Starting phenix.real_space_refine on Sat Aug 8 13:01:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vpd_65239/08_2026/9vpd_65239.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vpd_65239/08_2026/9vpd_65239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vpd_65239/08_2026/9vpd_65239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vpd_65239/08_2026/9vpd_65239.map" model { file = "/net/cci-nas-00/data/ceres_data/9vpd_65239/08_2026/9vpd_65239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vpd_65239/08_2026/9vpd_65239.cif" } resolution = 2.3 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= 0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 81 5.16 5 C 17243 2.51 5 N 4967 2.21 5 O 5497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27808 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3868 Classifications: {'peptide': 508} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 489} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3641 Classifications: {'peptide': 477} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3794 Classifications: {'peptide': 498} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 479} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3558 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "E" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3539 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "F" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3539 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "G" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2115 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 979 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 369 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "J" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 370 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "S" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 752 Classifications: {'peptide': 188} Incomplete info: {'backbone_only': 179} Link IDs: {'PTRANS': 8, 'TRANS': 179} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 713 Unresolved non-hydrogen angles: 1024 Unresolved non-hydrogen dihedrals: 435 Unresolved non-hydrogen chiralities: 240 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 9, 'GLN:plan1': 6, 'TYR:plan': 5, 'GLU:plan': 13, 'ASN:plan1': 6, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 235 Chain: "b" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 404 Classifications: {'peptide': 101} Incomplete info: {'backbone_only': 101} Link IDs: {'TRANS': 100} Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 652 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 126 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 9, 'GLN:plan1': 11, 'ARG:plan': 9, 'HIS:plan': 4, 'TYR:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 234 Chain: "d" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 436 Classifications: {'peptide': 109} Incomplete info: {'backbone_only': 107} Link IDs: {'PTRANS': 6, 'TRANS': 102} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 451 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 136 Planarities with less than four sites: {'ASP:plan': 7, 'TRP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 5, 'GLN:plan1': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 197 Chain: "h" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 248 Classifications: {'peptide': 62} Incomplete info: {'backbone_only': 58} Link IDs: {'PTRANS': 5, 'TRANS': 56} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 5, 'PHE:plan': 5, 'ARG:plan': 4, 'GLU:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 151 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 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: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.23, per 1000 atoms: 0.19 Number of scatterers: 27808 At special positions: 0 Unit cell: (123.924, 143.639, 168.049, 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 81 16.00 P 15 15.00 Mg 5 11.99 O 5497 8.00 N 4967 7.00 C 17243 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: 1.75 Conformation dependent library (CDL) restraints added in 1.0 seconds 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6162 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 23 sheets defined 50.9% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 removed outlier: 3.510A pdb=" N LEU A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.544A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.879A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.911A pdb=" N GLY A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.996A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.623A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.737A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.638A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 removed outlier: 4.087A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.134A pdb=" N GLN A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 457 through 475 removed outlier: 4.163A pdb=" N THR A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 removed outlier: 4.086A pdb=" N LEU A 480 " --> pdb=" O HIS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 506 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.562A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.598A pdb=" N ILE B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 239 through 260 Proline residue: B 247 - end of helix removed outlier: 4.179A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.941A pdb=" N GLN B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 removed outlier: 3.806A pdb=" N ALA B 293 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 294 " --> pdb=" O ARG B 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 290 through 294' Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.832A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 346 removed outlier: 3.504A pdb=" N THR B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 380 through 399 removed outlier: 3.904A pdb=" N VAL B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 460 through 475 removed outlier: 3.827A pdb=" N SER B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.884A pdb=" N LEU B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 507 Processing helix chain 'C' and resid 7 through 18 removed outlier: 3.573A pdb=" N ARG C 15 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.699A pdb=" N ILE C 178 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 239 through 259 removed outlier: 3.628A pdb=" N LEU C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Proline residue: C 247 - end of helix removed outlier: 3.815A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.874A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.669A pdb=" N ALA C 293 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 296 No H-bonds generated for 'chain 'C' and resid 295 through 296' Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.772A pdb=" N HIS C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.707A pdb=" N GLY C 317 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 346 removed outlier: 3.559A pdb=" N THR C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 380 through 400 removed outlier: 3.527A pdb=" N GLY C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 400 " --> pdb=" O GLN C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 429 removed outlier: 3.678A pdb=" N LYS C 429 " --> pdb=" O THR C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 452 through 456 removed outlier: 3.641A pdb=" N LYS C 455 " --> pdb=" O TYR C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 476 removed outlier: 4.072A pdb=" N SER C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 507 removed outlier: 3.559A pdb=" N ALA C 506 " --> pdb=" O THR C 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 130 removed outlier: 3.648A pdb=" N MET D 130 " --> pdb=" O PHE D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 165 through 177 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 229 through 249 removed outlier: 3.671A pdb=" N ARG D 235 " --> pdb=" O GLY D 231 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 274 removed outlier: 4.089A pdb=" N THR D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL D 272 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 288 through 298 removed outlier: 3.705A pdb=" N MET D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 320 removed outlier: 3.583A pdb=" N ASP D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 317 through 320' Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 368 through 393 removed outlier: 3.867A pdb=" N ASP D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE D 391 " --> pdb=" O SER D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.505A pdb=" N LEU D 400 " --> pdb=" O MET D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 418 Processing helix chain 'D' and resid 425 through 430 Processing helix chain 'D' and resid 437 through 451 Processing helix chain 'D' and resid 457 through 462 Processing helix chain 'D' and resid 466 through 480 removed outlier: 3.607A pdb=" N ALA D 470 " --> pdb=" O PRO D 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.642A pdb=" N THR E 94 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 95 " --> pdb=" O PRO E 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 91 through 95' Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 193 through 208 Processing helix chain 'E' and resid 229 through 234 removed outlier: 3.564A pdb=" N ARG E 233 " --> pdb=" O PRO E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 250 removed outlier: 3.767A pdb=" N PHE E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 277 removed outlier: 3.543A pdb=" N PHE E 265 " --> pdb=" O ASN E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 298 removed outlier: 3.966A pdb=" N MET E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 320 Processing helix chain 'E' and resid 323 through 330 Processing helix chain 'E' and resid 340 through 345 Processing helix chain 'E' and resid 363 through 368 Processing helix chain 'E' and resid 368 through 396 removed outlier: 3.918A pdb=" N ASP E 390 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE E 391 " --> pdb=" O SER E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 400 Processing helix chain 'E' and resid 401 through 419 removed outlier: 3.672A pdb=" N LYS E 405 " --> pdb=" O SER E 401 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR E 407 " --> pdb=" O GLU E 403 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER E 419 " --> pdb=" O GLN E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 424 No H-bonds generated for 'chain 'E' and resid 422 through 424' Processing helix chain 'E' and resid 425 through 430 removed outlier: 3.726A pdb=" N GLY E 430 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 451 removed outlier: 3.576A pdb=" N THR E 441 " --> pdb=" O PRO E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'E' and resid 466 through 479 removed outlier: 3.619A pdb=" N ALA E 470 " --> pdb=" O PRO E 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 95 removed outlier: 3.827A pdb=" N LEU F 95 " --> pdb=" O PRO F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 147 Processing helix chain 'F' and resid 165 through 180 Processing helix chain 'F' and resid 193 through 207 Processing helix chain 'F' and resid 229 through 235 removed outlier: 3.808A pdb=" N ARG F 235 " --> pdb=" O GLY F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 249 removed outlier: 3.626A pdb=" N PHE F 247 " --> pdb=" O VAL F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 276 removed outlier: 3.746A pdb=" N THR F 266 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA F 274 " --> pdb=" O SER F 270 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 298 Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 323 through 330 Processing helix chain 'F' and resid 331 through 333 No H-bonds generated for 'chain 'F' and resid 331 through 333' Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 369 through 395 removed outlier: 4.419A pdb=" N ASP F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE F 391 " --> pdb=" O SER F 387 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE F 394 " --> pdb=" O ASP F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 418 Processing helix chain 'F' and resid 425 through 430 Processing helix chain 'F' and resid 437 through 451 Processing helix chain 'F' and resid 457 through 461 Processing helix chain 'F' and resid 466 through 479 removed outlier: 3.617A pdb=" N ALA F 470 " --> pdb=" O PRO F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 55 Proline residue: G 40 - end of helix removed outlier: 4.516A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 100 Processing helix chain 'G' and resid 109 through 116 removed outlier: 3.669A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.653A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 186 removed outlier: 3.785A pdb=" N SER G 186 " --> pdb=" O ASP G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 192 Processing helix chain 'G' and resid 199 through 271 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 105 through 121 removed outlier: 3.853A pdb=" N LEU H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 2 through 7 Processing helix chain 'I' and resid 10 through 24 Processing helix chain 'I' and resid 27 through 36 removed outlier: 4.276A pdb=" N ALA I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 19 removed outlier: 3.805A pdb=" N GLY J 19 " --> pdb=" O VAL J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 54 removed outlier: 3.842A pdb=" N LYS J 24 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 28 Processing helix chain 'S' and resid 31 through 46 removed outlier: 3.542A pdb=" N GLN S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 56 Processing helix chain 'S' and resid 61 through 77 Processing helix chain 'S' and resid 79 through 92 Processing helix chain 'S' and resid 93 through 96 removed outlier: 4.551A pdb=" N THR S 96 " --> pdb=" O GLY S 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 93 through 96' Processing helix chain 'S' and resid 97 through 113 removed outlier: 3.516A pdb=" N VAL S 101 " --> pdb=" O ASN S 97 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL S 111 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS S 112 " --> pdb=" O MET S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 142 Processing helix chain 'S' and resid 174 through 188 Processing helix chain 'b' and resid 110 through 119 Processing helix chain 'b' and resid 122 through 185 removed outlier: 3.693A pdb=" N GLN b 183 " --> pdb=" O LYS b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 209 removed outlier: 3.962A pdb=" N GLN b 209 " --> pdb=" O SER b 205 " (cutoff:3.500A) Processing helix chain 'd' and resid 14 through 18 removed outlier: 3.629A pdb=" N ILE d 18 " --> pdb=" O PHE d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 44 removed outlier: 4.084A pdb=" N SER d 29 " --> pdb=" O ALA d 25 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 58 Processing helix chain 'd' and resid 62 through 76 removed outlier: 3.527A pdb=" N VAL d 66 " --> pdb=" O LYS d 62 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 87 Processing helix chain 'd' and resid 88 through 99 removed outlier: 3.944A pdb=" N GLU d 92 " --> pdb=" O GLN d 88 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU d 93 " --> pdb=" O VAL d 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL d 97 " --> pdb=" O GLU d 93 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS d 98 " --> pdb=" O LYS d 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 102 through 112 Processing helix chain 'h' and resid 8 through 25 Processing helix chain 'h' and resid 31 through 51 removed outlier: 3.722A pdb=" N TYR h 35 " --> pdb=" O ALA h 31 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN h 36 " --> pdb=" O GLY h 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.461A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 43 current: chain 'A' and resid 60 through 66 removed outlier: 5.603A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 75 current: chain 'C' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 43 current: chain 'C' and resid 60 through 66 removed outlier: 6.471A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 75 current: chain 'D' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 24 through 29 current: chain 'D' and resid 50 through 58 removed outlier: 6.633A pdb=" N ARG D 63 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS D 56 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR D 61 " --> pdb=" O HIS D 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 61 through 66 current: chain 'E' and resid 24 through 28 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 24 through 28 current: chain 'E' and resid 50 through 58 removed outlier: 6.562A pdb=" N ARG E 63 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N HIS E 56 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR E 61 " --> pdb=" O HIS E 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.899A pdb=" N ALA A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 109 Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 328 removed outlier: 7.331A pdb=" N ILE A 168 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE A 350 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 28 through 33 removed outlier: 6.441A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU B 51 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.007A pdb=" N ALA B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.583A pdb=" N ALA B 264 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 167 through 169 removed outlier: 6.402A pdb=" N ILE B 167 " --> pdb=" O ILE B 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 26 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 26 through 27 current: chain 'S' and resid 147 through 149 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 147 through 149 current: chain 'S' and resid 169 through 173 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.263A pdb=" N ALA C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.714A pdb=" N ILE C 230 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA C 264 " --> pdb=" O THR C 322 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 326 through 328 removed outlier: 6.368A pdb=" N ILE C 167 " --> pdb=" O ILE C 327 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.251A pdb=" N GLN D 116 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 136 through 137 removed outlier: 4.253A pdb=" N TYR D 150 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 220 through 224 removed outlier: 6.152A pdb=" N PHE D 187 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLY D 224 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY D 189 " --> pdb=" O GLY D 224 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL D 255 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL D 311 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU D 257 " --> pdb=" O VAL D 311 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ALA D 313 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE D 259 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TYR D 315 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 160 " --> pdb=" O ILE D 314 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 87 through 89 Processing sheet with id=AB8, first strand: chain 'E' and resid 220 through 225 removed outlier: 6.843A pdb=" N SER E 185 " --> pdb=" O ALA E 220 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL E 222 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE E 187 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY E 224 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY E 189 " --> pdb=" O GLY E 224 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL E 186 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL E 255 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL E 311 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU E 257 " --> pdb=" O VAL E 311 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ALA E 313 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE E 259 " --> pdb=" O ALA E 313 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 14 through 21 removed outlier: 6.557A pdb=" N ASP F 26 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL F 20 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL F 24 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N HIS F 56 " --> pdb=" O THR F 61 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS F 78 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 87 through 89 Processing sheet with id=AC2, first strand: chain 'F' and resid 98 through 99 removed outlier: 3.590A pdb=" N TYR F 184 " --> pdb=" O ASP F 254 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE F 156 " --> pdb=" O GLN F 312 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE F 314 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU F 158 " --> pdb=" O ILE F 314 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 170 through 178 removed outlier: 6.518A pdb=" N SER G 170 " --> pdb=" O ARG G 166 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE G 162 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N HIS G 66 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE G 68 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL G 108 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY G 70 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N VAL G 103 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N PHE G 128 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR G 127 " --> pdb=" O VAL I 45 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 26 through 31 removed outlier: 6.430A pdb=" N PHE H 20 " --> pdb=" O PHE H 27 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASN H 29 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE H 18 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.713A pdb=" N GLN H 35 " --> pdb=" O HIS H 66 " (cutoff:3.500A) 1434 hydrogen bonds defined for protein. 4152 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: 5.18 Time building geometry restraints manager: 2.41 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: 9607 1.34 - 1.45: 2752 1.45 - 1.57: 15624 1.57 - 1.69: 24 1.69 - 1.80: 154 Bond restraints: 28161 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.58e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.47e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.27e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.03e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 4.03e+01 ... (remaining 28156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 37844 4.79 - 9.59: 59 9.59 - 14.38: 1 14.38 - 19.17: 4 19.17 - 23.97: 2 Bond angle restraints: 37910 Sorted by residual: angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 115.90 23.97 1.00e+00 1.00e+00 5.74e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.99 21.88 1.00e+00 1.00e+00 4.79e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 118.01 18.82 1.00e+00 1.00e+00 3.54e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 121.53 18.34 1.00e+00 1.00e+00 3.36e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 121.43 15.40 1.00e+00 1.00e+00 2.37e+02 ... (remaining 37905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.49: 15962 30.49 - 60.99: 539 60.99 - 91.48: 63 91.48 - 121.97: 0 121.97 - 152.46: 1 Dihedral angle restraints: 16565 sinusoidal: 6476 harmonic: 10089 Sorted by residual: dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 147.54 152.46 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" CA GLN H 132 " pdb=" C GLN H 132 " pdb=" N ILE H 133 " pdb=" CA ILE H 133 " ideal model delta harmonic sigma weight residual 180.00 152.83 27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLN E 312 " pdb=" C GLN E 312 " pdb=" N ALA E 313 " pdb=" CA ALA E 313 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 16562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2756 0.039 - 0.078: 1030 0.078 - 0.116: 280 0.116 - 0.155: 85 0.155 - 0.194: 2 Chirality restraints: 4153 Sorted by residual: chirality pdb=" CA GLN H 132 " pdb=" N GLN H 132 " pdb=" C GLN H 132 " pdb=" CB GLN H 132 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.51 -0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA ILE B 202 " pdb=" N ILE B 202 " pdb=" C ILE B 202 " pdb=" CB ILE B 202 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 4150 not shown) Planarity restraints: 5057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 457 " -0.046 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO C 458 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 458 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 458 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 132 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C GLN H 132 " 0.044 2.00e-02 2.50e+03 pdb=" O GLN H 132 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE H 133 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 338 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO B 339 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " -0.027 5.00e-02 4.00e+02 ... (remaining 5054 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 170 2.46 - 3.07: 20574 3.07 - 3.68: 39534 3.68 - 4.29: 63283 4.29 - 4.90: 108746 Nonbonded interactions: 232307 Sorted by model distance: nonbonded pdb=" OG SER E 310 " pdb=" OE1 GLN E 312 " model vdw 1.847 3.040 nonbonded pdb=" OH TYR D 385 " pdb=" OE2 GLU J 30 " model vdw 1.887 3.040 nonbonded pdb=" OE2 GLU D 196 " pdb=" O HOH D 701 " model vdw 1.907 3.040 nonbonded pdb=" OE2 GLU F 196 " pdb=" O HOH F 701 " model vdw 1.968 3.040 nonbonded pdb=" OG SER C 237 " pdb=" OE1 GLU F 298 " model vdw 1.981 3.040 ... (remaining 232302 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 23 through 401 or resid 411 through 508 or resid 600 throu \ gh 601)) selection = chain 'B' selection = (chain 'C' and (resid 23 through 401 or resid 411 through 601)) } ncs_group { reference = (chain 'D' and resid 13 through 479) selection = (chain 'E' and resid 13 through 479) selection = (chain 'F' and resid 13 through 479) } 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: 3.070 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: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.120 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 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 : 0.006 0.075 28161 Z= 0.293 Angle : 0.682 23.966 37910 Z= 0.438 Chirality : 0.045 0.194 4153 Planarity : 0.003 0.068 5057 Dihedral : 15.097 152.465 10403 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.16 % 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: -0.84 (0.14), residues: 3812 helix: 0.53 (0.13), residues: 1681 sheet: -1.58 (0.21), residues: 605 loop : -1.25 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 143 TYR 0.013 0.002 TYR B 248 PHE 0.027 0.001 PHE H 20 TRP 0.002 0.001 TRP I 4 HIS 0.010 0.001 HIS E 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.29 (28161) covalent geometry : angle 0.68158 / 0.44 (37910) hydrogen bonds : bond 0.14680 / 10.06 ( 1434) hydrogen bonds : angle 6.63984 / 4.59 ( 4152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 826 time to evaluate : 1.219 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: A 508 PHE cc_start: 0.4363 (t80) cc_final: 0.4019 (t80) REVERT: B 462 THR cc_start: 0.8396 (p) cc_final: 0.7239 (p) REVERT: B 508 PHE cc_start: 0.5536 (t80) cc_final: 0.4830 (t80) outliers start: 0 outliers final: 7 residues processed: 826 average time/residue: 0.5558 time to fit residues: 540.6443 Evaluate side-chains 493 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 486 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 115 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 9.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 HIS A 349 GLN A 471 HIS A 503 ASN B 113 ASN B 215 GLN B 475 GLN C 208 GLN C 215 GLN C 471 HIS D 100 ASN D 176 ASN ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 GLN E 371 HIS E 415 GLN E 455 HIS F 176 ASN F 455 HIS G 17 GLN I 16 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.165346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.127990 restraints weight = 49376.588| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.79 r_work: 0.3659 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 28161 Z= 0.209 Angle : 0.742 10.438 37910 Z= 0.382 Chirality : 0.047 0.201 4153 Planarity : 0.005 0.060 5057 Dihedral : 7.124 147.487 4268 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.58 % Allowed : 15.03 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.16 % 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: -0.07 (0.14), residues: 3812 helix: 1.32 (0.13), residues: 1705 sheet: -1.25 (0.22), residues: 526 loop : -1.11 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 34 TYR 0.020 0.002 TYR I 11 PHE 0.027 0.002 PHE G 138 TRP 0.005 0.001 TRP I 4 HIS 0.011 0.002 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (28161) covalent geometry : angle 0.74191 / 0.38 (37910) hydrogen bonds : bond 0.04873 / 3.25 ( 1434) hydrogen bonds : angle 4.81164 / 3.35 ( 4152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 525 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7857 (p) REVERT: A 436 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6431 (tpp) REVERT: B 102 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: B 215 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6122 (mp-120) REVERT: B 266 ILE cc_start: 0.8553 (mt) cc_final: 0.8351 (tt) REVERT: B 312 MET cc_start: 0.8159 (mmm) cc_final: 0.7925 (mmm) REVERT: C 373 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7687 (mtt-85) REVERT: C 396 GLN cc_start: 0.8254 (mt0) cc_final: 0.8005 (mt0) REVERT: D 95 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5392 (mp) REVERT: D 171 MET cc_start: 0.8547 (tpp) cc_final: 0.8262 (mmm) REVERT: D 360 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.8186 (ttm-80) REVERT: D 477 LEU cc_start: 0.7945 (mt) cc_final: 0.7744 (mt) REVERT: E 59 GLU cc_start: 0.7468 (tp30) cc_final: 0.7231 (tp30) REVERT: E 356 ASP cc_start: 0.8802 (m-30) cc_final: 0.8490 (m-30) REVERT: E 379 GLN cc_start: 0.8007 (mt0) cc_final: 0.7644 (mt0) REVERT: F 88 ILE cc_start: 0.7985 (pt) cc_final: 0.7784 (pp) REVERT: F 203 GLU cc_start: 0.7431 (tp30) cc_final: 0.7102 (tm-30) REVERT: F 293 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8152 (ttm) REVERT: F 389 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7857 (mm-40) REVERT: F 416 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8214 (mtm-85) REVERT: G 20 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8107 (t) REVERT: G 23 MET cc_start: 0.7690 (mmm) cc_final: 0.7168 (tpt) REVERT: I 42 ILE cc_start: 0.2340 (OUTLIER) cc_final: 0.1855 (pt) outliers start: 98 outliers final: 34 residues processed: 584 average time/residue: 0.5660 time to fit residues: 390.0756 Evaluate side-chains 445 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 401 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 373 ARG Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 447 GLN Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 293 MET Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 416 ARG Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 42 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 54 optimal weight: 4.9990 chunk 282 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 375 optimal weight: 50.0000 chunk 103 optimal weight: 0.9980 chunk 214 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 358 optimal weight: 0.0040 chunk 15 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 GLN B 190 ASN B 471 HIS ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 GLN D 100 ASN D 297 GLN D 312 GLN D 415 GLN E 455 HIS F 116 GLN F 181 HIS F 297 GLN F 423 GLN F 455 HIS G 163 ASN J 49 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.147473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107912 restraints weight = 48051.101| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.75 r_work: 0.3376 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 28161 Z= 0.144 Angle : 0.622 12.425 37910 Z= 0.315 Chirality : 0.044 0.201 4153 Planarity : 0.004 0.063 5057 Dihedral : 6.461 132.388 4252 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.79 % Allowed : 18.61 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.16 % 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: 0.47 (0.14), residues: 3812 helix: 1.90 (0.13), residues: 1680 sheet: -1.02 (0.22), residues: 530 loop : -0.93 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.001 ARG G 33 TYR 0.027 0.001 TYR I 11 PHE 0.026 0.001 PHE G 138 TRP 0.003 0.001 TRP I 4 HIS 0.007 0.001 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (28161) covalent geometry : angle 0.62244 / 0.31 (37910) hydrogen bonds : bond 0.04278 / 2.86 ( 1434) hydrogen bonds : angle 4.34828 / 3.03 ( 4152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 442 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: A 107 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8426 (p) REVERT: B 157 VAL cc_start: 0.8938 (m) cc_final: 0.8702 (p) REVERT: B 172 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8435 (mt0) REVERT: B 463 LYS cc_start: 0.8759 (tptp) cc_final: 0.8539 (tppt) REVERT: B 465 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 89 LYS cc_start: 0.6391 (OUTLIER) cc_final: 0.6017 (mtpp) REVERT: C 143 ARG cc_start: 0.7969 (ttp-170) cc_final: 0.7439 (ptp-170) REVERT: D 95 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6182 (mp) REVERT: D 358 THR cc_start: 0.8681 (t) cc_final: 0.8259 (p) REVERT: D 360 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8292 (ttm-80) REVERT: D 477 LEU cc_start: 0.8023 (mt) cc_final: 0.7789 (mt) REVERT: E 319 ASP cc_start: 0.8681 (t0) cc_final: 0.8342 (t0) REVERT: E 356 ASP cc_start: 0.8889 (m-30) cc_final: 0.8510 (m-30) REVERT: E 376 ARG cc_start: 0.7896 (mmm-85) cc_final: 0.7588 (mmm-85) REVERT: E 379 GLN cc_start: 0.8119 (mt0) cc_final: 0.7750 (mt0) REVERT: E 397 MET cc_start: 0.6143 (ppp) cc_final: 0.5688 (tmm) REVERT: E 447 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6584 (mt0) REVERT: F 116 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: F 203 GLU cc_start: 0.7845 (tp30) cc_final: 0.7488 (tm-30) REVERT: F 358 THR cc_start: 0.8595 (t) cc_final: 0.8199 (p) REVERT: F 389 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7726 (mm-40) REVERT: F 469 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7696 (mt-10) REVERT: G 110 ASP cc_start: 0.5783 (m-30) cc_final: 0.5559 (m-30) REVERT: H 18 PHE cc_start: 0.4105 (t80) cc_final: 0.3648 (t80) REVERT: H 77 VAL cc_start: 0.4831 (m) cc_final: 0.4631 (m) REVERT: H 102 MET cc_start: 0.4998 (mmm) cc_final: 0.4514 (mmm) outliers start: 104 outliers final: 33 residues processed: 509 average time/residue: 0.6140 time to fit residues: 367.2089 Evaluate side-chains 409 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 369 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 447 GLN Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 116 GLN Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 108 optimal weight: 0.0670 chunk 267 optimal weight: 0.9990 chunk 326 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 361 optimal weight: 0.6980 chunk 284 optimal weight: 4.9990 chunk 110 optimal weight: 0.0170 chunk 76 optimal weight: 3.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN B 172 GLN B 190 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 312 GLN D 415 GLN D 447 GLN E 447 GLN E 455 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.124655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.082248 restraints weight = 46326.054| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.72 r_work: 0.2971 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.8546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 28161 Z= 0.163 Angle : 0.663 11.928 37910 Z= 0.339 Chirality : 0.045 0.276 4153 Planarity : 0.004 0.088 5057 Dihedral : 6.237 95.187 4252 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.54 % Allowed : 20.39 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.16 % 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: 0.64 (0.14), residues: 3812 helix: 2.00 (0.13), residues: 1708 sheet: -0.69 (0.22), residues: 511 loop : -0.94 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 113 TYR 0.021 0.001 TYR A 452 PHE 0.025 0.002 PHE G 138 TRP 0.003 0.001 TRP I 4 HIS 0.015 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (28161) covalent geometry : angle 0.66315 / 0.34 (37910) hydrogen bonds : bond 0.05141 / 3.40 ( 1434) hydrogen bonds : angle 4.25884 / 2.97 ( 4152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 423 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8989 (t) cc_final: 0.8638 (p) REVERT: A 26 GLU cc_start: 0.8185 (mp0) cc_final: 0.7783 (pm20) REVERT: A 52 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8414 (tpp) REVERT: A 67 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8521 (mt-10) REVERT: A 132 LYS cc_start: 0.8735 (pmtt) cc_final: 0.8254 (pptt) REVERT: A 501 VAL cc_start: 0.9064 (t) cc_final: 0.8797 (m) REVERT: B 67 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8308 (mp0) REVERT: B 383 MET cc_start: 0.8511 (mmm) cc_final: 0.7925 (tpp) REVERT: B 456 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7492 (mt) REVERT: C 143 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.8003 (ptp-170) REVERT: D 95 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7288 (mp) REVERT: D 126 GLU cc_start: 0.7596 (pm20) cc_final: 0.6869 (pm20) REVERT: D 129 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7582 (mt-10) REVERT: D 358 THR cc_start: 0.9020 (t) cc_final: 0.8727 (p) REVERT: D 402 GLU cc_start: 0.7627 (pp20) cc_final: 0.7127 (pm20) REVERT: E 59 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8204 (tp30) REVERT: E 71 GLU cc_start: 0.8696 (pp20) cc_final: 0.8495 (pm20) REVERT: E 319 ASP cc_start: 0.8746 (t0) cc_final: 0.8512 (t0) REVERT: E 341 ARG cc_start: 0.8930 (tpp80) cc_final: 0.8625 (tpp-160) REVERT: E 376 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8296 (mmm-85) REVERT: E 379 GLN cc_start: 0.8442 (mt0) cc_final: 0.8002 (mt0) REVERT: E 397 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6071 (tpt) REVERT: F 95 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7726 (mp) REVERT: F 108 GLU cc_start: 0.8747 (tp30) cc_final: 0.8534 (tp30) REVERT: F 126 GLU cc_start: 0.8460 (pm20) cc_final: 0.7914 (pm20) REVERT: F 129 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7898 (mt-10) REVERT: F 203 GLU cc_start: 0.8316 (tp30) cc_final: 0.7902 (tm-30) REVERT: F 204 MET cc_start: 0.8432 (tpp) cc_final: 0.8222 (mtt) REVERT: F 213 LYS cc_start: 0.8745 (tppt) cc_final: 0.8498 (ptpp) REVERT: F 358 THR cc_start: 0.9030 (t) cc_final: 0.8762 (p) REVERT: F 373 ASP cc_start: 0.8954 (m-30) cc_final: 0.8749 (m-30) REVERT: F 416 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7928 (mtm-85) REVERT: G 21 LYS cc_start: 0.8803 (tppt) cc_final: 0.8585 (tppp) REVERT: G 84 SER cc_start: 0.7973 (OUTLIER) cc_final: 0.7658 (p) REVERT: H 34 ARG cc_start: 0.6853 (tpm-80) cc_final: 0.6560 (tpt90) REVERT: H 102 MET cc_start: 0.5142 (mmm) cc_final: 0.4589 (mmm) REVERT: J 29 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8542 (tm-30) REVERT: J 32 ARG cc_start: 0.8450 (tmm160) cc_final: 0.8112 (ptt90) outliers start: 97 outliers final: 33 residues processed: 489 average time/residue: 0.5870 time to fit residues: 333.4455 Evaluate side-chains 357 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 316 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 416 ARG Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 260 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 264 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 362 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 190 ASN C 46 ASN C 78 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 GLN G 82 HIS ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.112658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.071200 restraints weight = 46414.896| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.70 r_work: 0.2763 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 1.0412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28161 Z= 0.191 Angle : 0.671 10.588 37910 Z= 0.348 Chirality : 0.046 0.245 4153 Planarity : 0.004 0.039 5057 Dihedral : 6.353 89.917 4252 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.83 % Allowed : 21.38 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.16 % 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: 0.69 (0.14), residues: 3812 helix: 2.00 (0.13), residues: 1715 sheet: -0.45 (0.22), residues: 520 loop : -0.96 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 381 TYR 0.017 0.002 TYR G 44 PHE 0.023 0.002 PHE J 34 TRP 0.005 0.002 TRP I 4 HIS 0.006 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (28161) covalent geometry : angle 0.67134 / 0.35 (37910) hydrogen bonds : bond 0.06182 / 4.09 ( 1434) hydrogen bonds : angle 4.36400 / 3.02 ( 4152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 345 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8388 (mp0) cc_final: 0.8177 (mp0) REVERT: A 67 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8451 (mt-10) REVERT: A 94 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9132 (mm) REVERT: A 132 LYS cc_start: 0.8884 (pmtt) cc_final: 0.8494 (pptt) REVERT: B 374 VAL cc_start: 0.9284 (t) cc_final: 0.8993 (m) REVERT: C 69 ASP cc_start: 0.8557 (m-30) cc_final: 0.8324 (p0) REVERT: C 143 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.8338 (ptp-170) REVERT: C 381 ARG cc_start: 0.8457 (mtp85) cc_final: 0.8217 (mmm-85) REVERT: C 416 GLN cc_start: 0.8484 (tt0) cc_final: 0.8253 (tp40) REVERT: D 46 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8734 (pm20) REVERT: D 126 GLU cc_start: 0.7994 (pm20) cc_final: 0.7402 (mp0) REVERT: D 129 GLU cc_start: 0.8490 (mm-30) cc_final: 0.7836 (mt-10) REVERT: D 214 ASP cc_start: 0.7965 (m-30) cc_final: 0.7625 (p0) REVERT: D 358 THR cc_start: 0.8996 (t) cc_final: 0.8740 (p) REVERT: D 403 GLU cc_start: 0.8334 (mp0) cc_final: 0.7804 (mp0) REVERT: D 423 GLN cc_start: 0.8638 (tt0) cc_final: 0.8272 (tm-30) REVERT: D 428 PHE cc_start: 0.8905 (m-80) cc_final: 0.8704 (m-80) REVERT: D 476 LYS cc_start: 0.7967 (tppp) cc_final: 0.7690 (mtmt) REVERT: E 41 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8444 (pt0) REVERT: E 59 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8225 (tp30) REVERT: E 171 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8797 (mtt) REVERT: E 397 MET cc_start: 0.7149 (ppp) cc_final: 0.6705 (tpt) REVERT: E 404 ASP cc_start: 0.8293 (m-30) cc_final: 0.7958 (m-30) REVERT: F 129 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8501 (mm-30) REVERT: F 203 GLU cc_start: 0.8661 (tp30) cc_final: 0.8398 (tm-30) REVERT: F 211 ASN cc_start: 0.9248 (t0) cc_final: 0.8753 (t0) REVERT: F 416 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8666 (mtt90) REVERT: F 418 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8564 (mt) REVERT: F 476 LYS cc_start: 0.8401 (tppt) cc_final: 0.8101 (mppt) REVERT: G 21 LYS cc_start: 0.9009 (tppt) cc_final: 0.8786 (ttpp) REVERT: G 66 HIS cc_start: 0.8105 (m90) cc_final: 0.7892 (m-70) REVERT: G 134 ARG cc_start: 0.9023 (mtp-110) cc_final: 0.8606 (mmm-85) REVERT: G 155 PHE cc_start: 0.7592 (p90) cc_final: 0.6980 (p90) REVERT: G 161 ILE cc_start: 0.8690 (mm) cc_final: 0.8395 (mm) REVERT: J 29 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8382 (tm-30) REVERT: J 32 ARG cc_start: 0.8583 (tmm160) cc_final: 0.8018 (ptt90) REVERT: J 40 GLU cc_start: 0.8361 (tp30) cc_final: 0.7965 (mt-10) outliers start: 105 outliers final: 30 residues processed: 424 average time/residue: 0.7341 time to fit residues: 358.6688 Evaluate side-chains 315 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 416 ARG Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 260 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 275 optimal weight: 0.9980 chunk 310 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 272 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 202 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN D 261 ASN E 38 ASN F 447 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.113445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.072714 restraints weight = 46142.989| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.68 r_work: 0.2793 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 1.0578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28161 Z= 0.123 Angle : 0.575 9.889 37910 Z= 0.293 Chirality : 0.043 0.212 4153 Planarity : 0.004 0.039 5057 Dihedral : 6.024 85.564 4252 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.26 % Allowed : 23.02 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.16 % 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: 1.03 (0.14), residues: 3812 helix: 2.32 (0.13), residues: 1711 sheet: -0.18 (0.23), residues: 516 loop : -0.87 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 35 TYR 0.021 0.001 TYR G 171 PHE 0.014 0.001 PHE H 18 TRP 0.004 0.001 TRP I 4 HIS 0.006 0.001 HIS G 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (28161) covalent geometry : angle 0.57524 / 0.29 (37910) hydrogen bonds : bond 0.04832 / 3.20 ( 1434) hydrogen bonds : angle 4.05868 / 2.82 ( 4152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 302 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8372 (mp0) cc_final: 0.8159 (mp0) REVERT: A 52 MET cc_start: 0.9061 (tpp) cc_final: 0.8678 (tpp) REVERT: A 67 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8506 (mt-10) REVERT: A 132 LYS cc_start: 0.8815 (pmtt) cc_final: 0.8452 (pptt) REVERT: A 312 MET cc_start: 0.9167 (mmm) cc_final: 0.8961 (mmp) REVERT: B 54 GLU cc_start: 0.8219 (pp20) cc_final: 0.7736 (pp20) REVERT: B 124 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.9031 (mmmt) REVERT: B 374 VAL cc_start: 0.9274 (t) cc_final: 0.9023 (m) REVERT: C 132 LYS cc_start: 0.8864 (pptt) cc_final: 0.8391 (tttp) REVERT: C 143 ARG cc_start: 0.8512 (ttp-170) cc_final: 0.8282 (ptp-170) REVERT: C 312 MET cc_start: 0.9413 (mmp) cc_final: 0.9159 (mmm) REVERT: C 381 ARG cc_start: 0.8442 (mtp85) cc_final: 0.8167 (mmm-85) REVERT: C 416 GLN cc_start: 0.8557 (tt0) cc_final: 0.8321 (tp40) REVERT: D 95 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8042 (mp) REVERT: D 116 GLN cc_start: 0.7925 (mp-120) cc_final: 0.7486 (mp10) REVERT: D 129 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7957 (mt-10) REVERT: D 214 ASP cc_start: 0.8003 (m-30) cc_final: 0.7791 (p0) REVERT: D 358 THR cc_start: 0.8943 (t) cc_final: 0.8728 (p) REVERT: D 360 ARG cc_start: 0.8930 (ttm-80) cc_final: 0.8629 (ttm-80) REVERT: D 402 GLU cc_start: 0.7898 (pm20) cc_final: 0.7490 (pm20) REVERT: D 403 GLU cc_start: 0.8056 (mp0) cc_final: 0.7693 (mp0) REVERT: D 423 GLN cc_start: 0.8625 (tt0) cc_final: 0.8295 (tm-30) REVERT: D 476 LYS cc_start: 0.7988 (tppp) cc_final: 0.7593 (mtmt) REVERT: D 479 GLU cc_start: 0.8125 (tp30) cc_final: 0.7711 (tm-30) REVERT: E 41 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8339 (pt0) REVERT: E 59 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8115 (tp30) REVERT: E 211 ASN cc_start: 0.8979 (t0) cc_final: 0.8637 (t160) REVERT: E 228 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8613 (mm-30) REVERT: E 397 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7168 (tpt) REVERT: E 404 ASP cc_start: 0.8330 (m-30) cc_final: 0.8104 (m-30) REVERT: F 47 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8286 (p) REVERT: F 126 GLU cc_start: 0.8276 (pm20) cc_final: 0.8055 (mm-30) REVERT: F 129 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8399 (mt-10) REVERT: F 203 GLU cc_start: 0.8487 (tp30) cc_final: 0.8277 (tm-30) REVERT: F 204 MET cc_start: 0.8730 (tpp) cc_final: 0.8521 (mtt) REVERT: F 211 ASN cc_start: 0.9209 (t0) cc_final: 0.8762 (t0) REVERT: F 250 GLN cc_start: 0.8971 (tp40) cc_final: 0.8377 (tm-30) REVERT: F 416 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8717 (mtt90) REVERT: F 418 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8437 (mt) REVERT: G 21 LYS cc_start: 0.8952 (tppt) cc_final: 0.8750 (ttpp) REVERT: G 66 HIS cc_start: 0.8016 (m90) cc_final: 0.7674 (m-70) REVERT: G 134 ARG cc_start: 0.9021 (mtp-110) cc_final: 0.8627 (mmm-85) REVERT: G 155 PHE cc_start: 0.7670 (p90) cc_final: 0.6955 (p90) REVERT: G 161 ILE cc_start: 0.8793 (mm) cc_final: 0.8524 (mm) REVERT: H 18 PHE cc_start: 0.4287 (t80) cc_final: 0.3584 (t80) REVERT: J 29 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8355 (tm-30) REVERT: J 32 ARG cc_start: 0.8473 (tmm160) cc_final: 0.8028 (ptt90) outliers start: 62 outliers final: 24 residues processed: 344 average time/residue: 0.7333 time to fit residues: 291.0294 Evaluate side-chains 311 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 416 ARG Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 260 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 276 optimal weight: 0.0670 chunk 231 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 107 optimal weight: 0.0010 chunk 55 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 282 optimal weight: 0.6980 chunk 37 optimal weight: 0.0980 overall best weight: 0.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN G 205 GLN ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.115387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075412 restraints weight = 46537.986| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.69 r_work: 0.2854 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 1.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28161 Z= 0.104 Angle : 0.545 10.013 37910 Z= 0.277 Chirality : 0.042 0.193 4153 Planarity : 0.003 0.042 5057 Dihedral : 5.679 87.899 4252 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.86 % Allowed : 22.95 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.16 % 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: 1.35 (0.14), residues: 3812 helix: 2.56 (0.13), residues: 1703 sheet: 0.03 (0.23), residues: 520 loop : -0.67 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 30 TYR 0.035 0.001 TYR I 11 PHE 0.012 0.001 PHE H 18 TRP 0.003 0.001 TRP I 4 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (28161) covalent geometry : angle 0.54528 / 0.28 (37910) hydrogen bonds : bond 0.03970 / 2.63 ( 1434) hydrogen bonds : angle 3.85941 / 2.68 ( 4152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8378 (mp0) cc_final: 0.8145 (mp0) REVERT: A 52 MET cc_start: 0.9031 (tpp) cc_final: 0.8660 (tpp) REVERT: A 67 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: A 132 LYS cc_start: 0.8785 (pmtt) cc_final: 0.8434 (pptt) REVERT: A 383 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8545 (tpp) REVERT: B 54 GLU cc_start: 0.8129 (pp20) cc_final: 0.7615 (pp20) REVERT: B 124 LYS cc_start: 0.9220 (mtpp) cc_final: 0.9007 (mmmt) REVERT: B 374 VAL cc_start: 0.9175 (t) cc_final: 0.8917 (m) REVERT: B 434 SER cc_start: 0.9270 (OUTLIER) cc_final: 0.8816 (p) REVERT: C 26 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7491 (pm20) REVERT: C 132 LYS cc_start: 0.8894 (pptt) cc_final: 0.8413 (tttp) REVERT: C 143 ARG cc_start: 0.8518 (ttp-170) cc_final: 0.8304 (ptp-170) REVERT: C 312 MET cc_start: 0.9402 (mmp) cc_final: 0.9100 (mmm) REVERT: C 416 GLN cc_start: 0.8552 (tt0) cc_final: 0.8275 (tp40) REVERT: D 16 ARG cc_start: 0.8508 (mtp-110) cc_final: 0.8308 (mtp-110) REVERT: D 129 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7909 (mt-10) REVERT: D 211 ASN cc_start: 0.8946 (t0) cc_final: 0.7758 (t0) REVERT: D 214 ASP cc_start: 0.8033 (m-30) cc_final: 0.7707 (p0) REVERT: D 358 THR cc_start: 0.8962 (t) cc_final: 0.8748 (p) REVERT: D 403 GLU cc_start: 0.7968 (mp0) cc_final: 0.7568 (mp0) REVERT: D 423 GLN cc_start: 0.8535 (tt0) cc_final: 0.8212 (tm-30) REVERT: D 476 LYS cc_start: 0.8010 (tppp) cc_final: 0.7619 (mtmt) REVERT: D 479 GLU cc_start: 0.8131 (tp30) cc_final: 0.7710 (tm-30) REVERT: E 16 ARG cc_start: 0.8428 (mtp-110) cc_final: 0.8060 (mtm-85) REVERT: E 41 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8377 (tt0) REVERT: E 59 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8029 (tp30) REVERT: E 228 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8587 (mm-30) REVERT: E 404 ASP cc_start: 0.8298 (m-30) cc_final: 0.8079 (m-30) REVERT: F 47 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8400 (p) REVERT: F 129 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8357 (mt-10) REVERT: F 211 ASN cc_start: 0.9227 (t0) cc_final: 0.8690 (t0) REVERT: F 418 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8156 (mt) REVERT: G 155 PHE cc_start: 0.7651 (p90) cc_final: 0.6967 (p90) REVERT: G 161 ILE cc_start: 0.8809 (mm) cc_final: 0.8474 (mm) REVERT: G 190 MET cc_start: 0.5934 (pp-130) cc_final: 0.5499 (pp-130) REVERT: H 16 MET cc_start: 0.0994 (mtm) cc_final: -0.0227 (tpt) REVERT: J 29 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8200 (tm-30) REVERT: J 32 ARG cc_start: 0.8410 (tmm160) cc_final: 0.7958 (ptt90) outliers start: 51 outliers final: 18 residues processed: 331 average time/residue: 0.7778 time to fit residues: 294.5403 Evaluate side-chains 288 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 260 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 237 optimal weight: 5.9990 chunk 190 optimal weight: 0.5980 chunk 301 optimal weight: 4.9990 chunk 353 optimal weight: 7.9990 chunk 221 optimal weight: 0.0970 chunk 204 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 336 optimal weight: 9.9990 chunk 354 optimal weight: 8.9990 chunk 338 optimal weight: 30.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.109533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.070083 restraints weight = 46774.532| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.00 r_work: 0.2711 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 1.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28161 Z= 0.174 Angle : 0.620 11.451 37910 Z= 0.320 Chirality : 0.045 0.200 4153 Planarity : 0.004 0.049 5057 Dihedral : 6.007 89.297 4252 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.71 % Allowed : 23.86 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.16 % 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: 1.27 (0.14), residues: 3812 helix: 2.42 (0.13), residues: 1716 sheet: 0.11 (0.23), residues: 528 loop : -0.71 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 35 TYR 0.021 0.002 TYR G 171 PHE 0.019 0.002 PHE F 265 TRP 0.005 0.002 TRP I 4 HIS 0.007 0.001 HIS D 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (28161) covalent geometry : angle 0.62030 / 0.32 (37910) hydrogen bonds : bond 0.05915 / 3.93 ( 1434) hydrogen bonds : angle 4.10660 / 2.85 ( 4152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 286 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8331 (mp0) cc_final: 0.8087 (mp0) REVERT: A 52 MET cc_start: 0.8998 (tpp) cc_final: 0.8654 (tpp) REVERT: A 67 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8313 (mt-10) REVERT: A 132 LYS cc_start: 0.8813 (pmtt) cc_final: 0.8482 (pptt) REVERT: B 54 GLU cc_start: 0.8042 (pp20) cc_final: 0.7494 (pp20) REVERT: B 124 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9086 (mmmt) REVERT: B 374 VAL cc_start: 0.9126 (t) cc_final: 0.8925 (m) REVERT: C 26 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: C 132 LYS cc_start: 0.8931 (pptt) cc_final: 0.8610 (tttp) REVERT: C 143 ARG cc_start: 0.8478 (ttp-170) cc_final: 0.8264 (ptp-170) REVERT: C 312 MET cc_start: 0.9435 (mmp) cc_final: 0.9172 (mmm) REVERT: C 416 GLN cc_start: 0.8591 (tt0) cc_final: 0.8324 (tp40) REVERT: D 129 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7956 (mt-10) REVERT: D 204 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8584 (mtp) REVERT: D 358 THR cc_start: 0.8843 (t) cc_final: 0.8596 (p) REVERT: D 402 GLU cc_start: 0.7840 (pm20) cc_final: 0.7561 (pm20) REVERT: D 403 GLU cc_start: 0.7984 (mp0) cc_final: 0.7638 (mp0) REVERT: D 423 GLN cc_start: 0.8488 (tt0) cc_final: 0.8190 (tm-30) REVERT: E 16 ARG cc_start: 0.8235 (mtp-110) cc_final: 0.7937 (mtm-85) REVERT: E 41 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8282 (tt0) REVERT: E 59 GLU cc_start: 0.8540 (mm-30) cc_final: 0.7993 (tp30) REVERT: E 108 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8501 (mt-10) REVERT: E 211 ASN cc_start: 0.8891 (t0) cc_final: 0.8493 (t0) REVERT: E 228 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8534 (mm-30) REVERT: E 404 ASP cc_start: 0.8282 (m-30) cc_final: 0.8001 (m-30) REVERT: F 129 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8269 (mt-10) REVERT: G 155 PHE cc_start: 0.7817 (p90) cc_final: 0.7148 (p90) REVERT: G 190 MET cc_start: 0.6358 (pp-130) cc_final: 0.6068 (pp-130) REVERT: G 194 ASP cc_start: 0.6169 (t0) cc_final: 0.5958 (p0) REVERT: H 16 MET cc_start: 0.0418 (mtm) cc_final: -0.0664 (tpt) REVERT: H 34 ARG cc_start: 0.7774 (tpt90) cc_final: 0.7431 (tmt-80) REVERT: J 29 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8092 (tm-30) REVERT: J 32 ARG cc_start: 0.8381 (tmm160) cc_final: 0.7947 (ptt90) REVERT: J 35 ARG cc_start: 0.8562 (ttm110) cc_final: 0.8353 (ttm-80) outliers start: 47 outliers final: 20 residues processed: 326 average time/residue: 0.7233 time to fit residues: 270.6786 Evaluate side-chains 287 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 263 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 260 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 118 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 318 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 354 optimal weight: 9.9990 chunk 329 optimal weight: 0.9990 chunk 360 optimal weight: 50.0000 chunk 365 optimal weight: 40.0000 chunk 342 optimal weight: 20.0000 chunk 362 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 415 GLN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN D 431 HIS ** G 82 HIS ** 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 = 0.3513 r_free = 0.3513 target = 0.106818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.067351 restraints weight = 46497.701| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.00 r_work: 0.2669 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 1.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 28161 Z= 0.231 Angle : 0.668 12.039 37910 Z= 0.346 Chirality : 0.047 0.167 4153 Planarity : 0.004 0.041 5057 Dihedral : 6.343 87.114 4252 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.61 % Allowed : 24.22 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.16 % 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 (0.14), residues: 3812 helix: 2.27 (0.13), residues: 1708 sheet: 0.11 (0.22), residues: 513 loop : -0.85 (0.14), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 373 TYR 0.022 0.002 TYR G 44 PHE 0.016 0.002 PHE F 265 TRP 0.005 0.002 TRP I 4 HIS 0.013 0.002 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.23 (28161) covalent geometry : angle 0.66786 / 0.35 (37910) hydrogen bonds : bond 0.06642 / 4.42 ( 1434) hydrogen bonds : angle 4.30583 / 2.98 ( 4152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8354 (mp0) cc_final: 0.8121 (mp0) REVERT: A 52 MET cc_start: 0.9062 (tpp) cc_final: 0.8712 (tpp) REVERT: A 67 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8463 (mt-10) REVERT: A 132 LYS cc_start: 0.8876 (pmtt) cc_final: 0.8574 (pptt) REVERT: B 54 GLU cc_start: 0.8117 (pp20) cc_final: 0.7576 (pp20) REVERT: B 124 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9143 (mmmt) REVERT: C 132 LYS cc_start: 0.8914 (pptt) cc_final: 0.8649 (tttp) REVERT: C 143 ARG cc_start: 0.8465 (ttp-170) cc_final: 0.8247 (ptp-170) REVERT: C 312 MET cc_start: 0.9493 (mmp) cc_final: 0.9251 (mmm) REVERT: C 416 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8361 (tp40) REVERT: D 129 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8052 (mt-10) REVERT: D 211 ASN cc_start: 0.9201 (t0) cc_final: 0.8801 (t0) REVERT: D 214 ASP cc_start: 0.8770 (p0) cc_final: 0.8382 (p0) REVERT: D 358 THR cc_start: 0.8909 (t) cc_final: 0.8633 (p) REVERT: D 402 GLU cc_start: 0.7875 (pm20) cc_final: 0.7586 (pm20) REVERT: D 403 GLU cc_start: 0.7927 (mp0) cc_final: 0.7606 (mp0) REVERT: D 423 GLN cc_start: 0.8604 (tt0) cc_final: 0.8301 (tm-30) REVERT: E 16 ARG cc_start: 0.8265 (mtp-110) cc_final: 0.7958 (mtm-85) REVERT: E 59 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8072 (tp30) REVERT: E 108 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8532 (mt-10) REVERT: E 211 ASN cc_start: 0.8965 (t0) cc_final: 0.8523 (t0) REVERT: E 228 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8551 (mm-30) REVERT: E 404 ASP cc_start: 0.8421 (m-30) cc_final: 0.8164 (m-30) REVERT: F 129 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8355 (mt-10) REVERT: G 84 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8295 (p) REVERT: G 155 PHE cc_start: 0.7971 (p90) cc_final: 0.7341 (p90) REVERT: H 16 MET cc_start: 0.1025 (mtm) cc_final: -0.0524 (tpt) REVERT: H 34 ARG cc_start: 0.7942 (tpt90) cc_final: 0.7595 (tmt-80) REVERT: H 98 VAL cc_start: 0.8117 (m) cc_final: 0.7697 (p) REVERT: J 29 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8229 (tm-30) REVERT: J 32 ARG cc_start: 0.8373 (tmm160) cc_final: 0.7812 (ptt90) REVERT: J 35 ARG cc_start: 0.8629 (ttm110) cc_final: 0.8397 (ttm-80) REVERT: J 39 LYS cc_start: 0.9000 (tmmm) cc_final: 0.8750 (tmmt) outliers start: 44 outliers final: 22 residues processed: 303 average time/residue: 0.7543 time to fit residues: 263.3340 Evaluate side-chains 280 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 260 LYS Chi-restraints excluded: chain H residue 102 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 22 optimal weight: 2.9990 chunk 299 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 333 optimal weight: 9.9990 chunk 322 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.104604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.066134 restraints weight = 46701.299| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.93 r_work: 0.2644 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 1.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 28161 Z= 0.260 Angle : 0.707 15.905 37910 Z= 0.365 Chirality : 0.048 0.176 4153 Planarity : 0.005 0.056 5057 Dihedral : 6.501 83.145 4252 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.57 % Allowed : 24.44 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.16 % 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: 0.91 (0.14), residues: 3812 helix: 2.14 (0.13), residues: 1715 sheet: 0.16 (0.23), residues: 496 loop : -0.99 (0.14), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 373 TYR 0.021 0.002 TYR G 44 PHE 0.027 0.002 PHE H 18 TRP 0.004 0.001 TRP I 4 HIS 0.018 0.002 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.26 (28161) covalent geometry : angle 0.70748 / 0.37 (37910) hydrogen bonds : bond 0.07068 / 4.70 ( 1434) hydrogen bonds : angle 4.42468 / 3.06 ( 4152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 270 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8416 (mp0) cc_final: 0.8164 (mp0) REVERT: A 52 MET cc_start: 0.9108 (tpp) cc_final: 0.8748 (tpp) REVERT: A 67 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8609 (mt-10) REVERT: A 132 LYS cc_start: 0.8944 (pmtt) cc_final: 0.8589 (pptt) REVERT: B 54 GLU cc_start: 0.8349 (pp20) cc_final: 0.7791 (pp20) REVERT: B 124 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9184 (mmmt) REVERT: C 132 LYS cc_start: 0.8946 (pptt) cc_final: 0.8637 (tttp) REVERT: C 143 ARG cc_start: 0.8552 (ttp-170) cc_final: 0.8327 (ptp-170) REVERT: C 312 MET cc_start: 0.9553 (mmp) cc_final: 0.9348 (mmm) REVERT: C 416 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8370 (tp40) REVERT: D 116 GLN cc_start: 0.8340 (mp10) cc_final: 0.7747 (mp10) REVERT: D 129 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8124 (mt-10) REVERT: D 218 LYS cc_start: 0.9147 (mttp) cc_final: 0.8819 (mtpt) REVERT: D 358 THR cc_start: 0.8924 (t) cc_final: 0.8629 (p) REVERT: D 423 GLN cc_start: 0.8753 (tt0) cc_final: 0.8367 (tm-30) REVERT: E 16 ARG cc_start: 0.8477 (mtp-110) cc_final: 0.8212 (mtm-85) REVERT: E 59 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8214 (tp30) REVERT: E 108 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8674 (mt-10) REVERT: E 116 GLN cc_start: 0.8851 (mp10) cc_final: 0.8328 (mp-120) REVERT: E 206 GLU cc_start: 0.8894 (tp30) cc_final: 0.8610 (tp30) REVERT: E 404 ASP cc_start: 0.8507 (m-30) cc_final: 0.8276 (m-30) REVERT: F 13 THR cc_start: 0.6927 (p) cc_final: 0.6651 (t) REVERT: F 129 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8439 (mt-10) REVERT: F 203 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8382 (tm-30) REVERT: F 206 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8597 (pp20) REVERT: G 84 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8292 (p) REVERT: G 124 PHE cc_start: 0.8262 (m-80) cc_final: 0.7901 (m-10) REVERT: G 155 PHE cc_start: 0.7958 (p90) cc_final: 0.7326 (p90) REVERT: J 29 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8437 (tm-30) REVERT: J 32 ARG cc_start: 0.8452 (tmm160) cc_final: 0.7936 (ptt90) REVERT: J 35 ARG cc_start: 0.8694 (ttm110) cc_final: 0.8481 (ttm-80) REVERT: J 39 LYS cc_start: 0.9020 (tmmm) cc_final: 0.8785 (tmmt) outliers start: 43 outliers final: 26 residues processed: 303 average time/residue: 0.7679 time to fit residues: 267.2574 Evaluate side-chains 277 residues out of total 3150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain J residue 49 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 305 optimal weight: 3.9990 chunk 367 optimal weight: 0.0870 chunk 318 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 371 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 299 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN J 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.107274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.068321 restraints weight = 46274.128| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.67 r_work: 0.2714 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 1.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28161 Z= 0.136 Angle : 0.610 14.563 37910 Z= 0.313 Chirality : 0.043 0.165 4153 Planarity : 0.004 0.040 5057 Dihedral : 6.212 87.804 4252 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.13 % Allowed : 25.06 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.16 % 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: 1.19 (0.14), residues: 3812 helix: 2.40 (0.13), residues: 1695 sheet: 0.29 (0.23), residues: 503 loop : -0.83 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 373 TYR 0.021 0.001 TYR B 358 PHE 0.013 0.001 PHE H 18 TRP 0.005 0.001 TRP I 4 HIS 0.020 0.001 HIS J 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (28161) covalent geometry : angle 0.60987 / 0.31 (37910) hydrogen bonds : bond 0.05330 / 3.53 ( 1434) hydrogen bonds : angle 4.15093 / 2.88 ( 4152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14346.97 seconds wall clock time: 243 minutes 40.90 seconds (14620.90 seconds total)