Starting phenix.real_space_refine on Mon Jul 6 17:07:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p2y_13174/07_2026/7p2y_13174.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p2y_13174/07_2026/7p2y_13174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7p2y_13174/07_2026/7p2y_13174.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p2y_13174/07_2026/7p2y_13174.cif" model { file = "/net/cci-nas-00/data/ceres_data/7p2y_13174/07_2026/7p2y_13174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p2y_13174/07_2026/7p2y_13174.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p2y_13174/07_2026/7p2y_13174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p2y_13174/07_2026/7p2y_13174.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 1.066 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 12 5.49 5 Mg 4 5.21 5 S 147 5.16 5 C 23664 2.51 5 N 6317 2.21 5 O 7028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37172 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3846 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 490} Chain: "B" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3892 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 495} Chain: "C" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3850 Classifications: {'peptide': 509} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 491} Chain: "D" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "E" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 440} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3533 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 441} Chain: "G" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "H" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "J" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "K" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "L" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "O" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "P" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "Q" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "R" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "S" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2104 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 15, 'TRANS': 261} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 3, 'HIS:plan': 3, 'PHE:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "b" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1162 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "d" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1347 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1010 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "g" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2243 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain: "p" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1185 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.28, per 1000 atoms: 0.20 Number of scatterers: 37172 At special positions: 0 Unit cell: (136.85, 137.7, 239.7, 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 147 16.00 P 12 15.00 Mg 4 11.99 O 7028 8.00 N 6317 7.00 C 23664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.2 seconds 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8930 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 28 sheets defined 60.5% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 17 through 25 removed outlier: 3.717A pdb=" N ASP A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.362A pdb=" N SER A 82 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.773A pdb=" N MET A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.615A pdb=" N THR A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix removed outlier: 3.727A pdb=" N TYR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.551A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.737A pdb=" N HIS A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 340 through 348 removed outlier: 3.526A pdb=" N SER A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 378 through 383 removed outlier: 3.930A pdb=" N SER A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN A 383 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 393 through 408 removed outlier: 3.578A pdb=" N GLU A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.509A pdb=" N GLN A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 removed outlier: 3.604A pdb=" N SER A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 480 Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.901A pdb=" N THR A 490 " --> pdb=" O GLN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 511 removed outlier: 3.559A pdb=" N GLU A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 21 through 27 removed outlier: 4.713A pdb=" N THR B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.611A pdb=" N ARG B 140 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.562A pdb=" N THR B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.516A pdb=" N THR B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 4.342A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 removed outlier: 3.561A pdb=" N GLN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.704A pdb=" N ARG B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 314 Processing helix chain 'B' and resid 334 through 337 Processing helix chain 'B' and resid 340 through 350 removed outlier: 3.597A pdb=" N ILE B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 Processing helix chain 'B' and resid 378 through 383 removed outlier: 4.092A pdb=" N SER B 381 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 404 removed outlier: 4.776A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLY B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.501A pdb=" N GLN B 409 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 464 through 480 Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 494 through 511 Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.605A pdb=" N LEU C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.946A pdb=" N SER C 82 " --> pdb=" O ASN C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 217 through 220 removed outlier: 3.678A pdb=" N ALA C 220 " --> pdb=" O GLY C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 220' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 240 - end of helix removed outlier: 3.589A pdb=" N MET C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.512A pdb=" N GLN C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.900A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 340 through 350 removed outlier: 3.665A pdb=" N ILE C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 363 Processing helix chain 'C' and resid 378 through 383 removed outlier: 3.820A pdb=" N SER C 381 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 404 removed outlier: 4.718A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLY C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 404 " --> pdb=" O GLN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 5.090A pdb=" N GLN C 409 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA C 411 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 432 removed outlier: 3.598A pdb=" N ARG C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 454 Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'C' and resid 464 through 480 Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 494 through 512 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.838A pdb=" N THR D 82 " --> pdb=" O GLY D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 136 Processing helix chain 'D' and resid 153 through 166 Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 211 through 217 removed outlier: 3.505A pdb=" N ARG D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 231 removed outlier: 3.516A pdb=" N ALA D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 259 removed outlier: 3.829A pdb=" N THR D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 275 through 285 removed outlier: 4.028A pdb=" N LEU D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 327 through 333 Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 355 through 376 Processing helix chain 'D' and resid 377 through 382 removed outlier: 3.609A pdb=" N ILE D 381 " --> pdb=" O ASP D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 3.615A pdb=" N GLU D 386 " --> pdb=" O GLY D 383 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 387 " --> pdb=" O MET D 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 383 through 387' Processing helix chain 'D' and resid 388 through 405 Processing helix chain 'D' and resid 411 through 415 removed outlier: 4.269A pdb=" N VAL D 414 " --> pdb=" O VAL D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 438 Processing helix chain 'D' and resid 444 through 449 removed outlier: 3.901A pdb=" N TYR D 449 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 464 removed outlier: 3.891A pdb=" N VAL D 457 " --> pdb=" O GLY D 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.855A pdb=" N THR E 82 " --> pdb=" O GLY E 79 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 83 " --> pdb=" O THR E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 153 through 169 Processing helix chain 'E' and resid 181 through 195 Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 211 through 232 removed outlier: 3.859A pdb=" N ARG E 215 " --> pdb=" O PRO E 211 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ALA E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 263 removed outlier: 3.836A pdb=" N THR E 253 " --> pdb=" O ILE E 249 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY E 256 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 285 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 310 through 318 removed outlier: 3.898A pdb=" N THR E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA E 318 " --> pdb=" O ALA E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 333 removed outlier: 3.723A pdb=" N ALA E 331 " --> pdb=" O SER E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 373 removed outlier: 3.826A pdb=" N TYR E 359 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 382 Processing helix chain 'E' and resid 391 through 405 removed outlier: 3.637A pdb=" N VAL E 395 " --> pdb=" O ASP E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 438 Processing helix chain 'E' and resid 444 through 449 removed outlier: 3.736A pdb=" N TYR E 449 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 464 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.653A pdb=" N THR F 82 " --> pdb=" O GLY F 79 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 83 " --> pdb=" O THR F 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 79 through 83' Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 153 through 169 Processing helix chain 'F' and resid 181 through 195 removed outlier: 3.571A pdb=" N SER F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 199 removed outlier: 3.824A pdb=" N ASP F 199 " --> pdb=" O ASN F 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 196 through 199' Processing helix chain 'F' and resid 211 through 232 removed outlier: 3.810A pdb=" N ARG F 215 " --> pdb=" O PRO F 211 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA F 219 " --> pdb=" O ARG F 215 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 264 removed outlier: 3.813A pdb=" N TYR F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 285 removed outlier: 3.774A pdb=" N LEU F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 Processing helix chain 'F' and resid 310 through 317 Processing helix chain 'F' and resid 327 through 333 removed outlier: 3.603A pdb=" N ALA F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 355 Processing helix chain 'F' and resid 356 through 383 removed outlier: 4.275A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY F 383 " --> pdb=" O ILE F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 387 Processing helix chain 'F' and resid 388 through 405 Processing helix chain 'F' and resid 411 through 416 removed outlier: 4.414A pdb=" N PHE F 415 " --> pdb=" O VAL F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 437 Processing helix chain 'F' and resid 444 through 449 removed outlier: 3.531A pdb=" N TYR F 449 " --> pdb=" O GLN F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 464 Processing helix chain 'G' and resid 3 through 41 removed outlier: 3.852A pdb=" N GLY G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 60 Processing helix chain 'G' and resid 60 through 76 Processing helix chain 'H' and resid 3 through 41 removed outlier: 3.680A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 60 Processing helix chain 'H' and resid 60 through 76 Processing helix chain 'J' and resid 2 through 41 removed outlier: 3.597A pdb=" N GLY J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY J 28 " --> pdb=" O ALA J 24 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 60 Processing helix chain 'J' and resid 60 through 76 Processing helix chain 'K' and resid 2 through 41 removed outlier: 3.770A pdb=" N ARG K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 60 Processing helix chain 'K' and resid 60 through 76 Processing helix chain 'L' and resid 2 through 41 removed outlier: 3.548A pdb=" N GLY L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 60 Processing helix chain 'L' and resid 60 through 76 Processing helix chain 'O' and resid 2 through 41 removed outlier: 3.691A pdb=" N ILE O 16 " --> pdb=" O SER O 12 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE O 25 " --> pdb=" O LEU O 21 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 60 Processing helix chain 'O' and resid 60 through 76 Processing helix chain 'P' and resid 3 through 41 removed outlier: 3.746A pdb=" N ARG P 33 " --> pdb=" O LEU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 60 Processing helix chain 'P' and resid 60 through 76 Processing helix chain 'Q' and resid 3 through 41 removed outlier: 3.590A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG Q 33 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 Processing helix chain 'Q' and resid 60 through 75 Processing helix chain 'R' and resid 2 through 41 removed outlier: 3.614A pdb=" N GLY R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 60 Processing helix chain 'R' and resid 60 through 76 Processing helix chain 'S' and resid 2 through 41 removed outlier: 3.702A pdb=" N GLY S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE S 25 " --> pdb=" O LEU S 21 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY S 28 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG S 33 " --> pdb=" O LEU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 60 Processing helix chain 'S' and resid 60 through 76 removed outlier: 3.543A pdb=" N GLY S 68 " --> pdb=" O MET S 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 26 Processing helix chain 'a' and resid 28 through 33 removed outlier: 3.982A pdb=" N TRP a 31 " --> pdb=" O ASP a 28 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU a 33 " --> pdb=" O THR a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 52 through 73 removed outlier: 4.325A pdb=" N ILE a 62 " --> pdb=" O GLY a 58 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL a 70 " --> pdb=" O LEU a 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 101 Processing helix chain 'a' and resid 107 through 125 removed outlier: 3.530A pdb=" N MET a 125 " --> pdb=" O LEU a 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 128 No H-bonds generated for 'chain 'a' and resid 126 through 128' Processing helix chain 'a' and resid 131 through 144 removed outlier: 4.378A pdb=" N PHE a 139 " --> pdb=" O GLN a 135 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL a 140 " --> pdb=" O VAL a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 147 through 154 removed outlier: 3.688A pdb=" N TYR a 153 " --> pdb=" O PRO a 149 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE a 154 " --> pdb=" O HIS a 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 161 through 181 removed outlier: 3.928A pdb=" N THR a 165 " --> pdb=" O ASP a 161 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 191 Processing helix chain 'a' and resid 201 through 209 Processing helix chain 'a' and resid 210 through 222 removed outlier: 4.593A pdb=" N PHE a 221 " --> pdb=" O GLU a 217 " (cutoff:3.500A) Processing helix chain 'a' and resid 222 through 247 removed outlier: 4.210A pdb=" N ILE a 226 " --> pdb=" O LEU a 222 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA a 247 " --> pdb=" O PHE a 243 " (cutoff:3.500A) Processing helix chain 'a' and resid 258 through 288 removed outlier: 3.963A pdb=" N THR a 270 " --> pdb=" O ILE a 266 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU a 271 " --> pdb=" O LEU a 267 " (cutoff:3.500A) Processing helix chain 'b' and resid 6 through 23 removed outlier: 4.181A pdb=" N GLN b 10 " --> pdb=" O THR b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 32 removed outlier: 3.568A pdb=" N ALA b 32 " --> pdb=" O PRO b 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 32 through 132 removed outlier: 3.910A pdb=" N ARG b 36 " --> pdb=" O ALA b 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA b 46 " --> pdb=" O ASP b 42 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS b 49 " --> pdb=" O ASN b 45 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA b 50 " --> pdb=" O ALA b 46 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU b 64 " --> pdb=" O GLN b 60 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU b 65 " --> pdb=" O VAL b 61 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA b 83 " --> pdb=" O ALA b 79 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA b 84 " --> pdb=" O ASN b 80 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN b 85 " --> pdb=" O ARG b 81 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER b 115 " --> pdb=" O GLN b 111 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 134 through 139 Processing helix chain 'd' and resid 4 through 8 Processing helix chain 'd' and resid 8 through 23 Processing helix chain 'd' and resid 24 through 41 Processing helix chain 'd' and resid 41 through 49 Processing helix chain 'd' and resid 54 through 67 Processing helix chain 'd' and resid 71 through 84 removed outlier: 3.678A pdb=" N ASN d 84 " --> pdb=" O LEU d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 86 through 88 No H-bonds generated for 'chain 'd' and resid 86 through 88' Processing helix chain 'd' and resid 89 through 105 Processing helix chain 'd' and resid 119 through 131 Processing helix chain 'd' and resid 132 through 134 No H-bonds generated for 'chain 'd' and resid 132 through 134' Processing helix chain 'd' and resid 165 through 176 removed outlier: 3.644A pdb=" N LEU d 169 " --> pdb=" O ALA d 165 " (cutoff:3.500A) Processing helix chain 'e' and resid 91 through 127 removed outlier: 4.756A pdb=" N ALA e 97 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG e 98 " --> pdb=" O ILE e 94 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER e 114 " --> pdb=" O SER e 110 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA e 115 " --> pdb=" O ASP e 111 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA e 119 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA e 120 " --> pdb=" O ALA e 116 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA e 122 " --> pdb=" O LEU e 118 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA e 125 " --> pdb=" O LEU e 121 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN e 127 " --> pdb=" O GLU e 123 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 133 Processing helix chain 'g' and resid 3 through 42 removed outlier: 3.735A pdb=" N ILE g 7 " --> pdb=" O ASN g 3 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA g 40 " --> pdb=" O GLN g 36 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN g 41 " --> pdb=" O GLU g 37 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY g 42 " --> pdb=" O ARG g 38 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 60 removed outlier: 3.764A pdb=" N ALA g 46 " --> pdb=" O GLY g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 109 removed outlier: 3.692A pdb=" N GLU g 108 " --> pdb=" O LYS g 104 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN g 109 " --> pdb=" O ALA g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 129 Processing helix chain 'g' and resid 145 through 162 removed outlier: 3.829A pdb=" N LEU g 149 " --> pdb=" O SER g 145 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLY g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N SER g 152 " --> pdb=" O GLN g 148 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL g 153 " --> pdb=" O LEU g 149 " (cutoff:3.500A) Processing helix chain 'g' and resid 213 through 288 removed outlier: 3.763A pdb=" N GLU g 236 " --> pdb=" O GLN g 232 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN g 237 " --> pdb=" O GLY g 233 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU g 265 " --> pdb=" O LYS g 261 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 139 removed outlier: 3.718A pdb=" N GLY p 9 " --> pdb=" O LEU p 5 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS p 23 " --> pdb=" O ALA p 19 " (cutoff:3.500A) Proline residue: p 27 - end of helix removed outlier: 3.849A pdb=" N GLN p 58 " --> pdb=" O LEU p 54 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA p 59 " --> pdb=" O ALA p 55 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA p 67 " --> pdb=" O GLN p 63 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN p 80 " --> pdb=" O ILE p 76 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG p 81 " --> pdb=" O GLU p 77 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU p 99 " --> pdb=" O ALA p 95 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG p 121 " --> pdb=" O ARG p 117 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN p 123 " --> pdb=" O GLU p 119 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 156 removed outlier: 4.050A pdb=" N ALA p 154 " --> pdb=" O SER p 150 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 removed outlier: 6.574A pdb=" N ARG A 41 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU A 67 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 61 " --> pdb=" O LEU A 77 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 3 through 10 current: chain 'A' and resid 89 through 91 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36 removed outlier: 6.574A pdb=" N ARG A 41 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU A 67 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 61 " --> pdb=" O LEU A 77 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 61 through 67 current: chain 'D' and resid 29 through 32 removed outlier: 6.807A pdb=" N ARG D 51 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLN D 44 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL D 49 " --> pdb=" O GLN D 44 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL D 13 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 3 through 10 current: chain 'A' and resid 89 through 91 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.615A pdb=" N VAL A 100 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 109 removed outlier: 3.714A pdb=" N ILE A 199 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 257 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 4.735A pdb=" N VAL A 160 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 330 through 332 removed outlier: 6.458A pdb=" N ILE A 168 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 169 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N GLN A 353 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N GLY A 372 " --> pdb=" O GLN A 353 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N PHE A 355 " --> pdb=" O ASN A 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 36 removed outlier: 6.623A pdb=" N ARG B 41 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN B 66 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 4 through 10 current: chain 'B' and resid 89 through 95 Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 36 removed outlier: 6.623A pdb=" N ARG B 41 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN B 66 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 61 through 67 current: chain 'F' and resid 29 through 32 removed outlier: 4.588A pdb=" N THR F 38 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ARG F 51 " --> pdb=" O GLN F 42 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLN F 44 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL F 49 " --> pdb=" O GLN F 44 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL F 13 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 4 through 10 current: chain 'B' and resid 89 through 95 Processing sheet with id=AA9, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.043A pdb=" N LEU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 147 removed outlier: 4.498A pdb=" N VAL B 160 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 330 through 332 removed outlier: 6.375A pdb=" N ILE B 168 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU B 167 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU B 356 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE B 169 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'd' and resid 138 through 144 removed outlier: 8.038A pdb=" N VAL d 108 " --> pdb=" O THR d 139 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N SER d 141 " --> pdb=" O VAL d 108 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL d 110 " --> pdb=" O SER d 141 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLU d 143 " --> pdb=" O VAL d 110 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE d 112 " --> pdb=" O GLU d 143 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASN C 28 " --> pdb=" O CYS C 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 91 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.999A pdb=" N LEU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.821A pdb=" N ILE C 199 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 330 through 332 removed outlier: 6.368A pdb=" N ILE C 168 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU C 167 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU C 356 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE C 169 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 375 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AB9, first strand: chain 'D' and resid 86 through 87 removed outlier: 6.317A pdb=" N MET D 87 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 178 " --> pdb=" O ASP D 247 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL D 242 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE D 298 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU D 244 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA D 300 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL D 246 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N TYR D 302 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY D 148 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS D 143 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL D 324 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY D 145 " --> pdb=" O VAL D 324 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 124 through 125 removed outlier: 3.527A pdb=" N LEU D 125 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE D 138 " --> pdb=" O LEU D 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 4 through 10 removed outlier: 6.760A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL E 13 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL E 49 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN E 44 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG E 51 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 77 Processing sheet with id=AC4, first strand: chain 'E' and resid 86 through 87 removed outlier: 6.711A pdb=" N MET E 87 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL E 174 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL E 242 " --> pdb=" O THR E 296 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ILE E 298 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU E 244 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ALA E 300 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL E 246 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL E 144 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS E 143 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL E 324 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY E 145 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 124 through 125 removed outlier: 3.579A pdb=" N LEU E 125 " --> pdb=" O PHE E 138 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE E 138 " --> pdb=" O LEU E 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 75 through 78 removed outlier: 4.473A pdb=" N GLU F 104 " --> pdb=" O VAL F 78 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 86 through 87 removed outlier: 5.963A pdb=" N MET F 87 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN F 207 " --> pdb=" O MET F 87 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP F 247 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL F 178 " --> pdb=" O ASP F 247 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL F 242 " --> pdb=" O THR F 296 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE F 298 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU F 244 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA F 300 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL F 246 " --> pdb=" O ALA F 300 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS F 143 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL F 324 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY F 145 " --> pdb=" O VAL F 324 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 14 through 20 removed outlier: 5.403A pdb=" N SER e 14 " --> pdb=" O SER e 10 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER e 10 " --> pdb=" O SER e 14 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN e 5 " --> pdb=" O VAL e 76 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL e 78 " --> pdb=" O GLN e 5 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP e 7 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA e 80 " --> pdb=" O ASP e 7 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL e 9 " --> pdb=" O ALA e 80 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY e 67 " --> pdb=" O LEU e 45 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU e 69 " --> pdb=" O THR e 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'e' and resid 31 through 34 removed outlier: 3.630A pdb=" N MET e 22 " --> pdb=" O LEU e 53 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LYS e 26 " --> pdb=" O PRO e 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'g' and resid 133 through 137 removed outlier: 6.397A pdb=" N VAL g 133 " --> pdb=" O VAL g 113 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE g 115 " --> pdb=" O VAL g 133 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY g 135 " --> pdb=" O PHE g 115 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL g 76 " --> pdb=" O GLN g 114 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ALA g 116 " --> pdb=" O VAL g 76 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR g 78 " --> pdb=" O ALA g 116 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE g 118 " --> pdb=" O TYR g 78 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE g 80 " --> pdb=" O ILE g 118 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARG g 75 " --> pdb=" O ARG g 167 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N TYR g 169 " --> pdb=" O ARG g 75 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY g 77 " --> pdb=" O TYR g 169 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL g 171 " --> pdb=" O GLY g 77 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE g 79 " --> pdb=" O VAL g 171 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ASN g 173 " --> pdb=" O ILE g 79 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N VAL g 81 " --> pdb=" O ASN g 173 " (cutoff:3.500A) removed outlier: 12.213A pdb=" N PHE g 175 " --> pdb=" O VAL g 81 " (cutoff:3.500A) 2244 hydrogen bonds defined for protein. 6567 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: 9.44 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12421 1.34 - 1.46: 7221 1.46 - 1.58: 17817 1.58 - 1.70: 18 1.70 - 1.82: 277 Bond restraints: 37754 Sorted by residual: bond pdb=" C1' ADP D 502 " pdb=" N9 ADP D 502 " ideal model delta sigma weight residual 1.485 1.339 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O3A ATP C 602 " pdb=" PB ATP C 602 " ideal model delta sigma weight residual 1.592 1.663 -0.071 1.10e-02 8.26e+03 4.19e+01 bond pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 1.592 1.663 -0.071 1.10e-02 8.26e+03 4.14e+01 bond pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 1.592 1.662 -0.070 1.10e-02 8.26e+03 4.08e+01 bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.335 0.052 1.00e-02 1.00e+04 2.70e+01 ... (remaining 37749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 50910 3.42 - 6.83: 248 6.83 - 10.25: 20 10.25 - 13.66: 6 13.66 - 17.08: 1 Bond angle restraints: 51185 Sorted by residual: angle pdb=" C5 ATP A 601 " pdb=" C4 ATP A 601 " pdb=" N3 ATP A 601 " ideal model delta sigma weight residual 126.80 119.27 7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" C5 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 126.80 119.29 7.51 1.00e+00 1.00e+00 5.64e+01 angle pdb=" C5 ATP C 602 " pdb=" C4 ATP C 602 " pdb=" N3 ATP C 602 " ideal model delta sigma weight residual 126.80 119.33 7.47 1.00e+00 1.00e+00 5.58e+01 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 132.72 7.15 1.00e+00 1.00e+00 5.12e+01 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 132.79 7.08 1.00e+00 1.00e+00 5.01e+01 ... (remaining 51180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.81: 22385 31.81 - 63.62: 338 63.62 - 95.43: 29 95.43 - 127.23: 0 127.23 - 159.04: 1 Dihedral angle restraints: 22753 sinusoidal: 8809 harmonic: 13944 Sorted by residual: dihedral pdb=" O1B ADP D 502 " pdb=" O3A ADP D 502 " pdb=" PB ADP D 502 " pdb=" PA ADP D 502 " ideal model delta sinusoidal sigma weight residual 300.00 140.95 159.04 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" CA GLY E 206 " pdb=" C GLY E 206 " pdb=" N GLN E 207 " pdb=" CA GLN E 207 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ASP F 194 " pdb=" C ASP F 194 " pdb=" N SER F 195 " pdb=" CA SER F 195 " ideal model delta harmonic sigma weight residual 180.00 157.54 22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 22750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4842 0.053 - 0.106: 986 0.106 - 0.159: 164 0.159 - 0.212: 3 0.212 - 0.266: 2 Chirality restraints: 5997 Sorted by residual: chirality pdb=" C1' ADP D 502 " pdb=" C2' ADP D 502 " pdb=" N9 ADP D 502 " pdb=" O4' ADP D 502 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C2' ADP D 502 " pdb=" C1' ADP D 502 " pdb=" C3' ADP D 502 " pdb=" O2' ADP D 502 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA MET E 159 " pdb=" N MET E 159 " pdb=" C MET E 159 " pdb=" CB MET E 159 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 5994 not shown) Planarity restraints: 6637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET p 22 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C MET p 22 " -0.047 2.00e-02 2.50e+03 pdb=" O MET p 22 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS p 23 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA b 19 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ALA b 19 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA b 19 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE b 20 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 23 " 0.013 2.00e-02 2.50e+03 1.32e-02 3.51e+00 pdb=" CG TYR a 23 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR a 23 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR a 23 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR a 23 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR a 23 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR a 23 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR a 23 " -0.002 2.00e-02 2.50e+03 ... (remaining 6634 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 462 2.65 - 3.21: 36497 3.21 - 3.78: 55252 3.78 - 4.34: 75808 4.34 - 4.90: 126114 Nonbonded interactions: 294133 Sorted by model distance: nonbonded pdb=" OG1 THR A 177 " pdb="MG MG A 602 " model vdw 2.088 2.170 nonbonded pdb=" OG1 THR B 177 " pdb="MG MG B 602 " model vdw 2.095 2.170 nonbonded pdb=" OG1 THR C 177 " pdb="MG MG C 601 " model vdw 2.096 2.170 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 2.096 2.170 nonbonded pdb="MG MG D 501 " pdb=" O1B ADP D 502 " model vdw 2.126 2.170 ... (remaining 294128 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 511) selection = (chain 'B' and resid 6 through 511) selection = (chain 'C' and resid 6 through 511) } ncs_group { reference = (chain 'D' and resid 2 through 464) selection = (chain 'E' and resid 2 through 464) selection = (chain 'F' and resid 2 through 464) } ncs_group { reference = chain 'G' selection = chain 'H' selection = (chain 'J' and resid 2 through 80) selection = (chain 'K' and resid 2 through 80) selection = (chain 'L' and resid 2 through 80) selection = (chain 'O' and resid 2 through 80) selection = chain 'P' selection = chain 'Q' selection = (chain 'R' and resid 2 through 80) selection = (chain 'S' and resid 2 through 80) } ncs_group { reference = chain 'b' selection = (chain 'p' and ((resid 3 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 155 or (resid 156 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2)))) } 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=0.75 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: 5.950 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 32.910 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.110 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 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 0.146 37754 Z= 0.228 Angle : 0.698 17.078 51185 Z= 0.415 Chirality : 0.043 0.266 5997 Planarity : 0.004 0.044 6637 Dihedral : 11.759 159.042 13823 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.08 % Allowed : 0.23 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.12), residues: 4860 helix: 1.32 (0.10), residues: 2621 sheet: -0.98 (0.20), residues: 578 loop : -1.52 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG b 36 TYR 0.033 0.001 TYR a 23 PHE 0.031 0.002 PHE a 101 TRP 0.014 0.001 TRP a 261 HIS 0.005 0.001 HIS a 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.23 (37754) covalent geometry : angle 0.69829 / 0.42 (51185) hydrogen bonds : bond 0.17449 / 11.82 ( 2229) hydrogen bonds : angle 6.15166 / 4.28 ( 6567) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 470 time to evaluate : 1.391 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: C 110 ASP cc_start: 0.8388 (t70) cc_final: 0.8005 (t0) REVERT: C 337 ASP cc_start: 0.8860 (t70) cc_final: 0.8655 (t0) REVERT: F 210 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8285 (mt-10) REVERT: G 64 MET cc_start: 0.9439 (mmp) cc_final: 0.9201 (mmp) REVERT: H 36 GLU cc_start: 0.8899 (tt0) cc_final: 0.8604 (tm-30) REVERT: H 52 MET cc_start: 0.9179 (tmm) cc_final: 0.8918 (tmm) REVERT: H 60 ASP cc_start: 0.8807 (m-30) cc_final: 0.8518 (m-30) REVERT: H 64 MET cc_start: 0.9099 (mmp) cc_final: 0.8658 (mmm) REVERT: J 36 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7633 (mm-30) REVERT: J 52 MET cc_start: 0.9418 (tmm) cc_final: 0.9203 (tmm) REVERT: K 52 MET cc_start: 0.9080 (tmm) cc_final: 0.8576 (tmm) REVERT: O 36 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8373 (tm-30) REVERT: O 52 MET cc_start: 0.9049 (tmm) cc_final: 0.8753 (tmm) REVERT: Q 52 MET cc_start: 0.9280 (tmm) cc_final: 0.8940 (tmm) REVERT: R 49 GLN cc_start: 0.9290 (tt0) cc_final: 0.8948 (tt0) REVERT: R 52 MET cc_start: 0.9153 (tmm) cc_final: 0.8856 (tmm) REVERT: S 49 GLN cc_start: 0.9101 (tt0) cc_final: 0.8810 (mt0) REVERT: a 100 THR cc_start: 0.9070 (p) cc_final: 0.8647 (p) REVERT: a 123 ASN cc_start: 0.8797 (t0) cc_final: 0.8171 (t0) REVERT: a 126 ASP cc_start: 0.8399 (m-30) cc_final: 0.7726 (m-30) REVERT: a 221 PHE cc_start: 0.8208 (p90) cc_final: 0.7941 (p90) REVERT: a 236 MET cc_start: 0.8535 (mmp) cc_final: 0.8084 (mmp) REVERT: a 240 GLU cc_start: 0.8886 (pt0) cc_final: 0.8580 (pt0) REVERT: b 16 PHE cc_start: 0.8218 (m-10) cc_final: 0.7548 (m-10) REVERT: b 17 PHE cc_start: 0.8988 (t80) cc_final: 0.8618 (t80) REVERT: b 45 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.6890 (p0) REVERT: b 54 LEU cc_start: 0.9173 (mm) cc_final: 0.8873 (tp) REVERT: d 69 ASP cc_start: 0.8978 (m-30) cc_final: 0.7780 (t0) REVERT: d 83 ASP cc_start: 0.8983 (m-30) cc_final: 0.8757 (m-30) REVERT: e 5 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7814 (tp-100) REVERT: e 7 ASP cc_start: 0.8193 (m-30) cc_final: 0.7876 (m-30) REVERT: e 22 MET cc_start: 0.7765 (tmm) cc_final: 0.7474 (tmm) REVERT: e 99 LYS cc_start: 0.8864 (mmmm) cc_final: 0.8531 (mmtt) REVERT: e 103 GLN cc_start: 0.9217 (tm-30) cc_final: 0.8917 (tm-30) REVERT: e 113 ASP cc_start: 0.8571 (t0) cc_final: 0.8348 (t0) REVERT: g 156 MET cc_start: 0.8332 (mmm) cc_final: 0.8098 (mmt) REVERT: p 14 PHE cc_start: 0.9017 (m-80) cc_final: 0.8564 (m-80) REVERT: p 53 ASP cc_start: 0.9179 (m-30) cc_final: 0.8200 (m-30) REVERT: p 129 VAL cc_start: 0.8956 (t) cc_final: 0.8716 (m) outliers start: 3 outliers final: 0 residues processed: 473 average time/residue: 0.2280 time to fit residues: 173.7570 Evaluate side-chains 365 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 363 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain b residue 45 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.5980 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 470 optimal weight: 7.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 426 GLN C 201 GLN E 111 GLN E 164 ASN F 284 GLN F 299 GLN P 47 GLN S 41 GLN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 151 GLN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.078755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.055756 restraints weight = 109078.117| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.27 r_work: 0.2721 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 37754 Z= 0.220 Angle : 0.641 7.961 51185 Z= 0.335 Chirality : 0.045 0.200 5997 Planarity : 0.004 0.056 6637 Dihedral : 6.033 174.894 5284 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.76 % Allowed : 5.69 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.12), residues: 4860 helix: 1.48 (0.10), residues: 2672 sheet: -0.72 (0.20), residues: 597 loop : -1.52 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG b 91 TYR 0.015 0.001 TYR a 283 PHE 0.020 0.002 PHE b 16 TRP 0.021 0.002 TRP a 255 HIS 0.004 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (37754) covalent geometry : angle 0.64067 / 0.34 (51185) hydrogen bonds : bond 0.06033 / 4.05 ( 2229) hydrogen bonds : angle 4.90326 / 3.41 ( 6567) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 407 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 337 ASP cc_start: 0.9024 (t70) cc_final: 0.8727 (t0) REVERT: G 60 ASP cc_start: 0.9019 (t0) cc_final: 0.8230 (t0) REVERT: G 64 MET cc_start: 0.9545 (mmp) cc_final: 0.9010 (mmp) REVERT: H 60 ASP cc_start: 0.9255 (m-30) cc_final: 0.8977 (m-30) REVERT: H 64 MET cc_start: 0.9396 (mmp) cc_final: 0.9000 (mmm) REVERT: J 52 MET cc_start: 0.9704 (tmm) cc_final: 0.9446 (tmm) REVERT: K 52 MET cc_start: 0.9246 (tmm) cc_final: 0.8688 (tmm) REVERT: O 36 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8663 (tm-30) REVERT: O 52 MET cc_start: 0.9357 (tmm) cc_final: 0.9009 (tmm) REVERT: O 64 MET cc_start: 0.9575 (tpp) cc_final: 0.9355 (mmm) REVERT: Q 52 MET cc_start: 0.9467 (tmm) cc_final: 0.9222 (tmm) REVERT: R 49 GLN cc_start: 0.9350 (tt0) cc_final: 0.8971 (tt0) REVERT: R 52 MET cc_start: 0.9441 (tmm) cc_final: 0.9119 (tmm) REVERT: S 49 GLN cc_start: 0.9184 (tt0) cc_final: 0.8842 (mt0) REVERT: S 52 MET cc_start: 0.9472 (tmm) cc_final: 0.9199 (tmm) REVERT: S 53 PHE cc_start: 0.9287 (m-10) cc_final: 0.9043 (m-10) REVERT: a 122 MET cc_start: 0.8972 (mtp) cc_final: 0.8650 (mtp) REVERT: a 123 ASN cc_start: 0.9094 (t0) cc_final: 0.8391 (t0) REVERT: a 168 MET cc_start: 0.9487 (mmm) cc_final: 0.9119 (mmm) REVERT: a 184 LYS cc_start: 0.8134 (mppt) cc_final: 0.7312 (tptp) REVERT: a 221 PHE cc_start: 0.8779 (p90) cc_final: 0.8529 (p90) REVERT: a 236 MET cc_start: 0.8998 (mmp) cc_final: 0.7291 (mtm) REVERT: a 237 TYR cc_start: 0.9477 (t80) cc_final: 0.9260 (t80) REVERT: a 240 GLU cc_start: 0.9117 (pt0) cc_final: 0.8819 (pt0) REVERT: a 277 MET cc_start: 0.9578 (tmm) cc_final: 0.9289 (tmm) REVERT: b 16 PHE cc_start: 0.9005 (m-10) cc_final: 0.8801 (m-10) REVERT: b 17 PHE cc_start: 0.9264 (t80) cc_final: 0.8762 (t80) REVERT: b 54 LEU cc_start: 0.9294 (mm) cc_final: 0.9080 (tp) REVERT: b 151 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: b 155 LYS cc_start: 0.8475 (mmmt) cc_final: 0.8252 (tptm) REVERT: d 69 ASP cc_start: 0.9224 (m-30) cc_final: 0.7876 (t0) REVERT: e 22 MET cc_start: 0.8347 (tmm) cc_final: 0.7412 (tmm) REVERT: g 156 MET cc_start: 0.8410 (mmm) cc_final: 0.8191 (mmt) REVERT: p 53 ASP cc_start: 0.8827 (m-30) cc_final: 0.8607 (m-30) REVERT: p 129 VAL cc_start: 0.8831 (t) cc_final: 0.8572 (m) outliers start: 29 outliers final: 13 residues processed: 419 average time/residue: 0.2261 time to fit residues: 154.4853 Evaluate side-chains 382 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 368 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain P residue 79 PHE Chi-restraints excluded: chain a residue 124 LEU Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain a residue 270 THR Chi-restraints excluded: chain a residue 284 LEU Chi-restraints excluded: chain b residue 151 GLN Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain g residue 39 MET Chi-restraints excluded: chain g residue 189 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 258 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 432 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 341 optimal weight: 3.9990 chunk 336 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 376 optimal weight: 0.0980 chunk 245 optimal weight: 0.0980 chunk 265 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 486 GLN J 41 GLN P 41 GLN ** S 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 151 HIS ** a 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 37 GLN ** b 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 173 ASN p 138 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.081003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.058066 restraints weight = 107677.313| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.20 r_work: 0.2781 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 37754 Z= 0.123 Angle : 0.562 7.348 51185 Z= 0.291 Chirality : 0.042 0.180 5997 Planarity : 0.004 0.047 6637 Dihedral : 5.513 160.861 5279 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.81 % Allowed : 7.59 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.12), residues: 4860 helix: 1.70 (0.10), residues: 2674 sheet: -0.29 (0.21), residues: 564 loop : -1.42 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 81 TYR 0.012 0.001 TYR a 283 PHE 0.018 0.001 PHE S 75 TRP 0.014 0.001 TRP a 255 HIS 0.004 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (37754) covalent geometry : angle 0.56186 / 0.29 (51185) hydrogen bonds : bond 0.04991 / 3.34 ( 2229) hydrogen bonds : angle 4.43195 / 3.08 ( 6567) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 421 time to evaluate : 1.336 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: C 49 MET cc_start: 0.8408 (mtm) cc_final: 0.8165 (mtp) REVERT: C 110 ASP cc_start: 0.8597 (t70) cc_final: 0.8227 (t0) REVERT: C 337 ASP cc_start: 0.8966 (t70) cc_final: 0.8687 (t0) REVERT: G 43 GLU cc_start: 0.8940 (pm20) cc_final: 0.8724 (pm20) REVERT: G 60 ASP cc_start: 0.9033 (t0) cc_final: 0.8563 (t0) REVERT: G 64 MET cc_start: 0.9526 (mmp) cc_final: 0.9013 (mmp) REVERT: H 36 GLU cc_start: 0.9195 (tt0) cc_final: 0.8774 (tm-30) REVERT: H 40 ARG cc_start: 0.9042 (mmm-85) cc_final: 0.8638 (mmm-85) REVERT: H 52 MET cc_start: 0.9521 (tmm) cc_final: 0.9228 (tmm) REVERT: H 60 ASP cc_start: 0.9202 (m-30) cc_final: 0.8854 (m-30) REVERT: H 64 MET cc_start: 0.9357 (mmp) cc_final: 0.8932 (mmm) REVERT: J 36 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8027 (mm-30) REVERT: J 52 MET cc_start: 0.9684 (tmm) cc_final: 0.9424 (tmm) REVERT: K 52 MET cc_start: 0.9243 (tmm) cc_final: 0.8723 (tmm) REVERT: O 36 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8210 (tm-30) REVERT: O 52 MET cc_start: 0.9339 (tmm) cc_final: 0.9009 (tmm) REVERT: Q 49 GLN cc_start: 0.9314 (tt0) cc_final: 0.8990 (tt0) REVERT: Q 52 MET cc_start: 0.9435 (tmm) cc_final: 0.9230 (tmm) REVERT: R 49 GLN cc_start: 0.9316 (tt0) cc_final: 0.8974 (tt0) REVERT: R 52 MET cc_start: 0.9426 (tmm) cc_final: 0.9126 (tmm) REVERT: R 64 MET cc_start: 0.9307 (mmm) cc_final: 0.8701 (mmm) REVERT: S 14 ILE cc_start: 0.9360 (tp) cc_final: 0.9077 (tp) REVERT: S 18 PHE cc_start: 0.9168 (m-10) cc_final: 0.8945 (m-10) REVERT: S 49 GLN cc_start: 0.9151 (tt0) cc_final: 0.8618 (mt0) REVERT: S 52 MET cc_start: 0.9471 (tmm) cc_final: 0.9134 (tmm) REVERT: S 53 PHE cc_start: 0.9291 (m-10) cc_final: 0.8998 (m-10) REVERT: a 21 MET cc_start: 0.9539 (mmp) cc_final: 0.8879 (ptm) REVERT: a 122 MET cc_start: 0.9069 (mtp) cc_final: 0.8838 (mtp) REVERT: a 123 ASN cc_start: 0.9017 (t0) cc_final: 0.8218 (t0) REVERT: a 168 MET cc_start: 0.9409 (mmm) cc_final: 0.8999 (mmm) REVERT: a 184 LYS cc_start: 0.8038 (mppt) cc_final: 0.7281 (tptp) REVERT: a 221 PHE cc_start: 0.8738 (p90) cc_final: 0.8488 (p90) REVERT: a 235 ASN cc_start: 0.8545 (m110) cc_final: 0.7998 (m-40) REVERT: a 236 MET cc_start: 0.8938 (mmp) cc_final: 0.7320 (mtm) REVERT: a 237 TYR cc_start: 0.9515 (t80) cc_final: 0.9260 (t80) REVERT: a 240 GLU cc_start: 0.9072 (pt0) cc_final: 0.8720 (pt0) REVERT: b 17 PHE cc_start: 0.9166 (t80) cc_final: 0.8954 (t80) REVERT: b 82 ARG cc_start: 0.9531 (ttp80) cc_final: 0.9291 (ptp90) REVERT: b 155 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8306 (tptm) REVERT: d 69 ASP cc_start: 0.9179 (m-30) cc_final: 0.7893 (t0) REVERT: d 168 LYS cc_start: 0.8733 (mmmt) cc_final: 0.8359 (mptt) REVERT: e 22 MET cc_start: 0.8471 (tmm) cc_final: 0.7582 (tmm) REVERT: e 63 TYR cc_start: 0.8266 (t80) cc_final: 0.8022 (t80) REVERT: g 156 MET cc_start: 0.8389 (mmm) cc_final: 0.8176 (mmt) REVERT: p 53 ASP cc_start: 0.8858 (m-30) cc_final: 0.8616 (m-30) REVERT: p 129 VAL cc_start: 0.8858 (t) cc_final: 0.8600 (m) REVERT: p 134 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8607 (mmmm) outliers start: 31 outliers final: 12 residues processed: 439 average time/residue: 0.2262 time to fit residues: 162.3157 Evaluate side-chains 395 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 383 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain P residue 79 PHE Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain a residue 284 LEU Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain e residue 110 SER Chi-restraints excluded: chain g residue 39 MET Chi-restraints excluded: chain g residue 189 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 1 optimal weight: 20.0000 chunk 380 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 477 optimal weight: 6.9990 chunk 311 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 169 HIS E 407 GLN ** S 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.078504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.055674 restraints weight = 109252.757| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.17 r_work: 0.2721 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 37754 Z= 0.243 Angle : 0.622 8.635 51185 Z= 0.322 Chirality : 0.044 0.232 5997 Planarity : 0.004 0.044 6637 Dihedral : 5.507 154.430 5279 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.02 % Allowed : 9.44 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.12), residues: 4860 helix: 1.67 (0.10), residues: 2683 sheet: -0.42 (0.21), residues: 587 loop : -1.38 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 175 TYR 0.015 0.001 TYR D 252 PHE 0.022 0.001 PHE G 53 TRP 0.017 0.002 TRP g 206 HIS 0.005 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.24 (37754) covalent geometry : angle 0.62225 / 0.32 (51185) hydrogen bonds : bond 0.05223 / 3.49 ( 2229) hydrogen bonds : angle 4.52978 / 3.15 ( 6567) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 391 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 337 ASP cc_start: 0.9018 (t70) cc_final: 0.8708 (t0) REVERT: F 159 MET cc_start: 0.8917 (mtm) cc_final: 0.8576 (mtm) REVERT: G 52 MET cc_start: 0.9579 (tmm) cc_final: 0.9348 (tmm) REVERT: G 60 ASP cc_start: 0.9088 (t0) cc_final: 0.8645 (t0) REVERT: G 64 MET cc_start: 0.9559 (mmp) cc_final: 0.9061 (mmp) REVERT: H 36 GLU cc_start: 0.9215 (tt0) cc_final: 0.8759 (tm-30) REVERT: H 40 ARG cc_start: 0.9111 (mmm-85) cc_final: 0.8392 (mmm-85) REVERT: H 60 ASP cc_start: 0.9269 (m-30) cc_final: 0.8918 (m-30) REVERT: H 64 MET cc_start: 0.9379 (mmp) cc_final: 0.8935 (mmm) REVERT: J 36 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8151 (mm-30) REVERT: J 52 MET cc_start: 0.9705 (tmm) cc_final: 0.9431 (tmm) REVERT: K 52 MET cc_start: 0.9243 (tmm) cc_final: 0.8646 (tmm) REVERT: L 1 MET cc_start: 0.8451 (ppp) cc_final: 0.8167 (ppp) REVERT: O 36 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8376 (tm-30) REVERT: O 52 MET cc_start: 0.9325 (tmm) cc_final: 0.8952 (tmm) REVERT: P 36 GLU cc_start: 0.9273 (tp30) cc_final: 0.8988 (tp30) REVERT: Q 49 GLN cc_start: 0.9368 (tt0) cc_final: 0.9054 (tt0) REVERT: Q 52 MET cc_start: 0.9474 (tmm) cc_final: 0.9247 (tmm) REVERT: R 49 GLN cc_start: 0.9341 (tt0) cc_final: 0.9003 (tt0) REVERT: R 52 MET cc_start: 0.9445 (tmm) cc_final: 0.9151 (tmm) REVERT: R 64 MET cc_start: 0.9306 (mmm) cc_final: 0.8961 (mmm) REVERT: S 18 PHE cc_start: 0.9145 (m-10) cc_final: 0.8906 (m-10) REVERT: S 49 GLN cc_start: 0.9149 (tt0) cc_final: 0.8761 (mt0) REVERT: S 52 MET cc_start: 0.9518 (tmm) cc_final: 0.9120 (tmm) REVERT: a 123 ASN cc_start: 0.8832 (t0) cc_final: 0.8389 (t0) REVERT: a 168 MET cc_start: 0.9436 (mmm) cc_final: 0.9032 (mmm) REVERT: a 184 LYS cc_start: 0.8035 (mppt) cc_final: 0.7222 (tptp) REVERT: a 221 PHE cc_start: 0.8814 (p90) cc_final: 0.8567 (p90) REVERT: a 240 GLU cc_start: 0.9094 (pt0) cc_final: 0.8777 (pt0) REVERT: a 277 MET cc_start: 0.9509 (tmm) cc_final: 0.9294 (tmm) REVERT: b 17 PHE cc_start: 0.9237 (t80) cc_final: 0.8849 (t80) REVERT: b 91 ARG cc_start: 0.8642 (tpt-90) cc_final: 0.8415 (tpt-90) REVERT: b 102 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8250 (mmm-85) REVERT: b 155 LYS cc_start: 0.8583 (mmmt) cc_final: 0.8336 (tptm) REVERT: d 69 ASP cc_start: 0.9256 (m-30) cc_final: 0.7877 (t0) REVERT: d 168 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8472 (mptt) REVERT: e 22 MET cc_start: 0.8454 (tmm) cc_final: 0.7575 (tmm) REVERT: p 53 ASP cc_start: 0.8826 (m-30) cc_final: 0.8498 (m-30) REVERT: p 129 VAL cc_start: 0.8779 (t) cc_final: 0.8553 (m) REVERT: p 134 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8595 (mmmm) outliers start: 39 outliers final: 21 residues processed: 414 average time/residue: 0.2160 time to fit residues: 146.4289 Evaluate side-chains 393 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 372 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain P residue 79 PHE Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 270 THR Chi-restraints excluded: chain a residue 284 LEU Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 141 ASP Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain e residue 110 SER Chi-restraints excluded: chain g residue 39 MET Chi-restraints excluded: chain g residue 150 THR Chi-restraints excluded: chain g residue 189 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 116 optimal weight: 2.9990 chunk 476 optimal weight: 8.9990 chunk 89 optimal weight: 0.0470 chunk 188 optimal weight: 0.0060 chunk 198 optimal weight: 0.9980 chunk 229 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 chunk 394 optimal weight: 0.9980 chunk 289 optimal weight: 10.0000 chunk 413 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 overall best weight: 0.8096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 41 GLN ** S 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 235 ASN a 272 GLN b 31 ASN ** b 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 103 GLN ** b 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 146 ASN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.081325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.058458 restraints weight = 105828.247| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.13 r_work: 0.2804 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37754 Z= 0.121 Angle : 0.557 11.616 51185 Z= 0.285 Chirality : 0.042 0.212 5997 Planarity : 0.004 0.049 6637 Dihedral : 5.203 138.204 5279 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.02 % Allowed : 10.54 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.12), residues: 4860 helix: 1.82 (0.10), residues: 2677 sheet: -0.14 (0.22), residues: 568 loop : -1.30 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 328 TYR 0.011 0.001 TYR E 250 PHE 0.021 0.001 PHE G 53 TRP 0.015 0.001 TRP g 206 HIS 0.003 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (37754) covalent geometry : angle 0.55692 / 0.29 (51185) hydrogen bonds : bond 0.04620 / 3.09 ( 2229) hydrogen bonds : angle 4.25154 / 2.96 ( 6567) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 409 time to evaluate : 1.063 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 263 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8541 (t0) REVERT: C 49 MET cc_start: 0.8328 (mtm) cc_final: 0.8047 (mtp) REVERT: C 110 ASP cc_start: 0.8556 (t70) cc_final: 0.8152 (t0) REVERT: C 337 ASP cc_start: 0.8943 (t70) cc_final: 0.8621 (t0) REVERT: D 247 ASP cc_start: 0.8955 (t0) cc_final: 0.8678 (t70) REVERT: F 159 MET cc_start: 0.8915 (mtm) cc_final: 0.8038 (mtp) REVERT: F 191 GLU cc_start: 0.8907 (tt0) cc_final: 0.8606 (tt0) REVERT: G 52 MET cc_start: 0.9574 (tmm) cc_final: 0.9315 (tmm) REVERT: G 60 ASP cc_start: 0.9100 (t0) cc_final: 0.8417 (t0) REVERT: G 64 MET cc_start: 0.9548 (mmp) cc_final: 0.9068 (mmm) REVERT: H 36 GLU cc_start: 0.9182 (tt0) cc_final: 0.8888 (tm-30) REVERT: H 40 ARG cc_start: 0.9071 (mmm-85) cc_final: 0.8767 (mmm-85) REVERT: H 52 MET cc_start: 0.9526 (tmm) cc_final: 0.9207 (tmm) REVERT: H 60 ASP cc_start: 0.9281 (m-30) cc_final: 0.8880 (m-30) REVERT: H 64 MET cc_start: 0.9369 (mmp) cc_final: 0.8879 (mmm) REVERT: J 36 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8007 (mm-30) REVERT: J 52 MET cc_start: 0.9676 (tmm) cc_final: 0.9401 (tmm) REVERT: J 65 ILE cc_start: 0.9646 (mm) cc_final: 0.9282 (mm) REVERT: K 52 MET cc_start: 0.9223 (tmm) cc_final: 0.8641 (tmm) REVERT: O 36 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8276 (tm-30) REVERT: O 52 MET cc_start: 0.9325 (tmm) cc_final: 0.8946 (tmm) REVERT: P 36 GLU cc_start: 0.9243 (tp30) cc_final: 0.8895 (tp30) REVERT: Q 49 GLN cc_start: 0.9330 (tt0) cc_final: 0.9003 (tt0) REVERT: Q 52 MET cc_start: 0.9441 (tmm) cc_final: 0.9233 (tmm) REVERT: R 49 GLN cc_start: 0.9283 (tt0) cc_final: 0.8887 (mt0) REVERT: R 52 MET cc_start: 0.9451 (tmm) cc_final: 0.9184 (tmm) REVERT: R 64 MET cc_start: 0.9285 (mmm) cc_final: 0.8922 (mmm) REVERT: S 49 GLN cc_start: 0.9118 (tt0) cc_final: 0.8708 (mt0) REVERT: S 52 MET cc_start: 0.9535 (tmm) cc_final: 0.9148 (tmm) REVERT: S 75 PHE cc_start: 0.8692 (m-80) cc_final: 0.8422 (m-10) REVERT: a 123 ASN cc_start: 0.8989 (t0) cc_final: 0.8226 (t0) REVERT: a 168 MET cc_start: 0.9438 (mmm) cc_final: 0.9133 (mmm) REVERT: a 179 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.7992 (t80) REVERT: a 184 LYS cc_start: 0.8053 (mppt) cc_final: 0.7287 (tptp) REVERT: a 221 PHE cc_start: 0.8775 (p90) cc_final: 0.8516 (p90) REVERT: a 236 MET cc_start: 0.8897 (mmp) cc_final: 0.7306 (mtt) REVERT: a 240 GLU cc_start: 0.9109 (pt0) cc_final: 0.8769 (pt0) REVERT: b 82 ARG cc_start: 0.9446 (ttp80) cc_final: 0.9187 (ptp90) REVERT: b 102 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.8263 (mmm-85) REVERT: d 69 ASP cc_start: 0.9272 (m-30) cc_final: 0.7879 (t0) REVERT: e 22 MET cc_start: 0.8473 (tmm) cc_final: 0.7565 (tmm) REVERT: e 111 ASP cc_start: 0.8378 (t0) cc_final: 0.8154 (t0) REVERT: g 156 MET cc_start: 0.8367 (mmm) cc_final: 0.8050 (mmt) REVERT: p 53 ASP cc_start: 0.8950 (m-30) cc_final: 0.8739 (m-30) REVERT: p 129 VAL cc_start: 0.8788 (t) cc_final: 0.8488 (m) REVERT: p 134 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8599 (mmmm) outliers start: 39 outliers final: 18 residues processed: 431 average time/residue: 0.2114 time to fit residues: 149.0511 Evaluate side-chains 406 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 386 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain P residue 79 PHE Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain b residue 100 ARG Chi-restraints excluded: chain b residue 117 ARG Chi-restraints excluded: chain d residue 166 LEU Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain e residue 110 SER Chi-restraints excluded: chain g residue 39 MET Chi-restraints excluded: chain g residue 189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 321 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 326 optimal weight: 0.9980 chunk 385 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 281 optimal weight: 0.7980 chunk 220 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 299 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 272 GLN b 31 ASN ** b 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 139 GLN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 GLN p 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.081036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.057931 restraints weight = 107492.598| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.11 r_work: 0.2783 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37754 Z= 0.124 Angle : 0.561 11.871 51185 Z= 0.286 Chirality : 0.042 0.325 5997 Planarity : 0.004 0.050 6637 Dihedral : 5.021 125.641 5279 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.94 % Allowed : 11.66 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4860 helix: 1.88 (0.10), residues: 2680 sheet: -0.00 (0.22), residues: 567 loop : -1.19 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 231 TYR 0.010 0.001 TYR E 250 PHE 0.020 0.001 PHE G 53 TRP 0.015 0.001 TRP g 206 HIS 0.003 0.001 HIS a 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (37754) covalent geometry : angle 0.56120 / 0.29 (51185) hydrogen bonds : bond 0.04435 / 2.97 ( 2229) hydrogen bonds : angle 4.18625 / 2.92 ( 6567) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 415 time to evaluate : 1.472 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: C 49 MET cc_start: 0.8418 (mtm) cc_final: 0.8154 (mtp) REVERT: C 110 ASP cc_start: 0.8594 (t70) cc_final: 0.8177 (t0) REVERT: C 337 ASP cc_start: 0.8966 (t70) cc_final: 0.8659 (t0) REVERT: D 247 ASP cc_start: 0.8964 (t0) cc_final: 0.8665 (t70) REVERT: E 450 MET cc_start: 0.8745 (mmm) cc_final: 0.8445 (mmt) REVERT: F 159 MET cc_start: 0.8955 (mtm) cc_final: 0.8580 (mtp) REVERT: G 40 ARG cc_start: 0.8627 (ttp-170) cc_final: 0.8402 (ttp-170) REVERT: G 52 MET cc_start: 0.9555 (tmm) cc_final: 0.9348 (tmm) REVERT: G 60 ASP cc_start: 0.9120 (t0) cc_final: 0.8419 (t0) REVERT: G 64 MET cc_start: 0.9528 (mmp) cc_final: 0.9008 (mmm) REVERT: H 36 GLU cc_start: 0.9125 (tt0) cc_final: 0.8790 (tm-30) REVERT: H 40 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8441 (mmm-85) REVERT: H 52 MET cc_start: 0.9481 (tmm) cc_final: 0.9169 (tmm) REVERT: H 60 ASP cc_start: 0.9225 (m-30) cc_final: 0.8813 (m-30) REVERT: H 64 MET cc_start: 0.9337 (mmp) cc_final: 0.8866 (mmm) REVERT: J 36 GLU cc_start: 0.8598 (mm-30) cc_final: 0.7957 (mm-30) REVERT: J 49 GLN cc_start: 0.9174 (tt0) cc_final: 0.8804 (tt0) REVERT: J 52 MET cc_start: 0.9682 (tmm) cc_final: 0.9401 (tmm) REVERT: J 64 MET cc_start: 0.8275 (ppp) cc_final: 0.8019 (ppp) REVERT: J 65 ILE cc_start: 0.9555 (mm) cc_final: 0.9225 (mm) REVERT: K 52 MET cc_start: 0.9227 (tmm) cc_final: 0.8637 (tmm) REVERT: K 73 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8673 (m-80) REVERT: O 36 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8310 (tm-30) REVERT: O 52 MET cc_start: 0.9258 (tmm) cc_final: 0.8898 (tmm) REVERT: O 64 MET cc_start: 0.9275 (mmm) cc_final: 0.9021 (mmm) REVERT: P 16 ILE cc_start: 0.9378 (mm) cc_final: 0.9176 (mm) REVERT: P 36 GLU cc_start: 0.9221 (tp30) cc_final: 0.8891 (tp30) REVERT: Q 49 GLN cc_start: 0.9355 (tt0) cc_final: 0.9013 (tt0) REVERT: R 49 GLN cc_start: 0.9281 (tt0) cc_final: 0.8872 (mt0) REVERT: R 52 MET cc_start: 0.9425 (tmm) cc_final: 0.9158 (tmm) REVERT: R 64 MET cc_start: 0.9275 (mmm) cc_final: 0.8516 (mmm) REVERT: S 18 PHE cc_start: 0.9107 (m-10) cc_final: 0.8854 (m-10) REVERT: S 49 GLN cc_start: 0.9125 (tt0) cc_final: 0.8713 (mt0) REVERT: S 52 MET cc_start: 0.9538 (tmm) cc_final: 0.9117 (tmm) REVERT: S 64 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8664 (tmm) REVERT: a 21 MET cc_start: 0.9478 (mmp) cc_final: 0.8779 (ptm) REVERT: a 123 ASN cc_start: 0.9037 (t0) cc_final: 0.8225 (t0) REVERT: a 179 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7919 (t80) REVERT: a 184 LYS cc_start: 0.8039 (mppt) cc_final: 0.7365 (tptp) REVERT: a 221 PHE cc_start: 0.8756 (p90) cc_final: 0.8524 (p90) REVERT: a 236 MET cc_start: 0.8838 (mmp) cc_final: 0.7361 (mtt) REVERT: a 240 GLU cc_start: 0.9058 (pt0) cc_final: 0.8702 (pt0) REVERT: b 17 PHE cc_start: 0.9148 (t80) cc_final: 0.8823 (t80) REVERT: b 102 ARG cc_start: 0.8592 (mmm-85) cc_final: 0.8292 (mmm-85) REVERT: b 155 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8240 (ptpp) REVERT: d 69 ASP cc_start: 0.9278 (m-30) cc_final: 0.7913 (t0) REVERT: e 22 MET cc_start: 0.8529 (tmm) cc_final: 0.7628 (tmm) REVERT: e 111 ASP cc_start: 0.8519 (t0) cc_final: 0.8282 (t0) REVERT: g 156 MET cc_start: 0.8478 (mmm) cc_final: 0.8084 (mmt) REVERT: p 14 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8789 (m-80) REVERT: p 16 PHE cc_start: 0.9101 (m-80) cc_final: 0.8429 (m-80) REVERT: p 81 ARG cc_start: 0.9077 (tmm-80) cc_final: 0.8797 (ttp80) REVERT: p 134 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8637 (mmmm) outliers start: 36 outliers final: 22 residues processed: 437 average time/residue: 0.2203 time to fit residues: 156.1097 Evaluate side-chains 414 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 388 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain P residue 79 PHE Chi-restraints excluded: chain S residue 64 MET Chi-restraints excluded: chain a residue 63 PHE Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 110 SER Chi-restraints excluded: chain g residue 39 MET Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 189 VAL Chi-restraints excluded: chain p residue 14 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 237 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 349 optimal weight: 8.9990 chunk 429 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 439 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 454 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 41 GLN ** S 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 103 GLN ** b 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 139 GLN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.079687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.056477 restraints weight = 108811.333| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.12 r_work: 0.2743 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 37754 Z= 0.197 Angle : 0.612 13.140 51185 Z= 0.311 Chirality : 0.044 0.349 5997 Planarity : 0.004 0.049 6637 Dihedral : 5.077 116.658 5279 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.10 % Allowed : 12.15 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.12), residues: 4860 helix: 1.86 (0.10), residues: 2687 sheet: -0.12 (0.21), residues: 579 loop : -1.20 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 328 TYR 0.013 0.001 TYR D 252 PHE 0.028 0.001 PHE Q 27 TRP 0.017 0.001 TRP g 206 HIS 0.006 0.001 HIS a 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (37754) covalent geometry : angle 0.61165 / 0.31 (51185) hydrogen bonds : bond 0.04650 / 3.10 ( 2229) hydrogen bonds : angle 4.30608 / 3.00 ( 6567) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 394 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 MET cc_start: 0.8590 (mtp) cc_final: 0.8329 (mtt) REVERT: B 263 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8604 (t0) REVERT: D 247 ASP cc_start: 0.9041 (t0) cc_final: 0.8741 (t70) REVERT: F 192 MET cc_start: 0.8984 (ttp) cc_final: 0.8767 (ttp) REVERT: G 60 ASP cc_start: 0.9128 (t0) cc_final: 0.8430 (t0) REVERT: G 64 MET cc_start: 0.9548 (mmp) cc_final: 0.9040 (mmm) REVERT: H 36 GLU cc_start: 0.9154 (tt0) cc_final: 0.8790 (tm-30) REVERT: H 40 ARG cc_start: 0.9129 (mmm-85) cc_final: 0.8461 (mmm-85) REVERT: H 49 GLN cc_start: 0.9331 (mt0) cc_final: 0.9055 (mt0) REVERT: H 52 MET cc_start: 0.9490 (tmm) cc_final: 0.9183 (tmm) REVERT: H 60 ASP cc_start: 0.9248 (m-30) cc_final: 0.8851 (m-30) REVERT: H 64 MET cc_start: 0.9359 (mmp) cc_final: 0.8878 (mmm) REVERT: J 36 GLU cc_start: 0.8643 (mm-30) cc_final: 0.7986 (mm-30) REVERT: J 52 MET cc_start: 0.9700 (tmm) cc_final: 0.9413 (tmm) REVERT: J 64 MET cc_start: 0.8197 (ppp) cc_final: 0.7922 (ppp) REVERT: J 65 ILE cc_start: 0.9554 (mm) cc_final: 0.9200 (mm) REVERT: K 52 MET cc_start: 0.9251 (tmm) cc_final: 0.8644 (tmm) REVERT: K 73 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8779 (m-80) REVERT: O 36 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8352 (tm-30) REVERT: O 52 MET cc_start: 0.9262 (tmm) cc_final: 0.8890 (tmm) REVERT: O 64 MET cc_start: 0.9314 (mmm) cc_final: 0.9063 (mmm) REVERT: P 36 GLU cc_start: 0.9269 (tp30) cc_final: 0.8954 (tp30) REVERT: R 49 GLN cc_start: 0.9309 (tt0) cc_final: 0.8904 (mt0) REVERT: R 52 MET cc_start: 0.9445 (tmm) cc_final: 0.9184 (tmm) REVERT: R 64 MET cc_start: 0.9282 (mmm) cc_final: 0.8949 (mmm) REVERT: S 18 PHE cc_start: 0.9118 (m-10) cc_final: 0.8891 (m-10) REVERT: S 49 GLN cc_start: 0.9133 (tt0) cc_final: 0.8749 (mt0) REVERT: S 52 MET cc_start: 0.9564 (tmm) cc_final: 0.9118 (tmm) REVERT: a 123 ASN cc_start: 0.9022 (t0) cc_final: 0.8202 (t0) REVERT: a 179 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.7963 (t80) REVERT: a 221 PHE cc_start: 0.8777 (p90) cc_final: 0.8546 (p90) REVERT: a 236 MET cc_start: 0.8871 (mmp) cc_final: 0.7155 (mtm) REVERT: a 240 GLU cc_start: 0.9058 (pt0) cc_final: 0.8733 (pt0) REVERT: a 277 MET cc_start: 0.9374 (tmm) cc_final: 0.9075 (tmm) REVERT: b 17 PHE cc_start: 0.9236 (t80) cc_final: 0.9006 (t80) REVERT: b 99 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8795 (pt0) REVERT: b 102 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8290 (mmm-85) REVERT: b 155 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8089 (ptpp) REVERT: d 69 ASP cc_start: 0.9282 (m-30) cc_final: 0.7956 (t0) REVERT: e 22 MET cc_start: 0.8570 (tmm) cc_final: 0.7668 (tmm) REVERT: e 111 ASP cc_start: 0.8540 (t0) cc_final: 0.8316 (t0) REVERT: g 156 MET cc_start: 0.8511 (mmm) cc_final: 0.7958 (mmt) REVERT: g 206 TRP cc_start: 0.7696 (p-90) cc_final: 0.7384 (p-90) REVERT: p 14 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.8819 (m-80) REVERT: p 16 PHE cc_start: 0.9082 (m-80) cc_final: 0.8410 (m-80) REVERT: p 81 ARG cc_start: 0.9091 (tmm-80) cc_final: 0.8808 (ttp80) REVERT: p 134 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8641 (mmmm) outliers start: 42 outliers final: 28 residues processed: 421 average time/residue: 0.2360 time to fit residues: 162.1393 Evaluate side-chains 416 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 384 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain P residue 79 PHE Chi-restraints excluded: chain a residue 63 PHE Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 110 SER Chi-restraints excluded: chain g residue 39 MET Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 189 VAL Chi-restraints excluded: chain p residue 14 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 45 optimal weight: 8.9990 chunk 173 optimal weight: 0.9980 chunk 419 optimal weight: 10.0000 chunk 283 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 chunk 278 optimal weight: 0.0670 chunk 410 optimal weight: 2.9990 chunk 91 optimal weight: 0.0010 chunk 201 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 182 optimal weight: 3.9990 overall best weight: 0.5326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 47 GLN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 139 GLN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.081838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.058601 restraints weight = 107284.350| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.13 r_work: 0.2791 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37754 Z= 0.118 Angle : 0.588 13.670 51185 Z= 0.296 Chirality : 0.042 0.342 5997 Planarity : 0.004 0.049 6637 Dihedral : 4.894 105.654 5279 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.86 % Allowed : 12.73 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.12), residues: 4860 helix: 1.90 (0.10), residues: 2688 sheet: 0.12 (0.22), residues: 568 loop : -1.10 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG b 100 TYR 0.013 0.001 TYR a 283 PHE 0.019 0.001 PHE G 53 TRP 0.015 0.001 TRP g 206 HIS 0.006 0.001 HIS a 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (37754) covalent geometry : angle 0.58753 / 0.30 (51185) hydrogen bonds : bond 0.04236 / 2.83 ( 2229) hydrogen bonds : angle 4.13937 / 2.89 ( 6567) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 413 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 MET cc_start: 0.8508 (mtp) cc_final: 0.8250 (mtt) REVERT: B 263 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8533 (t0) REVERT: C 49 MET cc_start: 0.8410 (mtm) cc_final: 0.8124 (mtp) REVERT: C 110 ASP cc_start: 0.8585 (t70) cc_final: 0.8170 (t0) REVERT: D 247 ASP cc_start: 0.8971 (t0) cc_final: 0.8670 (t0) REVERT: E 450 MET cc_start: 0.8713 (mmm) cc_final: 0.8438 (mmt) REVERT: F 192 MET cc_start: 0.8933 (ttp) cc_final: 0.8682 (ttp) REVERT: G 60 ASP cc_start: 0.9134 (t0) cc_final: 0.8760 (t0) REVERT: G 64 MET cc_start: 0.9528 (mmp) cc_final: 0.9243 (mmm) REVERT: H 36 GLU cc_start: 0.9103 (tt0) cc_final: 0.8831 (tm-30) REVERT: H 40 ARG cc_start: 0.9032 (mmm-85) cc_final: 0.8470 (mmm-85) REVERT: H 49 GLN cc_start: 0.9298 (mt0) cc_final: 0.8995 (mt0) REVERT: H 52 MET cc_start: 0.9485 (tmm) cc_final: 0.9171 (tmm) REVERT: J 36 GLU cc_start: 0.8604 (mm-30) cc_final: 0.7918 (mm-30) REVERT: J 49 GLN cc_start: 0.9177 (tt0) cc_final: 0.8798 (tt0) REVERT: J 52 MET cc_start: 0.9678 (tmm) cc_final: 0.9403 (tmm) REVERT: J 64 MET cc_start: 0.8121 (ppp) cc_final: 0.7838 (ppp) REVERT: J 65 ILE cc_start: 0.9538 (mm) cc_final: 0.9152 (mm) REVERT: K 52 MET cc_start: 0.9224 (tmm) cc_final: 0.8657 (tmm) REVERT: K 73 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8683 (m-80) REVERT: O 36 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8301 (tm-30) REVERT: O 52 MET cc_start: 0.9230 (tmm) cc_final: 0.8863 (tmm) REVERT: O 64 MET cc_start: 0.9230 (mmm) cc_final: 0.8983 (mmm) REVERT: P 16 ILE cc_start: 0.9369 (mm) cc_final: 0.9164 (mm) REVERT: P 36 GLU cc_start: 0.9245 (tp30) cc_final: 0.8910 (tp30) REVERT: R 49 GLN cc_start: 0.9258 (tt0) cc_final: 0.8855 (mt0) REVERT: R 52 MET cc_start: 0.9431 (tmm) cc_final: 0.9155 (tmm) REVERT: R 64 MET cc_start: 0.9274 (mmm) cc_final: 0.8486 (mmm) REVERT: S 18 PHE cc_start: 0.9136 (m-10) cc_final: 0.8905 (m-10) REVERT: S 49 GLN cc_start: 0.9095 (tt0) cc_final: 0.8462 (mt0) REVERT: S 52 MET cc_start: 0.9539 (tmm) cc_final: 0.9031 (tmm) REVERT: S 53 PHE cc_start: 0.9257 (m-10) cc_final: 0.8850 (m-10) REVERT: S 75 PHE cc_start: 0.8777 (m-10) cc_final: 0.8576 (m-10) REVERT: a 21 MET cc_start: 0.9497 (mmp) cc_final: 0.8772 (ptm) REVERT: a 104 LYS cc_start: 0.6109 (tttt) cc_final: 0.5366 (tttt) REVERT: a 123 ASN cc_start: 0.8980 (t0) cc_final: 0.8315 (t0) REVERT: a 179 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.7970 (t80) REVERT: a 184 LYS cc_start: 0.7925 (mppt) cc_final: 0.7148 (tptp) REVERT: a 221 PHE cc_start: 0.8714 (p90) cc_final: 0.8463 (p90) REVERT: a 236 MET cc_start: 0.8830 (mmp) cc_final: 0.7435 (mtt) REVERT: a 240 GLU cc_start: 0.9076 (pt0) cc_final: 0.8779 (pt0) REVERT: a 277 MET cc_start: 0.9356 (tmm) cc_final: 0.9042 (tmm) REVERT: b 17 PHE cc_start: 0.9218 (t80) cc_final: 0.8899 (t80) REVERT: b 100 ARG cc_start: 0.9110 (tpm170) cc_final: 0.8721 (tpm170) REVERT: b 102 ARG cc_start: 0.8579 (mmm-85) cc_final: 0.8280 (mmm-85) REVERT: b 155 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8266 (ptpt) REVERT: d 69 ASP cc_start: 0.9309 (m-30) cc_final: 0.7997 (t0) REVERT: e 22 MET cc_start: 0.8560 (tmm) cc_final: 0.7678 (tmm) REVERT: e 111 ASP cc_start: 0.8514 (t0) cc_final: 0.8266 (t0) REVERT: g 156 MET cc_start: 0.8411 (mmm) cc_final: 0.8004 (mmt) REVERT: p 14 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8788 (m-80) REVERT: p 16 PHE cc_start: 0.9084 (m-80) cc_final: 0.8416 (m-80) REVERT: p 81 ARG cc_start: 0.9113 (tmm-80) cc_final: 0.8805 (ttp80) REVERT: p 117 ARG cc_start: 0.6926 (mtt180) cc_final: 0.5482 (ttm110) outliers start: 33 outliers final: 17 residues processed: 432 average time/residue: 0.2301 time to fit residues: 162.4425 Evaluate side-chains 412 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 391 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain E residue 405 PHE Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain P residue 79 PHE Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain a residue 63 PHE Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 166 LEU Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain g residue 39 MET Chi-restraints excluded: chain g residue 189 VAL Chi-restraints excluded: chain p residue 14 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 97 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 chunk 344 optimal weight: 5.9990 chunk 312 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 443 optimal weight: 10.0000 chunk 371 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 196 ASN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 31 ASN b 139 GLN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.080280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.057027 restraints weight = 109284.269| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.15 r_work: 0.2754 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37754 Z= 0.171 Angle : 0.619 14.702 51185 Z= 0.311 Chirality : 0.043 0.368 5997 Planarity : 0.004 0.048 6637 Dihedral : 4.932 104.089 5279 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.81 % Allowed : 12.99 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.12), residues: 4860 helix: 1.89 (0.10), residues: 2702 sheet: 0.03 (0.21), residues: 586 loop : -1.09 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 81 TYR 0.019 0.001 TYR a 283 PHE 0.020 0.001 PHE p 17 TRP 0.009 0.001 TRP a 55 HIS 0.005 0.001 HIS a 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (37754) covalent geometry : angle 0.61918 / 0.31 (51185) hydrogen bonds : bond 0.04480 / 3.00 ( 2229) hydrogen bonds : angle 4.23860 / 2.96 ( 6567) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 389 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 MET cc_start: 0.8497 (mtp) cc_final: 0.8248 (mtt) REVERT: C 49 MET cc_start: 0.8451 (mtm) cc_final: 0.8103 (mtp) REVERT: D 247 ASP cc_start: 0.9032 (t0) cc_final: 0.8709 (t70) REVERT: E 450 MET cc_start: 0.8713 (mmm) cc_final: 0.8435 (mmt) REVERT: G 60 ASP cc_start: 0.9144 (t0) cc_final: 0.8765 (t0) REVERT: G 64 MET cc_start: 0.9556 (mmp) cc_final: 0.9257 (mmm) REVERT: H 36 GLU cc_start: 0.9131 (tt0) cc_final: 0.8839 (tm-30) REVERT: H 40 ARG cc_start: 0.9064 (mmm-85) cc_final: 0.8493 (mmm-85) REVERT: H 49 GLN cc_start: 0.9314 (mt0) cc_final: 0.9042 (mt0) REVERT: H 52 MET cc_start: 0.9492 (tmm) cc_final: 0.9174 (tmm) REVERT: J 36 GLU cc_start: 0.8635 (mm-30) cc_final: 0.7977 (mm-30) REVERT: J 49 GLN cc_start: 0.9197 (tt0) cc_final: 0.8851 (tt0) REVERT: J 52 MET cc_start: 0.9707 (tmm) cc_final: 0.9420 (tmm) REVERT: J 64 MET cc_start: 0.8191 (ppp) cc_final: 0.7931 (ppp) REVERT: J 65 ILE cc_start: 0.9545 (mm) cc_final: 0.9215 (mm) REVERT: K 52 MET cc_start: 0.9241 (tmm) cc_final: 0.8631 (tmm) REVERT: K 73 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8727 (m-80) REVERT: O 36 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8363 (tm-30) REVERT: O 52 MET cc_start: 0.9238 (tmm) cc_final: 0.8879 (tmm) REVERT: O 64 MET cc_start: 0.9257 (mmm) cc_final: 0.9007 (mmm) REVERT: P 36 GLU cc_start: 0.9285 (tp30) cc_final: 0.8961 (tp30) REVERT: R 49 GLN cc_start: 0.9296 (tt0) cc_final: 0.8889 (mt0) REVERT: R 52 MET cc_start: 0.9449 (tmm) cc_final: 0.9180 (tmm) REVERT: R 64 MET cc_start: 0.9245 (mmm) cc_final: 0.8445 (mmm) REVERT: S 18 PHE cc_start: 0.9177 (m-10) cc_final: 0.8908 (m-10) REVERT: S 49 GLN cc_start: 0.9103 (tt0) cc_final: 0.8545 (mt0) REVERT: S 52 MET cc_start: 0.9543 (tmm) cc_final: 0.8985 (tmm) REVERT: S 53 PHE cc_start: 0.9274 (m-10) cc_final: 0.8900 (m-10) REVERT: S 64 MET cc_start: 0.8974 (ttp) cc_final: 0.8347 (tmm) REVERT: a 21 MET cc_start: 0.9483 (mmp) cc_final: 0.8761 (ptm) REVERT: a 104 LYS cc_start: 0.5982 (tttt) cc_final: 0.5165 (tttt) REVERT: a 123 ASN cc_start: 0.8996 (t0) cc_final: 0.8396 (t0) REVERT: a 179 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8022 (t80) REVERT: a 184 LYS cc_start: 0.8021 (mppt) cc_final: 0.7160 (tptp) REVERT: a 221 PHE cc_start: 0.8748 (p90) cc_final: 0.8492 (p90) REVERT: a 236 MET cc_start: 0.8790 (mmp) cc_final: 0.7317 (mtt) REVERT: a 240 GLU cc_start: 0.9075 (pt0) cc_final: 0.8807 (pt0) REVERT: a 277 MET cc_start: 0.9344 (tmm) cc_final: 0.9012 (tmm) REVERT: b 102 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8304 (mmm-85) REVERT: b 155 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8159 (ptpt) REVERT: d 69 ASP cc_start: 0.9302 (m-30) cc_final: 0.8005 (t0) REVERT: e 22 MET cc_start: 0.8582 (tmm) cc_final: 0.7682 (tmm) REVERT: e 99 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8359 (mmmt) REVERT: e 111 ASP cc_start: 0.8553 (t0) cc_final: 0.8311 (t0) REVERT: g 156 MET cc_start: 0.8493 (mmm) cc_final: 0.7967 (mmt) REVERT: p 16 PHE cc_start: 0.9089 (m-80) cc_final: 0.8407 (m-80) REVERT: p 81 ARG cc_start: 0.9121 (tmm-80) cc_final: 0.8820 (ttp80) REVERT: p 117 ARG cc_start: 0.6978 (mtt180) cc_final: 0.5674 (ttm110) outliers start: 31 outliers final: 27 residues processed: 409 average time/residue: 0.2271 time to fit residues: 151.0594 Evaluate side-chains 412 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 383 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain P residue 79 PHE Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain a residue 23 TYR Chi-restraints excluded: chain a residue 63 PHE Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain b residue 20 PHE Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 166 LEU Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain g residue 39 MET Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 189 VAL Chi-restraints excluded: chain p residue 14 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 324 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 410 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 334 optimal weight: 0.0060 chunk 225 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 434 optimal weight: 4.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 139 GLN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.081330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.058072 restraints weight = 107721.173| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.15 r_work: 0.2776 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37754 Z= 0.126 Angle : 0.609 13.386 51185 Z= 0.305 Chirality : 0.043 0.368 5997 Planarity : 0.004 0.049 6637 Dihedral : 4.862 99.681 5279 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.78 % Allowed : 12.88 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.12), residues: 4860 helix: 1.95 (0.10), residues: 2682 sheet: 0.09 (0.22), residues: 584 loop : -1.05 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG b 81 TYR 0.019 0.001 TYR a 283 PHE 0.028 0.001 PHE p 17 TRP 0.031 0.001 TRP a 118 HIS 0.004 0.001 HIS a 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (37754) covalent geometry : angle 0.60860 / 0.31 (51185) hydrogen bonds : bond 0.04255 / 2.85 ( 2229) hydrogen bonds : angle 4.14946 / 2.90 ( 6567) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 396 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 MET cc_start: 0.8409 (mtp) cc_final: 0.8183 (mtt) REVERT: B 263 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8545 (t0) REVERT: C 49 MET cc_start: 0.8388 (mtm) cc_final: 0.8078 (mtp) REVERT: C 110 ASP cc_start: 0.8554 (t70) cc_final: 0.8167 (t0) REVERT: D 247 ASP cc_start: 0.9000 (t0) cc_final: 0.8674 (t70) REVERT: E 450 MET cc_start: 0.8725 (mmm) cc_final: 0.8451 (mmt) REVERT: F 36 GLU cc_start: 0.9071 (pp20) cc_final: 0.8426 (pp20) REVERT: G 60 ASP cc_start: 0.9130 (t0) cc_final: 0.8402 (t0) REVERT: G 64 MET cc_start: 0.9537 (mmp) cc_final: 0.9024 (mmm) REVERT: H 36 GLU cc_start: 0.9106 (tt0) cc_final: 0.8765 (tm-30) REVERT: H 40 ARG cc_start: 0.9041 (mmm-85) cc_final: 0.8285 (mmm-85) REVERT: H 49 GLN cc_start: 0.9308 (mt0) cc_final: 0.9018 (mt0) REVERT: H 52 MET cc_start: 0.9476 (tmm) cc_final: 0.9160 (tmm) REVERT: J 36 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7920 (mm-30) REVERT: J 49 GLN cc_start: 0.9178 (tt0) cc_final: 0.8787 (tt0) REVERT: J 52 MET cc_start: 0.9698 (tmm) cc_final: 0.9410 (tmm) REVERT: J 64 MET cc_start: 0.8190 (ppp) cc_final: 0.7894 (ppp) REVERT: J 65 ILE cc_start: 0.9533 (mm) cc_final: 0.9145 (mm) REVERT: K 52 MET cc_start: 0.9224 (tmm) cc_final: 0.8637 (tmm) REVERT: K 73 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8693 (m-80) REVERT: O 36 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8338 (tm-30) REVERT: O 52 MET cc_start: 0.9249 (tmm) cc_final: 0.8869 (tmm) REVERT: O 64 MET cc_start: 0.9238 (mmm) cc_final: 0.8995 (mmm) REVERT: P 16 ILE cc_start: 0.9397 (mm) cc_final: 0.9189 (mm) REVERT: P 36 GLU cc_start: 0.9275 (tp30) cc_final: 0.8958 (tp30) REVERT: R 49 GLN cc_start: 0.9268 (tt0) cc_final: 0.8859 (mt0) REVERT: R 52 MET cc_start: 0.9434 (tmm) cc_final: 0.9160 (tmm) REVERT: R 64 MET cc_start: 0.9259 (mmm) cc_final: 0.8487 (mmm) REVERT: S 18 PHE cc_start: 0.9172 (m-10) cc_final: 0.8927 (m-10) REVERT: S 49 GLN cc_start: 0.9074 (tt0) cc_final: 0.8470 (mt0) REVERT: S 52 MET cc_start: 0.9538 (tmm) cc_final: 0.9030 (tmm) REVERT: S 53 PHE cc_start: 0.9246 (m-10) cc_final: 0.8890 (m-10) REVERT: a 21 MET cc_start: 0.9496 (mmp) cc_final: 0.8810 (ptm) REVERT: a 104 LYS cc_start: 0.5982 (tttt) cc_final: 0.5188 (tttt) REVERT: a 123 ASN cc_start: 0.8989 (t0) cc_final: 0.8381 (t0) REVERT: a 179 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.8003 (t80) REVERT: a 184 LYS cc_start: 0.7972 (mppt) cc_final: 0.7164 (tptp) REVERT: a 221 PHE cc_start: 0.8729 (p90) cc_final: 0.8470 (p90) REVERT: a 236 MET cc_start: 0.8809 (mmp) cc_final: 0.7361 (mtt) REVERT: a 240 GLU cc_start: 0.9065 (pt0) cc_final: 0.8775 (pt0) REVERT: a 277 MET cc_start: 0.9339 (tmm) cc_final: 0.8993 (tmm) REVERT: b 17 PHE cc_start: 0.9188 (t80) cc_final: 0.8907 (t80) REVERT: b 102 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8300 (mmm-85) REVERT: b 155 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8188 (ptpt) REVERT: d 69 ASP cc_start: 0.9321 (m-30) cc_final: 0.7997 (t0) REVERT: e 4 MET cc_start: 0.9080 (ptt) cc_final: 0.8800 (ptm) REVERT: e 22 MET cc_start: 0.8561 (tmm) cc_final: 0.7646 (tmm) REVERT: e 99 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8325 (mmmt) REVERT: e 111 ASP cc_start: 0.8577 (t0) cc_final: 0.8298 (t0) REVERT: g 156 MET cc_start: 0.8418 (mmm) cc_final: 0.7948 (mmt) REVERT: p 16 PHE cc_start: 0.9092 (m-80) cc_final: 0.8416 (m-80) REVERT: p 81 ARG cc_start: 0.9114 (tmm-80) cc_final: 0.8787 (ttp80) REVERT: p 117 ARG cc_start: 0.6928 (mtt180) cc_final: 0.5498 (ttm110) outliers start: 30 outliers final: 23 residues processed: 412 average time/residue: 0.2174 time to fit residues: 146.6126 Evaluate side-chains 416 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 390 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain P residue 79 PHE Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain a residue 63 PHE Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 166 LEU Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain g residue 39 MET Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 189 VAL Chi-restraints excluded: chain p residue 14 PHE Chi-restraints excluded: chain p residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 306 optimal weight: 3.9990 chunk 428 optimal weight: 0.9980 chunk 366 optimal weight: 6.9990 chunk 313 optimal weight: 3.9990 chunk 310 optimal weight: 0.0000 chunk 61 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 416 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 318 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 196 ASN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 139 GLN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.079932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.057064 restraints weight = 108357.546| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.18 r_work: 0.2741 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37754 Z= 0.186 Angle : 0.636 13.657 51185 Z= 0.321 Chirality : 0.044 0.364 5997 Planarity : 0.004 0.049 6637 Dihedral : 4.948 98.932 5279 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.97 % Allowed : 13.02 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.12), residues: 4860 helix: 1.88 (0.10), residues: 2696 sheet: -0.02 (0.21), residues: 590 loop : -1.07 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 81 TYR 0.018 0.001 TYR a 283 PHE 0.033 0.001 PHE b 17 TRP 0.024 0.001 TRP a 118 HIS 0.005 0.001 HIS a 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (37754) covalent geometry : angle 0.63587 / 0.32 (51185) hydrogen bonds : bond 0.04561 / 3.04 ( 2229) hydrogen bonds : angle 4.27576 / 2.99 ( 6567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8979.72 seconds wall clock time: 154 minutes 21.42 seconds (9261.42 seconds total)