 0.8406 (m-30) cc_final: 0.8068 (t0) REVERT: Y 22 MET cc_start: 0.4737 (mmp) cc_final: 0.3994 (ttt) REVERT: Y 98 ARG cc_start: 0.8885 (mtp180) cc_final: 0.8581 (mmm-85) REVERT: a 6 MET cc_start: -0.0653 (ttt) cc_final: -0.0885 (ttt) REVERT: a 47 MET cc_start: 0.6768 (tmm) cc_final: 0.6426 (ptt) REVERT: a 97 LYS cc_start: 0.7291 (mttt) cc_final: 0.6642 (pttt) REVERT: a 157 VAL cc_start: 0.8583 (t) cc_final: 0.8297 (p) REVERT: a 216 TYR cc_start: 0.8427 (t80) cc_final: 0.8220 (t80) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.5102 time to fit residues: 280.9800 Evaluate side-chains 269 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 4.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 278 optimal weight: 1.9990 chunk 449 optimal weight: 50.0000 chunk 274 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 chunk 312 optimal weight: 9.9990 chunk 471 optimal weight: 7.9990 chunk 433 optimal weight: 6.9990 chunk 375 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 289 optimal weight: 4.9990 chunk 230 optimal weight: 0.0870 overall best weight: 2.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN a 214 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37392 Z= 0.202 Angle : 0.597 12.303 50637 Z= 0.304 Chirality : 0.042 0.414 5901 Planarity : 0.004 0.047 6546 Dihedral : 6.483 123.484 5367 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.19 % Favored : 96.79 % Rotamer: Outliers : 0.03 % Allowed : 0.37 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.12), residues: 4793 helix: 1.09 (0.10), residues: 2605 sheet: 0.31 (0.22), residues: 525 loop : -0.73 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP W 27 HIS 0.005 0.001 HIS H 38 PHE 0.027 0.001 PHE a 163 TYR 0.021 0.001 TYR G 205 ARG 0.011 0.000 ARG G 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 323 time to evaluate : 4.500 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 48 MET cc_start: 0.8540 (mpp) cc_final: 0.8285 (mmt) REVERT: A 245 MET cc_start: 0.8462 (mpp) cc_final: 0.8182 (mpp) REVERT: A 386 MET cc_start: 0.9116 (tpp) cc_final: 0.8578 (tpp) REVERT: A 448 LEU cc_start: 0.9580 (mt) cc_final: 0.9293 (mt) REVERT: A 468 GLU cc_start: 0.9061 (tt0) cc_final: 0.8793 (tm-30) REVERT: B 48 MET cc_start: 0.7873 (ptp) cc_final: 0.7353 (ptp) REVERT: B 52 MET cc_start: 0.7256 (mtm) cc_final: 0.7016 (mtm) REVERT: B 412 ASP cc_start: 0.7624 (m-30) cc_final: 0.7224 (t70) REVERT: B 439 MET cc_start: 0.9186 (mmm) cc_final: 0.8942 (mmm) REVERT: D 160 MET cc_start: 0.8372 (tpt) cc_final: 0.8081 (tpt) REVERT: D 275 MET cc_start: 0.8808 (tpp) cc_final: 0.8592 (tpt) REVERT: D 397 GLN cc_start: 0.9136 (tt0) cc_final: 0.8665 (tm-30) REVERT: E 193 MET cc_start: 0.8664 (mpp) cc_final: 0.8291 (mpp) REVERT: F 56 MET cc_start: 0.9053 (mmm) cc_final: 0.8845 (mmm) REVERT: F 136 MET cc_start: 0.9165 (mmp) cc_final: 0.8336 (mmp) REVERT: F 445 MET cc_start: 0.8239 (mmt) cc_final: 0.7522 (tmm) REVERT: G 31 MET cc_start: 0.9103 (tmm) cc_final: 0.8835 (tmm) REVERT: G 178 MET cc_start: 0.8608 (pmm) cc_final: 0.8329 (pmm) REVERT: H 49 MET cc_start: 0.3341 (ppp) cc_final: 0.3098 (ppp) REVERT: I 17 MET cc_start: 0.1732 (ppp) cc_final: 0.1513 (ppp) REVERT: J 11 MET cc_start: 0.8330 (tpp) cc_final: 0.8053 (mtt) REVERT: J 35 PHE cc_start: 0.7016 (t80) cc_final: 0.6810 (t80) REVERT: L 6 MET cc_start: 0.3964 (tmm) cc_final: 0.3726 (tmm) REVERT: L 75 MET cc_start: 0.6616 (ttt) cc_final: 0.6273 (mmt) REVERT: M 54 PHE cc_start: 0.7030 (m-80) cc_final: 0.6576 (t80) REVERT: N 37 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8243 (mm-30) REVERT: O 11 MET cc_start: 0.7407 (tpt) cc_final: 0.6713 (mtp) REVERT: O 16 MET cc_start: 0.6810 (tmm) cc_final: 0.6253 (tmm) REVERT: O 35 PHE cc_start: 0.7024 (t80) cc_final: 0.6176 (t80) REVERT: O 53 PHE cc_start: 0.7968 (t80) cc_final: 0.7537 (t80) REVERT: P 11 MET cc_start: 0.6389 (mpp) cc_final: 0.5988 (mpp) REVERT: P 30 ILE cc_start: 0.6769 (tt) cc_final: 0.6509 (pt) REVERT: Q 11 MET cc_start: 0.7573 (ppp) cc_final: 0.7306 (ppp) REVERT: Q 35 PHE cc_start: 0.6863 (t80) cc_final: 0.6463 (t80) REVERT: R 16 MET cc_start: 0.5167 (ttt) cc_final: 0.4839 (ttm) REVERT: R 17 MET cc_start: 0.7984 (mtt) cc_final: 0.7296 (tpt) REVERT: R 75 MET cc_start: 0.3593 (ttt) cc_final: 0.3348 (tmm) REVERT: S 17 MET cc_start: 0.5483 (ttt) cc_final: 0.5021 (tpt) REVERT: W 43 MET cc_start: 0.8960 (tpt) cc_final: 0.8414 (tpt) REVERT: X 22 MET cc_start: 0.4920 (ptp) cc_final: 0.4645 (ptm) REVERT: X 69 LYS cc_start: 0.5158 (tptt) cc_final: 0.4875 (tptm) REVERT: X 117 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7728 (tmm160) REVERT: X 141 ASP cc_start: 0.8354 (m-30) cc_final: 0.8017 (t0) REVERT: Y 22 MET cc_start: 0.4702 (mmp) cc_final: 0.3966 (ttt) REVERT: Y 98 ARG cc_start: 0.8850 (mtp180) cc_final: 0.8575 (mmm-85) REVERT: a 6 MET cc_start: -0.0680 (ttt) cc_final: -0.0884 (ttt) REVERT: a 47 MET cc_start: 0.6806 (tmm) cc_final: 0.6425 (ptt) REVERT: a 97 LYS cc_start: 0.7308 (mttt) cc_final: 0.6663 (pttt) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.4718 time to fit residues: 260.5261 Evaluate side-chains 270 residues out of total 3824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 298 optimal weight: 6.9990 chunk 399 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 345 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 104 optimal weight: 0.0980 chunk 375 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 385 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 overall best weight: 3.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN C 185 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 ASN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN a 214 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.058552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.041646 restraints weight = 254999.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.042680 restraints weight = 138436.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.043367 restraints weight = 88423.852| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37392 Z= 0.224 Angle : 0.612 10.494 50637 Z= 0.312 Chirality : 0.042 0.387 5901 Planarity : 0.004 0.047 6546 Dihedral : 6.484 124.834 5367 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.59 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.12), residues: 4793 helix: 1.08 (0.10), residues: 2603 sheet: 0.28 (0.22), residues: 526 loop : -0.72 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 107 HIS 0.007 0.001 HIS H 38 PHE 0.029 0.002 PHE a 163 TYR 0.020 0.001 TYR R 10 ARG 0.009 0.000 ARG X 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6991.63 seconds wall clock time: 128 minutes 23.64 seconds (7703.64 seconds total)