Starting phenix.real_space_refine on Fri Feb 23 05:09:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbu_27307/02_2024/8dbu_27307_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbu_27307/02_2024/8dbu_27307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbu_27307/02_2024/8dbu_27307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbu_27307/02_2024/8dbu_27307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbu_27307/02_2024/8dbu_27307_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbu_27307/02_2024/8dbu_27307_updated.pdb" } resolution = 3.4 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 179 5.16 5 C 23452 2.51 5 N 6307 2.21 5 O 6958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "R TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36917 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3826 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3877 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3849 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 18, 'TRANS': 491} Chain: "D" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 274} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1021 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "X" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1190 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 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: "E" 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: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.94, per 1000 atoms: 0.51 Number of scatterers: 36917 At special positions: 0 Unit cell: (181.272, 219.037, 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 179 16.00 P 16 15.00 Mg 5 11.99 O 6958 8.00 N 6307 7.00 C 23452 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: 16.33 Conformation dependent library (CDL) restraints added in 7.4 seconds 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8806 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 179 helices and 26 sheets defined 56.0% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.70 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 removed outlier: 3.595A pdb=" N ALA A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) 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 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.803A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.897A 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 288 through 300 removed outlier: 3.914A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 293 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.092A 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 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 407 removed outlier: 3.581A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 431 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 5.345A pdb=" N GLY A 465 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 466 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP A 478 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 494 through 509 Processing helix chain 'B' and resid 3 through 18 removed outlier: 3.821A pdb=" N ILE B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.516A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 238 through 252 removed outlier: 3.787A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.946A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 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 Processing helix chain 'B' and resid 384 through 407 removed outlier: 5.009A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 430 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 462 through 478 removed outlier: 4.477A pdb=" N SER B 466 " --> 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 510 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 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.766A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 238 through 252 removed outlier: 3.799A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.069A 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 288 through 300 removed outlier: 4.590A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 409 removed outlier: 4.304A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 478 removed outlier: 3.696A pdb=" N ILE C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 508 removed outlier: 3.858A pdb=" N LYS C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) 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: 3.833A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 213 through 232 removed outlier: 4.883A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 255 removed outlier: 3.672A pdb=" N GLU D 253 " --> pdb=" O ALA D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 281 removed outlier: 3.581A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG D 281 " --> pdb=" O VAL D 277 " (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: 4.233A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 removed outlier: 3.613A pdb=" N LEU D 328 " --> pdb=" O GLN D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 351 through 377 removed outlier: 4.286A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 376 " --> pdb=" O ASP D 372 " (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 removed outlier: 3.524A pdb=" N LEU D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 411 No H-bonds generated for 'chain 'D' and resid 408 through 411' Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.779A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 116 through 118 No H-bonds generated for 'chain 'E' and resid 116 through 118' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 169 removed outlier: 3.883A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU E 169 " --> pdb=" O ASN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 232 removed outlier: 4.342A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 257 removed outlier: 3.680A pdb=" N THR E 248 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 281 removed outlier: 4.303A pdb=" N ARG E 281 " --> pdb=" O VAL E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 306 through 314 removed outlier: 4.428A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N HIS E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 removed outlier: 4.210A pdb=" N LEU E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 377 removed outlier: 7.759A pdb=" N GLN E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N GLU E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS E 353 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (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 removed outlier: 3.623A pdb=" N ARG E 398 " --> pdb=" O ARG E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 433 through 435 No H-bonds generated for 'chain 'E' and resid 433 through 435' Processing helix chain 'E' and resid 449 through 458 removed outlier: 3.800A pdb=" N VAL E 453 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' 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 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 155 through 168 Processing helix chain 'F' and resid 183 through 196 Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 213 through 232 removed outlier: 4.895A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 271 through 281 removed outlier: 4.312A pdb=" N ARG F 281 " --> pdb=" O VAL F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 312 Processing helix chain 'F' and resid 323 through 328 removed outlier: 3.607A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) 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 376 removed outlier: 4.059A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (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 386 through 399 removed outlier: 3.624A pdb=" N LYS F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 3.850A pdb=" N GLU F 408 " --> pdb=" O PHE F 405 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL F 409 " --> pdb=" O VAL F 406 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR F 411 " --> pdb=" O GLU F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 432 Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 449 through 458 removed outlier: 3.822A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 56 removed outlier: 4.079A pdb=" N GLU G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA G 27 " --> pdb=" O MET G 23 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Proline residue: G 43 - end of helix removed outlier: 3.752A pdb=" N GLY G 53 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS G 54 " --> pdb=" O LYS G 50 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU G 55 " --> pdb=" O VAL G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 108 removed outlier: 3.837A pdb=" N LYS G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 149 through 160 Processing helix chain 'G' and resid 211 through 282 Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 91 through 107 removed outlier: 3.650A pdb=" N SER H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 135 removed outlier: 3.846A pdb=" N ALA H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS H 135 " --> pdb=" O ILE H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 41 removed outlier: 3.598A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 77 Proline residue: I 47 - end of helix removed outlier: 3.813A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 41 removed outlier: 4.031A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 60 removed outlier: 3.582A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 76 removed outlier: 3.870A pdb=" N ILE J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA J 67 " --> pdb=" O ILE J 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 41 removed outlier: 3.683A pdb=" N LEU L 8 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR L 10 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL L 15 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA L 20 " --> pdb=" O MET L 17 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA L 24 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE L 26 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY L 27 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY L 33 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG L 41 " --> pdb=" O GLY L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.698A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 4.182A pdb=" N ARG L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY L 58 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 3.576A pdb=" N VAL L 68 " --> pdb=" O MET L 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU L 70 " --> pdb=" O ALA L 67 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY L 71 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET L 75 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.622A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 Proline residue: M 47 - end of helix removed outlier: 3.535A pdb=" N GLN M 52 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.500A pdb=" N VAL M 68 " --> pdb=" O MET M 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.916A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 Proline residue: N 47 - end of helix removed outlier: 4.330A pdb=" N ARG N 50 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET N 57 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix removed outlier: 3.501A pdb=" N VAL N 68 " --> pdb=" O MET N 65 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE N 76 " --> pdb=" O TYR N 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 41 removed outlier: 3.513A pdb=" N LEU O 19 " --> pdb=" O MET O 16 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA O 24 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY O 27 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE O 28 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY O 32 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG O 41 " --> pdb=" O GLY O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.796A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 Processing helix chain 'P' and resid 4 through 41 removed outlier: 3.923A pdb=" N LEU P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 76 removed outlier: 3.855A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.674A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.504A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 4.334A pdb=" N ARG Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE Q 54 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.528A pdb=" N MET Q 75 " --> pdb=" O LEU Q 72 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE Q 76 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.677A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA R 21 " --> pdb=" O MET R 17 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 76 Proline residue: R 47 - end of helix removed outlier: 3.617A pdb=" N GLY R 58 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE R 63 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 3.516A pdb=" N PHE R 76 " --> pdb=" O TYR R 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 41 removed outlier: 4.708A pdb=" N TYR S 10 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL S 15 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU S 19 " --> pdb=" O MET S 16 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA S 20 " --> pdb=" O MET S 17 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA S 24 " --> pdb=" O ALA S 21 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE S 26 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 3.519A 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 removed outlier: 3.990A pdb=" N MET S 57 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY S 58 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 76 Processing helix chain 'W' and resid 4 through 20 Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.550A pdb=" N PHE W 33 " --> pdb=" O ASP W 29 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 47 Processing helix chain 'W' and resid 53 through 63 Processing helix chain 'W' and resid 72 through 81 Processing helix chain 'W' and resid 85 through 91 Proline residue: W 89 - end of helix Processing helix chain 'W' and resid 94 through 102 Processing helix chain 'W' and resid 119 through 131 Processing helix chain 'W' and resid 163 through 170 Processing helix chain 'X' and resid 5 through 23 Processing helix chain 'X' and resid 25 through 46 Processing helix chain 'X' and resid 51 through 135 removed outlier: 3.781A pdb=" N LEU X 56 " --> pdb=" O LYS X 52 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 154 Processing helix chain 'Y' and resid 4 through 24 removed outlier: 3.739A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 138 removed outlier: 4.521A pdb=" N ALA Y 50 " --> pdb=" O SER Y 46 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N HIS Y 51 " --> pdb=" O ALA Y 47 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS Y 52 " --> pdb=" O GLU Y 48 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP Y 53 " --> pdb=" O ARG Y 49 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN Y 73 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS Y 114 " --> pdb=" O GLU Y 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU Y 119 " --> pdb=" O ARG Y 115 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU Y 120 " --> pdb=" O ALA Y 116 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS Y 134 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 155 removed outlier: 3.520A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 15 Processing helix chain 'a' and resid 43 through 64 Processing helix chain 'a' and resid 74 through 93 removed outlier: 3.927A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET a 93 " --> pdb=" O SER a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 120 removed outlier: 4.355A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.392A 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 180 removed outlier: 6.933A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE a 174 " --> pdb=" O GLY a 170 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR a 175 " --> pdb=" O ILE a 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 228 removed outlier: 3.531A pdb=" N ILE a 189 " --> pdb=" O TRP a 186 " (cutoff:3.500A) Proline residue: a 190 - end of helix removed outlier: 4.039A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU a 196 " --> pdb=" O LEU a 193 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.519A pdb=" N LEU a 209 " --> pdb=" O SER a 206 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE a 212 " --> pdb=" O LEU a 209 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR a 216 " --> pdb=" O GLY a 213 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA a 217 " --> pdb=" O ASN a 214 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU a 228 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 4.051A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 4.070A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.738A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (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 107 through 109 removed outlier: 8.328A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL A 224 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 198 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.552A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.293A pdb=" N ASN B 27 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 70 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.354A 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 98 Processing sheet with id= G, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.309A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL B 224 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 198 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.689A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.345A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.343A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL C 224 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 198 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU C 327 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 351 through 355 Processing sheet with id= M, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.493A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= O, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.166A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 67 through 69 removed outlier: 6.618A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE E 50 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU E 36 " --> pdb=" O ASN E 33 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= R, first strand: chain 'E' and resid 317 through 320 removed outlier: 7.964A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLY E 149 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL E 296 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 4 through 9 removed outlier: 6.595A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP F 27 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N HIS F 73 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLU F 30 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU F 71 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N GLN F 32 " --> pdb=" O LYS F 69 " (cutoff:3.500A) removed outlier: 9.715A pdb=" N LYS F 69 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.658A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 317 through 319 removed outlier: 8.557A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR F 173 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE F 240 " --> pdb=" O TYR F 173 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL F 175 " --> pdb=" O PHE F 240 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 181 through 188 removed outlier: 6.588A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA G 134 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 42 through 45 removed outlier: 3.956A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR H 4 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER H 10 " --> pdb=" O GLN H 14 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLN H 14 " --> pdb=" O SER H 10 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 32 through 34 removed outlier: 3.899A pdb=" N ILE H 23 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN H 24 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N THR H 82 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'W' and resid 135 through 138 Processing sheet with id= Z, first strand: chain 'a' and resid 27 through 29 removed outlier: 3.566A pdb=" N SER a 27 " --> pdb=" O ASP a 22 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLN a 20 " --> pdb=" O VAL a 29 " (cutoff:3.500A) 2011 hydrogen bonds defined for protein. 5121 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: 13.12 Time building geometry restraints manager: 17.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6327 1.31 - 1.44: 8796 1.44 - 1.57: 21964 1.57 - 1.69: 27 1.69 - 1.82: 358 Bond restraints: 37472 Sorted by residual: bond pdb=" C PRO F 23 " pdb=" O PRO F 23 " ideal model delta sigma weight residual 1.234 1.187 0.046 1.14e-02 7.69e+03 1.63e+01 bond pdb=" CA SER B 375 " pdb=" CB SER B 375 " ideal model delta sigma weight residual 1.532 1.474 0.058 1.58e-02 4.01e+03 1.34e+01 bond pdb=" CA SER B 373 " pdb=" CB SER B 373 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.48e-02 4.57e+03 1.29e+01 bond pdb=" C ILE Q 63 " pdb=" N PRO Q 64 " ideal model delta sigma weight residual 1.335 1.372 -0.037 1.19e-02 7.06e+03 9.88e+00 bond pdb=" N LEU O 45 " pdb=" CA LEU O 45 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.32e-02 5.74e+03 8.88e+00 ... (remaining 37467 not shown) Histogram of bond angle deviations from ideal: 97.82 - 106.31: 1026 106.31 - 114.80: 22450 114.80 - 123.28: 26006 123.28 - 131.77: 1203 131.77 - 140.26: 36 Bond angle restraints: 50721 Sorted by residual: angle pdb=" N THR A 148 " pdb=" CA THR A 148 " pdb=" C THR A 148 " ideal model delta sigma weight residual 109.96 101.16 8.80 1.68e+00 3.54e-01 2.75e+01 angle pdb=" N VAL E 198 " pdb=" CA VAL E 198 " pdb=" C VAL E 198 " ideal model delta sigma weight residual 113.20 108.20 5.00 9.60e-01 1.09e+00 2.71e+01 angle pdb=" C HIS A 479 " pdb=" N ALA A 480 " pdb=" CA ALA A 480 " ideal model delta sigma weight residual 120.58 126.21 -5.63 1.32e+00 5.74e-01 1.82e+01 angle pdb=" C VAL A 146 " pdb=" N GLN A 147 " pdb=" CA GLN A 147 " ideal model delta sigma weight residual 122.84 117.31 5.53 1.30e+00 5.92e-01 1.81e+01 angle pdb=" N ILE O 46 " pdb=" CA ILE O 46 " pdb=" CB ILE O 46 " ideal model delta sigma weight residual 110.50 112.94 -2.44 6.30e-01 2.52e+00 1.50e+01 ... (remaining 50716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 22316 35.49 - 70.98: 409 70.98 - 106.47: 54 106.47 - 141.96: 3 141.96 - 177.45: 2 Dihedral angle restraints: 22784 sinusoidal: 9019 harmonic: 13765 Sorted by residual: dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 122.55 177.45 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP F 500 " pdb=" O5' ADP F 500 " pdb=" PA ADP F 500 " pdb=" O2A ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 125.32 174.69 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 179.58 120.43 1 2.00e+01 2.50e-03 3.62e+01 ... (remaining 22781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5503 0.099 - 0.197: 399 0.197 - 0.296: 7 0.296 - 0.394: 3 0.394 - 0.493: 2 Chirality restraints: 5914 Sorted by residual: chirality pdb=" CB ILE Q 63 " pdb=" CA ILE Q 63 " pdb=" CG1 ILE Q 63 " pdb=" CG2 ILE Q 63 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CA THR A 148 " pdb=" N THR A 148 " pdb=" C THR A 148 " pdb=" CB THR A 148 " both_signs ideal model delta sigma weight residual False 2.53 2.96 -0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA TYR F 26 " pdb=" N TYR F 26 " pdb=" C TYR F 26 " pdb=" CB TYR F 26 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 5911 not shown) Planarity restraints: 6540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG W 169 " -0.241 9.50e-02 1.11e+02 1.09e-01 9.44e+00 pdb=" NE ARG W 169 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG W 169 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG W 169 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG W 169 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 59 " 0.214 9.50e-02 1.11e+02 9.72e-02 8.76e+00 pdb=" NE ARG A 59 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 59 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 59 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 59 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 296 " 0.015 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C ARG A 296 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG A 296 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU A 297 " 0.017 2.00e-02 2.50e+03 ... (remaining 6537 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 63 2.50 - 3.10: 28163 3.10 - 3.70: 55281 3.70 - 4.30: 83891 4.30 - 4.90: 136724 Nonbonded interactions: 304122 Sorted by model distance: nonbonded pdb="MG MG D 501 " pdb=" O1G ATP D 502 " model vdw 1.900 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.006 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.062 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 2.101 2.170 nonbonded pdb=" OG1 THR D 156 " pdb="MG MG D 501 " model vdw 2.115 2.170 ... (remaining 304117 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' selection = (chain 'B' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) } ncs_group { reference = (chain 'D' and resid 2 through 459) selection = (chain 'E' and resid 2 through 459) selection = (chain 'F' and resid 2 through 459) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = (chain 'Y' and (resid 1 through 47 or resid 50 through 156)) } 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 individual isotropic 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.420 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 100.520 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.230 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 0.072 37472 Z= 0.282 Angle : 0.833 11.300 50721 Z= 0.461 Chirality : 0.052 0.493 5914 Planarity : 0.009 0.109 6540 Dihedral : 14.469 177.445 13978 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.58 % Favored : 98.40 % Rotamer: Outliers : 0.76 % Allowed : 4.88 % Favored : 94.36 % Cbeta Deviations : 0.07 % 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: -0.05 (0.11), residues: 4799 helix: 0.28 (0.09), residues: 2614 sheet: 0.25 (0.21), residues: 528 loop : -0.42 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP G 203 HIS 0.009 0.002 HIS G 57 PHE 0.042 0.003 PHE O 54 TYR 0.035 0.006 TYR G 205 ARG 0.031 0.004 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 517 time to evaluate : 4.596 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: C 386 MET cc_start: 0.8727 (mmm) cc_final: 0.8355 (mmt) REVERT: D 445 MET cc_start: 0.8889 (mmt) cc_final: 0.8677 (mmm) REVERT: E 56 MET cc_start: 0.9133 (mmm) cc_final: 0.8868 (mmp) REVERT: E 242 ASP cc_start: 0.7159 (t70) cc_final: 0.6163 (t70) REVERT: E 397 GLN cc_start: 0.8584 (tt0) cc_final: 0.8069 (tm-30) REVERT: F 136 MET cc_start: 0.8363 (mmm) cc_final: 0.8030 (mmm) REVERT: G 48 MET cc_start: 0.8608 (mmt) cc_final: 0.8214 (mmm) REVERT: H 53 VAL cc_start: 0.8848 (p) cc_final: 0.8578 (p) REVERT: H 63 TYR cc_start: 0.6661 (t80) cc_final: 0.6289 (t80) REVERT: H 127 GLN cc_start: 0.8193 (mt0) cc_final: 0.7871 (tt0) REVERT: J 11 MET cc_start: 0.5319 (tpp) cc_final: 0.5093 (tmm) REVERT: J 65 MET cc_start: 0.3343 (OUTLIER) cc_final: 0.3131 (mmp) REVERT: L 6 MET cc_start: 0.6287 (ttp) cc_final: 0.5968 (mtm) REVERT: L 17 MET cc_start: 0.7017 (mtm) cc_final: 0.6698 (tpp) REVERT: L 57 MET cc_start: 0.0866 (tmm) cc_final: 0.0394 (tpp) REVERT: M 17 MET cc_start: 0.6233 (mtm) cc_final: 0.3680 (tpt) REVERT: M 44 ASP cc_start: 0.6857 (m-30) cc_final: 0.5948 (t70) REVERT: M 75 MET cc_start: 0.3690 (ttp) cc_final: 0.3057 (tmm) REVERT: N 65 MET cc_start: 0.0914 (mtt) cc_final: 0.0644 (mtm) REVERT: O 37 GLU cc_start: 0.6882 (tt0) cc_final: 0.6577 (tp30) REVERT: O 65 MET cc_start: 0.4916 (mmt) cc_final: 0.4432 (mmm) REVERT: P 6 MET cc_start: 0.4010 (mmt) cc_final: 0.3586 (ptp) REVERT: P 11 MET cc_start: 0.5183 (tpp) cc_final: 0.4658 (mpp) REVERT: P 47 PRO cc_start: 0.5615 (Cg_endo) cc_final: 0.5050 (Cg_exo) REVERT: Q 11 MET cc_start: 0.7515 (tpt) cc_final: 0.6697 (mmp) REVERT: Q 17 MET cc_start: 0.7185 (mtm) cc_final: 0.6320 (tpt) REVERT: S 4 LEU cc_start: 0.3890 (tp) cc_final: 0.3626 (pt) REVERT: S 31 LEU cc_start: 0.6715 (tp) cc_final: 0.6093 (pp) REVERT: X 74 VAL cc_start: 0.8539 (m) cc_final: 0.8312 (m) REVERT: X 136 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6651 (mm) REVERT: X 150 ASP cc_start: 0.8174 (t0) cc_final: 0.7763 (m-30) REVERT: Y 24 TYR cc_start: 0.2664 (m-80) cc_final: 0.1869 (t80) REVERT: Y 26 TRP cc_start: 0.4381 (t60) cc_final: 0.3085 (m100) REVERT: Y 37 GLN cc_start: 0.5105 (mt0) cc_final: 0.4798 (tp40) REVERT: Y 73 GLN cc_start: 0.7455 (tp40) cc_final: 0.6664 (pt0) REVERT: Y 113 ARG cc_start: 0.7593 (ttt180) cc_final: 0.7317 (ttt180) REVERT: Y 115 ARG cc_start: 0.8810 (ttp80) cc_final: 0.8590 (tpt90) REVERT: a 65 LYS cc_start: 0.2966 (tttt) cc_final: 0.2478 (pttt) REVERT: a 168 MET cc_start: 0.6152 (mmt) cc_final: 0.5500 (tpp) outliers start: 29 outliers final: 5 residues processed: 535 average time/residue: 0.5577 time to fit residues: 462.9529 Evaluate side-chains 314 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 307 time to evaluate : 4.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain J residue 65 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 106 GLN Chi-restraints excluded: chain X residue 136 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 6.9990 chunk 358 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 370 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 275 optimal weight: 0.8980 chunk 429 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS C 479 HIS E 365 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN L 5 ASN P 3 ASN S 52 GLN Y 73 GLN Y 123 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 37472 Z= 0.357 Angle : 0.656 8.161 50721 Z= 0.349 Chirality : 0.044 0.279 5914 Planarity : 0.005 0.098 6540 Dihedral : 8.439 166.394 5373 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.54 % Favored : 98.44 % Rotamer: Outliers : 1.46 % Allowed : 8.93 % Favored : 89.61 % 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: 0.30 (0.12), residues: 4799 helix: 0.57 (0.10), residues: 2653 sheet: 0.40 (0.21), residues: 535 loop : -0.28 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP G 203 HIS 0.006 0.001 HIS B 215 PHE 0.019 0.002 PHE R 35 TYR 0.017 0.002 TYR P 10 ARG 0.010 0.001 ARG H 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 312 time to evaluate : 4.640 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 456 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8199 (mm) REVERT: B 1 MET cc_start: 0.2475 (ttm) cc_final: 0.0565 (mpp) REVERT: B 10 GLU cc_start: 0.9308 (tm-30) cc_final: 0.8941 (mp0) REVERT: C 180 ILE cc_start: 0.9087 (pt) cc_final: 0.8825 (mm) REVERT: E 56 MET cc_start: 0.9092 (mmm) cc_final: 0.8825 (mmp) REVERT: E 379 MET cc_start: 0.8255 (ttt) cc_final: 0.7986 (ttt) REVERT: E 397 GLN cc_start: 0.8680 (tt0) cc_final: 0.8129 (tm-30) REVERT: F 384 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8180 (tm-30) REVERT: H 52 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8120 (pt) REVERT: H 95 MET cc_start: 0.6644 (tpp) cc_final: 0.6375 (mmp) REVERT: L 6 MET cc_start: 0.6560 (ttp) cc_final: 0.6172 (mtm) REVERT: M 16 MET cc_start: 0.7273 (mtp) cc_final: 0.7065 (mmm) REVERT: M 75 MET cc_start: 0.3606 (ttp) cc_final: 0.3060 (mmp) REVERT: O 16 MET cc_start: -0.0961 (mtp) cc_final: -0.1449 (mtp) REVERT: P 6 MET cc_start: 0.3747 (mmt) cc_final: 0.3189 (ptp) REVERT: P 11 MET cc_start: 0.4952 (tpp) cc_final: 0.4316 (mtp) REVERT: Q 11 MET cc_start: 0.7299 (tpt) cc_final: 0.6700 (mmm) REVERT: Q 17 MET cc_start: 0.7298 (mtm) cc_final: 0.6494 (tpt) REVERT: R 22 ILE cc_start: 0.7347 (mt) cc_final: 0.7123 (mt) REVERT: Y 24 TYR cc_start: 0.2815 (m-80) cc_final: 0.2104 (t80) REVERT: Y 26 TRP cc_start: 0.4258 (t60) cc_final: 0.3095 (m100) REVERT: Y 37 GLN cc_start: 0.4938 (mt0) cc_final: 0.4638 (tp40) REVERT: Y 73 GLN cc_start: 0.7347 (tp-100) cc_final: 0.6316 (pt0) REVERT: Y 74 VAL cc_start: 0.8767 (p) cc_final: 0.8554 (m) REVERT: Y 89 GLU cc_start: 0.8894 (tp30) cc_final: 0.8480 (tm-30) REVERT: a 65 LYS cc_start: 0.2987 (tttt) cc_final: 0.2429 (pttt) REVERT: a 168 MET cc_start: 0.6129 (mmt) cc_final: 0.5409 (tpp) outliers start: 56 outliers final: 25 residues processed: 351 average time/residue: 0.5190 time to fit residues: 294.6168 Evaluate side-chains 298 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 271 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain a residue 121 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 357 optimal weight: 30.0000 chunk 292 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 430 optimal weight: 20.0000 chunk 464 optimal weight: 8.9990 chunk 383 optimal weight: 5.9990 chunk 426 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 345 optimal weight: 0.0270 overall best weight: 3.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN C 220 ASN C 294 HIS C 479 HIS F 368 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 ASN ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 106 GLN Y 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37472 Z= 0.271 Angle : 0.582 8.856 50721 Z= 0.304 Chirality : 0.042 0.293 5914 Planarity : 0.005 0.073 6540 Dihedral : 7.698 150.737 5365 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.62 % Allowed : 10.08 % Favored : 88.31 % 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: 0.54 (0.12), residues: 4799 helix: 0.80 (0.10), residues: 2649 sheet: 0.40 (0.21), residues: 556 loop : -0.21 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 203 HIS 0.005 0.001 HIS a 14 PHE 0.024 0.001 PHE R 53 TYR 0.019 0.001 TYR H 63 ARG 0.006 0.000 ARG Y 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 299 time to evaluate : 4.790 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: B 1 MET cc_start: 0.2708 (ttm) cc_final: 0.1410 (mtm) REVERT: B 10 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8918 (mp0) REVERT: C 187 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8690 (ptp-170) REVERT: E 46 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8752 (pp) REVERT: E 397 GLN cc_start: 0.8696 (tt0) cc_final: 0.8130 (tm-30) REVERT: E 445 MET cc_start: 0.8558 (mmt) cc_final: 0.8296 (mmt) REVERT: F 0 MET cc_start: 0.6711 (pmm) cc_final: 0.6489 (pmm) REVERT: H 49 MET cc_start: 0.6462 (ppp) cc_final: 0.6191 (ppp) REVERT: J 6 MET cc_start: 0.1630 (ptp) cc_final: 0.1257 (mmm) REVERT: L 6 MET cc_start: 0.6671 (ttp) cc_final: 0.6235 (mtm) REVERT: M 11 MET cc_start: 0.5070 (tpt) cc_final: 0.4838 (tpt) REVERT: M 17 MET cc_start: 0.5052 (mtp) cc_final: 0.2614 (tpt) REVERT: O 57 MET cc_start: 0.3697 (tmm) cc_final: 0.3291 (tmm) REVERT: P 6 MET cc_start: 0.3943 (mmt) cc_final: 0.3531 (ptp) REVERT: P 11 MET cc_start: 0.4621 (tpp) cc_final: 0.4048 (mpp) REVERT: Q 11 MET cc_start: 0.7073 (tpt) cc_final: 0.6446 (mmt) REVERT: Q 17 MET cc_start: 0.7315 (mtm) cc_final: 0.6453 (tpt) REVERT: X 104 GLN cc_start: 0.8501 (pp30) cc_final: 0.8208 (pt0) REVERT: X 147 ASP cc_start: 0.7306 (m-30) cc_final: 0.7035 (t70) REVERT: Y 24 TYR cc_start: 0.3009 (m-80) cc_final: 0.2777 (t80) REVERT: Y 26 TRP cc_start: 0.4247 (t60) cc_final: 0.3029 (m100) REVERT: Y 73 GLN cc_start: 0.7310 (tp-100) cc_final: 0.6299 (pt0) REVERT: Y 74 VAL cc_start: 0.8704 (p) cc_final: 0.8478 (m) REVERT: Y 82 ARG cc_start: 0.7098 (mmm160) cc_final: 0.6775 (mmm160) REVERT: a 65 LYS cc_start: 0.2948 (tttt) cc_final: 0.2447 (pttt) REVERT: a 168 MET cc_start: 0.6611 (mmt) cc_final: 0.5455 (tpp) outliers start: 62 outliers final: 34 residues processed: 345 average time/residue: 0.4851 time to fit residues: 277.4013 Evaluate side-chains 306 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 270 time to evaluate : 4.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 106 GLN Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 425 optimal weight: 5.9990 chunk 323 optimal weight: 30.0000 chunk 223 optimal weight: 0.0980 chunk 47 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 288 optimal weight: 8.9990 chunk 431 optimal weight: 30.0000 chunk 457 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 409 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN G 111 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 106 GLN Y 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37472 Z= 0.195 Angle : 0.555 10.710 50721 Z= 0.286 Chirality : 0.041 0.244 5914 Planarity : 0.004 0.047 6540 Dihedral : 7.304 147.811 5365 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.46 % Allowed : 10.99 % Favored : 87.55 % 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: 0.73 (0.12), residues: 4799 helix: 0.99 (0.10), residues: 2655 sheet: 0.39 (0.21), residues: 572 loop : -0.17 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 203 HIS 0.004 0.001 HIS C 479 PHE 0.018 0.001 PHE Q 54 TYR 0.013 0.001 TYR H 63 ARG 0.004 0.000 ARG H 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 282 time to evaluate : 5.062 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: B 1 MET cc_start: 0.2732 (ttm) cc_final: 0.1836 (mtm) REVERT: B 10 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8947 (mp0) REVERT: C 187 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8650 (ptp-170) REVERT: D 379 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6800 (mpp) REVERT: E 46 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8663 (pp) REVERT: E 397 GLN cc_start: 0.8689 (tt0) cc_final: 0.8100 (tm-30) REVERT: E 445 MET cc_start: 0.8615 (mmt) cc_final: 0.8296 (mmm) REVERT: H 95 MET cc_start: 0.6514 (mmm) cc_final: 0.6274 (mmm) REVERT: I 11 MET cc_start: -0.0038 (ttt) cc_final: -0.0428 (ttt) REVERT: J 6 MET cc_start: 0.1672 (ptp) cc_final: 0.1312 (mmm) REVERT: L 6 MET cc_start: 0.6633 (ttp) cc_final: 0.6161 (mtm) REVERT: M 17 MET cc_start: 0.4777 (mtp) cc_final: 0.2510 (tpt) REVERT: O 57 MET cc_start: 0.3551 (tmm) cc_final: 0.3126 (tmm) REVERT: P 6 MET cc_start: 0.3970 (mmt) cc_final: 0.3522 (ptp) REVERT: P 11 MET cc_start: 0.4632 (tpp) cc_final: 0.4040 (mpp) REVERT: Q 17 MET cc_start: 0.7254 (mtm) cc_final: 0.6474 (tpt) REVERT: Q 34 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7688 (mmmm) REVERT: X 104 GLN cc_start: 0.8518 (pp30) cc_final: 0.8240 (pt0) REVERT: X 115 ARG cc_start: 0.8524 (ptp-110) cc_final: 0.8280 (ptt-90) REVERT: X 147 ASP cc_start: 0.7467 (m-30) cc_final: 0.7117 (t70) REVERT: Y 24 TYR cc_start: 0.3077 (m-80) cc_final: 0.2832 (t80) REVERT: Y 26 TRP cc_start: 0.4345 (t60) cc_final: 0.3162 (m100) REVERT: Y 73 GLN cc_start: 0.7190 (tp-100) cc_final: 0.6266 (pt0) REVERT: Y 74 VAL cc_start: 0.8663 (p) cc_final: 0.8443 (m) REVERT: a 40 THR cc_start: 0.3224 (OUTLIER) cc_final: 0.3019 (p) REVERT: a 65 LYS cc_start: 0.2875 (tttt) cc_final: 0.2402 (pttt) REVERT: a 168 MET cc_start: 0.6590 (mmt) cc_final: 0.5338 (tpp) outliers start: 56 outliers final: 32 residues processed: 321 average time/residue: 0.4868 time to fit residues: 259.3929 Evaluate side-chains 303 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 267 time to evaluate : 4.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 106 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 121 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 340 optimal weight: 30.0000 chunk 188 optimal weight: 5.9990 chunk 390 optimal weight: 0.9990 chunk 316 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 233 optimal weight: 3.9990 chunk 410 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 106 GLN a 15 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 37472 Z= 0.325 Angle : 0.590 9.204 50721 Z= 0.303 Chirality : 0.042 0.211 5914 Planarity : 0.004 0.049 6540 Dihedral : 7.209 142.693 5365 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.88 % Allowed : 12.09 % Favored : 86.03 % 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: 0.77 (0.12), residues: 4799 helix: 1.08 (0.10), residues: 2641 sheet: 0.41 (0.21), residues: 558 loop : -0.25 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 235 HIS 0.006 0.001 HIS B 215 PHE 0.019 0.001 PHE H 16 TYR 0.015 0.001 TYR E 247 ARG 0.014 0.000 ARG Y 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 281 time to evaluate : 4.804 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: B 1 MET cc_start: 0.2919 (ttm) cc_final: 0.2104 (mtm) REVERT: B 10 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8945 (mp0) REVERT: B 504 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8783 (mm) REVERT: C 187 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8686 (ptp-170) REVERT: D 379 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6903 (mpp) REVERT: E 46 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8779 (pp) REVERT: E 397 GLN cc_start: 0.8761 (tt0) cc_final: 0.8227 (tm-30) REVERT: G 116 MET cc_start: 0.8320 (mmp) cc_final: 0.8119 (mmp) REVERT: H 16 PHE cc_start: 0.5624 (t80) cc_final: 0.5382 (t80) REVERT: H 49 MET cc_start: 0.6326 (ppp) cc_final: 0.5937 (ppp) REVERT: H 51 ARG cc_start: 0.7819 (tmm-80) cc_final: 0.7559 (tmm160) REVERT: H 95 MET cc_start: 0.6475 (mmm) cc_final: 0.6191 (mmm) REVERT: I 11 MET cc_start: -0.0100 (ttt) cc_final: -0.0606 (ttt) REVERT: I 17 MET cc_start: 0.4542 (ppp) cc_final: 0.4305 (ppp) REVERT: J 6 MET cc_start: 0.1572 (ptp) cc_final: 0.1273 (mmm) REVERT: L 6 MET cc_start: 0.6547 (ttp) cc_final: 0.6031 (mtm) REVERT: L 65 MET cc_start: 0.0586 (mmm) cc_final: -0.0486 (ptt) REVERT: M 17 MET cc_start: 0.4679 (mtp) cc_final: 0.2624 (tpt) REVERT: M 78 VAL cc_start: 0.0883 (OUTLIER) cc_final: 0.0641 (p) REVERT: O 57 MET cc_start: 0.3416 (tmm) cc_final: 0.3005 (tmm) REVERT: O 75 MET cc_start: 0.3066 (tmm) cc_final: 0.2742 (tmm) REVERT: P 6 MET cc_start: 0.4022 (mmt) cc_final: 0.3545 (ptp) REVERT: P 11 MET cc_start: 0.4415 (tpp) cc_final: 0.3780 (mpp) REVERT: Q 17 MET cc_start: 0.7322 (mtm) cc_final: 0.6326 (tpt) REVERT: Q 34 LYS cc_start: 0.7943 (mmtt) cc_final: 0.7728 (mppt) REVERT: R 75 MET cc_start: 0.3047 (ptm) cc_final: 0.2573 (tmm) REVERT: X 104 GLN cc_start: 0.8487 (pp30) cc_final: 0.8216 (pt0) REVERT: X 115 ARG cc_start: 0.8534 (ptp-110) cc_final: 0.8323 (ptt-90) REVERT: X 147 ASP cc_start: 0.7456 (m-30) cc_final: 0.7108 (t70) REVERT: Y 26 TRP cc_start: 0.4331 (t60) cc_final: 0.3147 (m100) REVERT: Y 73 GLN cc_start: 0.7250 (tp-100) cc_final: 0.6316 (pt0) REVERT: Y 74 VAL cc_start: 0.8691 (p) cc_final: 0.8476 (m) REVERT: a 40 THR cc_start: 0.3005 (OUTLIER) cc_final: 0.2688 (p) REVERT: a 65 LYS cc_start: 0.2954 (tttt) cc_final: 0.2428 (pttt) REVERT: a 168 MET cc_start: 0.6599 (mmt) cc_final: 0.5406 (tpp) outliers start: 72 outliers final: 49 residues processed: 332 average time/residue: 0.4639 time to fit residues: 259.6692 Evaluate side-chains 315 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 260 time to evaluate : 4.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 55 ASP Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 106 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 121 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 0.4980 chunk 411 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 268 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 457 optimal weight: 5.9990 chunk 379 optimal weight: 30.0000 chunk 211 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 240 optimal weight: 6.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN D 437 HIS ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 37472 Z= 0.354 Angle : 0.606 12.966 50721 Z= 0.311 Chirality : 0.042 0.215 5914 Planarity : 0.004 0.049 6540 Dihedral : 7.084 139.008 5362 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.93 % Allowed : 12.95 % Favored : 85.12 % 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: 0.71 (0.12), residues: 4799 helix: 1.03 (0.10), residues: 2656 sheet: 0.33 (0.21), residues: 556 loop : -0.27 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 235 HIS 0.006 0.001 HIS B 215 PHE 0.018 0.001 PHE Q 54 TYR 0.017 0.001 TYR E 247 ARG 0.009 0.000 ARG Y 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 269 time to evaluate : 4.790 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: B 1 MET cc_start: 0.3095 (ttm) cc_final: 0.2333 (mtm) REVERT: B 504 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8808 (mm) REVERT: C 187 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8713 (ptp-170) REVERT: D 379 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6942 (mpp) REVERT: D 445 MET cc_start: 0.8685 (mmm) cc_final: 0.8212 (tpp) REVERT: E 46 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8791 (pp) REVERT: E 397 GLN cc_start: 0.8797 (tt0) cc_final: 0.8196 (tm-30) REVERT: E 445 MET cc_start: 0.8469 (mmt) cc_final: 0.8092 (mmm) REVERT: G 116 MET cc_start: 0.8270 (mmp) cc_final: 0.8051 (mmp) REVERT: H 51 ARG cc_start: 0.7964 (tmm-80) cc_final: 0.7493 (tmm160) REVERT: I 11 MET cc_start: -0.0021 (ttt) cc_final: -0.0469 (ttt) REVERT: J 6 MET cc_start: 0.1651 (ptp) cc_final: 0.1432 (mmm) REVERT: L 6 MET cc_start: 0.6641 (ttp) cc_final: 0.6087 (ptt) REVERT: L 57 MET cc_start: 0.0334 (tpp) cc_final: -0.0062 (tpt) REVERT: L 65 MET cc_start: 0.0776 (mmm) cc_final: -0.0257 (ptt) REVERT: M 17 MET cc_start: 0.4716 (mtp) cc_final: 0.4389 (mtt) REVERT: O 57 MET cc_start: 0.3606 (tmm) cc_final: 0.3229 (tmm) REVERT: P 6 MET cc_start: 0.4012 (mmt) cc_final: 0.3328 (ptp) REVERT: P 11 MET cc_start: 0.4403 (tpp) cc_final: 0.3525 (mpp) REVERT: Q 17 MET cc_start: 0.7294 (mtm) cc_final: 0.6244 (tpt) REVERT: Q 34 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7667 (mppt) REVERT: W 156 ASP cc_start: 0.7734 (p0) cc_final: 0.7354 (p0) REVERT: X 104 GLN cc_start: 0.8518 (pp30) cc_final: 0.8238 (pt0) REVERT: X 115 ARG cc_start: 0.8481 (ptp-110) cc_final: 0.8275 (ptt-90) REVERT: X 147 ASP cc_start: 0.7320 (m-30) cc_final: 0.6962 (t70) REVERT: Y 26 TRP cc_start: 0.4339 (t60) cc_final: 0.3189 (m100) REVERT: Y 73 GLN cc_start: 0.7260 (tp-100) cc_final: 0.6317 (pt0) REVERT: Y 74 VAL cc_start: 0.8665 (p) cc_final: 0.8448 (m) REVERT: Y 96 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8113 (mp10) REVERT: a 65 LYS cc_start: 0.2906 (tttt) cc_final: 0.2319 (pttt) REVERT: a 168 MET cc_start: 0.6572 (mmt) cc_final: 0.5376 (tpp) outliers start: 74 outliers final: 55 residues processed: 318 average time/residue: 0.4641 time to fit residues: 248.2454 Evaluate side-chains 314 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 255 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain N residue 11 MET Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 16 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 55 ASP Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 78 GLN Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 260 optimal weight: 9.9990 chunk 334 optimal weight: 10.0000 chunk 258 optimal weight: 2.9990 chunk 385 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 455 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 chunk 277 optimal weight: 0.0470 chunk 210 optimal weight: 0.9980 overall best weight: 3.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS M 52 GLN ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37472 Z= 0.268 Angle : 0.582 14.354 50721 Z= 0.296 Chirality : 0.041 0.205 5914 Planarity : 0.004 0.057 6540 Dihedral : 6.919 136.713 5362 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.04 % Allowed : 13.57 % Favored : 84.39 % 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: 0.79 (0.12), residues: 4799 helix: 1.12 (0.10), residues: 2650 sheet: 0.23 (0.21), residues: 567 loop : -0.23 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 235 HIS 0.004 0.001 HIS B 215 PHE 0.019 0.001 PHE L 76 TYR 0.015 0.001 TYR E 247 ARG 0.004 0.000 ARG Y 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 265 time to evaluate : 4.123 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: B 1 MET cc_start: 0.3065 (ttm) cc_final: 0.2337 (mtm) REVERT: B 504 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8802 (mm) REVERT: C 187 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8683 (ptp-170) REVERT: C 200 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8105 (mt0) REVERT: D 379 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6933 (mpp) REVERT: D 445 MET cc_start: 0.8623 (mmm) cc_final: 0.8217 (tpp) REVERT: E 46 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8747 (pp) REVERT: E 397 GLN cc_start: 0.8790 (tt0) cc_final: 0.8198 (tm-30) REVERT: E 445 MET cc_start: 0.8499 (mmt) cc_final: 0.8128 (mmm) REVERT: G 31 MET cc_start: 0.8783 (ttp) cc_final: 0.8578 (ttp) REVERT: G 116 MET cc_start: 0.8189 (mmp) cc_final: 0.7954 (mmp) REVERT: G 155 MET cc_start: 0.8025 (tpp) cc_final: 0.7813 (tpp) REVERT: H 51 ARG cc_start: 0.8025 (tmm-80) cc_final: 0.7547 (tmm160) REVERT: H 95 MET cc_start: 0.6640 (mmm) cc_final: 0.6368 (mmm) REVERT: I 11 MET cc_start: 0.0064 (ttt) cc_final: -0.0347 (ttt) REVERT: J 37 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7822 (tp30) REVERT: L 6 MET cc_start: 0.6636 (ttp) cc_final: 0.6078 (ptt) REVERT: L 11 MET cc_start: 0.5033 (mmm) cc_final: 0.3814 (mtp) REVERT: L 65 MET cc_start: 0.1013 (mmm) cc_final: 0.0053 (ptt) REVERT: M 17 MET cc_start: 0.4591 (mtp) cc_final: 0.4279 (mtt) REVERT: P 6 MET cc_start: 0.3988 (mmt) cc_final: 0.3277 (ptp) REVERT: P 11 MET cc_start: 0.4754 (tpp) cc_final: 0.3880 (mpp) REVERT: Q 11 MET cc_start: 0.6910 (tpt) cc_final: 0.6002 (mmm) REVERT: Q 17 MET cc_start: 0.7314 (mtm) cc_final: 0.6272 (tpt) REVERT: Q 34 LYS cc_start: 0.7917 (mmtt) cc_final: 0.7659 (mppt) REVERT: X 78 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7616 (tp40) REVERT: X 82 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.8159 (ttp-110) REVERT: X 104 GLN cc_start: 0.8491 (pp30) cc_final: 0.8217 (pt0) REVERT: X 115 ARG cc_start: 0.8435 (ptp-110) cc_final: 0.8156 (ptt-90) REVERT: X 147 ASP cc_start: 0.7169 (m-30) cc_final: 0.6845 (t70) REVERT: Y 26 TRP cc_start: 0.4288 (t60) cc_final: 0.3148 (m100) REVERT: Y 73 GLN cc_start: 0.7393 (tp-100) cc_final: 0.6348 (pt0) REVERT: Y 74 VAL cc_start: 0.8541 (p) cc_final: 0.8254 (m) REVERT: Y 96 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8204 (mp10) REVERT: a 168 MET cc_start: 0.6566 (mmt) cc_final: 0.5366 (tpp) outliers start: 78 outliers final: 55 residues processed: 322 average time/residue: 0.4371 time to fit residues: 238.8370 Evaluate side-chains 315 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 253 time to evaluate : 4.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain N residue 11 MET Chi-restraints excluded: chain O residue 16 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 55 ASP Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 78 GLN Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 289 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 358 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37472 Z= 0.256 Angle : 0.586 12.191 50721 Z= 0.296 Chirality : 0.041 0.210 5914 Planarity : 0.004 0.048 6540 Dihedral : 6.792 135.434 5362 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.88 % Allowed : 13.94 % Favored : 84.18 % 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: 0.83 (0.12), residues: 4799 helix: 1.16 (0.10), residues: 2652 sheet: 0.28 (0.21), residues: 565 loop : -0.24 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 235 HIS 0.004 0.001 HIS B 215 PHE 0.015 0.001 PHE L 76 TYR 0.014 0.001 TYR E 247 ARG 0.003 0.000 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 267 time to evaluate : 4.146 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: B 1 MET cc_start: 0.3049 (ttm) cc_final: 0.2460 (mtp) REVERT: B 504 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8804 (mm) REVERT: C 187 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8666 (ptp-170) REVERT: C 200 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8045 (mt0) REVERT: D 379 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6947 (mpp) REVERT: D 445 MET cc_start: 0.8620 (mmm) cc_final: 0.8236 (tpp) REVERT: E 46 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8737 (pp) REVERT: E 397 GLN cc_start: 0.8797 (tt0) cc_final: 0.8203 (tm-30) REVERT: E 445 MET cc_start: 0.8498 (mmt) cc_final: 0.8129 (mmm) REVERT: G 31 MET cc_start: 0.8808 (ttp) cc_final: 0.8592 (ttp) REVERT: G 155 MET cc_start: 0.7968 (tpp) cc_final: 0.7766 (tpp) REVERT: H 51 ARG cc_start: 0.8249 (tmm-80) cc_final: 0.7863 (tmm160) REVERT: H 95 MET cc_start: 0.6647 (mmm) cc_final: 0.6374 (mmm) REVERT: I 11 MET cc_start: 0.0075 (ttt) cc_final: -0.0323 (ttt) REVERT: J 37 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7802 (tp30) REVERT: L 10 TYR cc_start: 0.4146 (OUTLIER) cc_final: 0.3068 (t80) REVERT: L 65 MET cc_start: 0.1310 (mmm) cc_final: 0.0347 (ptt) REVERT: M 17 MET cc_start: 0.4739 (mtp) cc_final: 0.4321 (mtt) REVERT: M 75 MET cc_start: 0.3216 (tpp) cc_final: 0.2784 (tpt) REVERT: P 6 MET cc_start: 0.4171 (mmt) cc_final: 0.3476 (ptp) REVERT: P 11 MET cc_start: 0.4790 (tpp) cc_final: 0.3972 (mpp) REVERT: Q 11 MET cc_start: 0.7026 (tpt) cc_final: 0.6092 (mmm) REVERT: Q 17 MET cc_start: 0.7346 (mtm) cc_final: 0.6294 (tpt) REVERT: X 78 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7680 (tp40) REVERT: X 82 ARG cc_start: 0.8464 (ttp-110) cc_final: 0.8189 (ttp-110) REVERT: X 104 GLN cc_start: 0.8451 (pp30) cc_final: 0.8176 (pt0) REVERT: X 115 ARG cc_start: 0.8470 (ptp-110) cc_final: 0.8196 (ptt-90) REVERT: X 147 ASP cc_start: 0.7256 (m-30) cc_final: 0.6950 (t70) REVERT: Y 26 TRP cc_start: 0.4242 (t60) cc_final: 0.3204 (m100) REVERT: Y 73 GLN cc_start: 0.7290 (tp-100) cc_final: 0.6305 (pt0) REVERT: Y 89 GLU cc_start: 0.8966 (tp30) cc_final: 0.8718 (pp20) REVERT: Y 96 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8344 (mp10) REVERT: a 168 MET cc_start: 0.6557 (mmt) cc_final: 0.5365 (tpp) outliers start: 72 outliers final: 52 residues processed: 320 average time/residue: 0.4833 time to fit residues: 259.3522 Evaluate side-chains 321 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 261 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain P residue 53 PHE Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 55 ASP Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 78 GLN Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 414 optimal weight: 0.7980 chunk 436 optimal weight: 50.0000 chunk 398 optimal weight: 8.9990 chunk 424 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 333 optimal weight: 30.0000 chunk 130 optimal weight: 0.9980 chunk 383 optimal weight: 9.9990 chunk 401 optimal weight: 4.9990 chunk 423 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN ** O 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN a 15 HIS ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 37472 Z= 0.266 Angle : 0.596 12.771 50721 Z= 0.300 Chirality : 0.041 0.286 5914 Planarity : 0.004 0.048 6540 Dihedral : 6.748 134.145 5362 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.88 % Allowed : 14.38 % Favored : 83.74 % 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: 0.86 (0.12), residues: 4799 helix: 1.21 (0.10), residues: 2649 sheet: 0.28 (0.21), residues: 563 loop : -0.26 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 235 HIS 0.004 0.001 HIS B 215 PHE 0.022 0.001 PHE L 76 TYR 0.014 0.001 TYR E 247 ARG 0.005 0.000 ARG Y 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 265 time to evaluate : 4.945 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: B 1 MET cc_start: 0.3368 (ttm) cc_final: 0.2785 (mtp) REVERT: B 504 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8793 (mm) REVERT: C 187 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8669 (ptp-170) REVERT: C 200 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: D 379 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6998 (mpp) REVERT: D 445 MET cc_start: 0.8606 (mmm) cc_final: 0.8230 (tpp) REVERT: E 46 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8741 (pp) REVERT: E 397 GLN cc_start: 0.8795 (tt0) cc_final: 0.8309 (tm-30) REVERT: E 445 MET cc_start: 0.8514 (mmt) cc_final: 0.8140 (mmm) REVERT: G 31 MET cc_start: 0.8779 (ttp) cc_final: 0.8548 (ttp) REVERT: H 51 ARG cc_start: 0.8265 (tmm-80) cc_final: 0.7762 (tmm160) REVERT: H 95 MET cc_start: 0.6653 (mmm) cc_final: 0.6378 (mmm) REVERT: I 11 MET cc_start: 0.0383 (ttt) cc_final: -0.0107 (ttt) REVERT: J 37 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: J 57 MET cc_start: 0.5720 (tmm) cc_final: 0.4875 (ttp) REVERT: L 10 TYR cc_start: 0.4171 (OUTLIER) cc_final: 0.3182 (t80) REVERT: L 65 MET cc_start: 0.1321 (mmm) cc_final: 0.0372 (ptt) REVERT: M 75 MET cc_start: 0.3142 (tpp) cc_final: 0.2772 (tpt) REVERT: P 6 MET cc_start: 0.4164 (mmt) cc_final: 0.3464 (ptp) REVERT: P 11 MET cc_start: 0.4530 (tpp) cc_final: 0.3943 (mpp) REVERT: Q 11 MET cc_start: 0.6873 (tpt) cc_final: 0.6047 (mmm) REVERT: Q 17 MET cc_start: 0.7230 (mtm) cc_final: 0.6232 (tpt) REVERT: X 78 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7560 (tp40) REVERT: X 104 GLN cc_start: 0.8461 (pp30) cc_final: 0.8154 (pt0) REVERT: X 115 ARG cc_start: 0.8423 (ptp-110) cc_final: 0.8097 (ptt-90) REVERT: Y 26 TRP cc_start: 0.4262 (t60) cc_final: 0.3118 (m100) REVERT: Y 73 GLN cc_start: 0.7290 (tp-100) cc_final: 0.6392 (pt0) REVERT: Y 89 GLU cc_start: 0.8950 (tp30) cc_final: 0.8703 (pp20) REVERT: Y 96 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8311 (mp10) REVERT: a 168 MET cc_start: 0.6565 (mmt) cc_final: 0.5375 (tpp) outliers start: 72 outliers final: 55 residues processed: 318 average time/residue: 0.4813 time to fit residues: 260.2615 Evaluate side-chains 318 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 255 time to evaluate : 4.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain P residue 53 PHE Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 78 GLN Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU 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: 4.9990 chunk 274 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 312 optimal weight: 9.9990 chunk 471 optimal weight: 5.9990 chunk 433 optimal weight: 20.0000 chunk 375 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 ASN ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 96 GLN ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 106 GLN a 15 HIS ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 37472 Z= 0.257 Angle : 0.605 15.191 50721 Z= 0.302 Chirality : 0.041 0.321 5914 Planarity : 0.004 0.049 6540 Dihedral : 6.665 131.415 5362 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.80 % Allowed : 14.59 % Favored : 83.61 % 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: 0.87 (0.12), residues: 4799 helix: 1.22 (0.10), residues: 2654 sheet: 0.29 (0.21), residues: 563 loop : -0.25 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 235 HIS 0.004 0.001 HIS G 57 PHE 0.021 0.001 PHE L 76 TYR 0.014 0.001 TYR E 247 ARG 0.007 0.000 ARG G 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 259 time to evaluate : 4.470 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: B 1 MET cc_start: 0.3521 (ttm) cc_final: 0.2971 (mtp) REVERT: B 504 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8793 (mm) REVERT: C 187 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8659 (ptp-170) REVERT: C 200 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8042 (mt0) REVERT: D 379 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6944 (mpp) REVERT: E 46 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8730 (pp) REVERT: E 397 GLN cc_start: 0.8797 (tt0) cc_final: 0.8315 (tm-30) REVERT: E 445 MET cc_start: 0.8512 (mmt) cc_final: 0.8137 (mmm) REVERT: G 31 MET cc_start: 0.8774 (ttp) cc_final: 0.8554 (ttp) REVERT: H 51 ARG cc_start: 0.8399 (tmm-80) cc_final: 0.7840 (tmm160) REVERT: H 95 MET cc_start: 0.6699 (mmm) cc_final: 0.6435 (mmm) REVERT: I 11 MET cc_start: 0.0387 (ttt) cc_final: -0.0103 (ttt) REVERT: J 37 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7767 (tp30) REVERT: J 57 MET cc_start: 0.5633 (tmm) cc_final: 0.4796 (ttp) REVERT: L 10 TYR cc_start: 0.3988 (OUTLIER) cc_final: 0.3183 (t80) REVERT: L 65 MET cc_start: 0.1320 (mmm) cc_final: 0.0380 (ptt) REVERT: M 75 MET cc_start: 0.3068 (tpp) cc_final: 0.2719 (tpt) REVERT: P 6 MET cc_start: 0.4103 (mmt) cc_final: 0.3364 (ptp) REVERT: P 11 MET cc_start: 0.4426 (tpp) cc_final: 0.3936 (mpp) REVERT: Q 11 MET cc_start: 0.6883 (tpt) cc_final: 0.6045 (mmm) REVERT: Q 17 MET cc_start: 0.7230 (mtm) cc_final: 0.6230 (tpt) REVERT: X 78 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7685 (tp40) REVERT: X 82 ARG cc_start: 0.8521 (ttp-110) cc_final: 0.8229 (ttp-110) REVERT: X 104 GLN cc_start: 0.8474 (pp30) cc_final: 0.8178 (pt0) REVERT: X 115 ARG cc_start: 0.8414 (ptp-110) cc_final: 0.8169 (ptt-90) REVERT: Y 26 TRP cc_start: 0.4207 (t60) cc_final: 0.3228 (m100) REVERT: Y 73 GLN cc_start: 0.7289 (tp-100) cc_final: 0.6495 (pt0) REVERT: Y 82 ARG cc_start: 0.6132 (mmm160) cc_final: 0.5293 (mmm160) REVERT: Y 89 GLU cc_start: 0.8986 (tp30) cc_final: 0.8734 (pp20) REVERT: Y 96 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8375 (mp10) REVERT: a 168 MET cc_start: 0.6541 (mmt) cc_final: 0.5368 (tpp) outliers start: 69 outliers final: 55 residues processed: 309 average time/residue: 0.4704 time to fit residues: 247.4593 Evaluate side-chains 318 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 255 time to evaluate : 4.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain N residue 11 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain P residue 53 PHE Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 55 ASP Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 78 GLN Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 298 optimal weight: 0.3980 chunk 399 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 345 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 375 optimal weight: 20.0000 chunk 157 optimal weight: 4.9990 chunk 385 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 HIS ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.082662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052555 restraints weight = 153803.716| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.95 r_work: 0.2894 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37472 Z= 0.175 Angle : 0.579 13.353 50721 Z= 0.288 Chirality : 0.040 0.360 5914 Planarity : 0.004 0.048 6540 Dihedral : 6.453 123.059 5362 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.59 % Allowed : 14.93 % Favored : 83.48 % 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: 0.99 (0.12), residues: 4799 helix: 1.30 (0.10), residues: 2643 sheet: 0.35 (0.21), residues: 565 loop : -0.18 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 235 HIS 0.004 0.001 HIS B 479 PHE 0.020 0.001 PHE L 76 TYR 0.013 0.001 TYR H 63 ARG 0.005 0.000 ARG Y 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7816.69 seconds wall clock time: 142 minutes 16.46 seconds (8536.46 seconds total)