Starting phenix.real_space_refine on Mon Aug 25 00:27:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9l_34572/08_2025/8h9l_34572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9l_34572/08_2025/8h9l_34572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h9l_34572/08_2025/8h9l_34572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9l_34572/08_2025/8h9l_34572.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h9l_34572/08_2025/8h9l_34572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9l_34572/08_2025/8h9l_34572.map" } resolution = 2.61 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= 0.000 sd= 0.028 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 13 5.49 5 Mg 5 5.21 5 S 85 5.16 5 C 15081 2.51 5 N 4170 2.21 5 O 4609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 207 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23963 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3706 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 467} Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3639 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3587 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 451} Chain breaks: 1 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3458 Classifications: {'peptide': 456} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3529 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3562 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 444} Chain: "G" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 623 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "J" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1437 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} 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: "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: "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} Time building chain proxies: 4.85, per 1000 atoms: 0.20 Number of scatterers: 23963 At special positions: 0 Unit cell: (125.56, 123.37, 134.32, 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 85 16.00 P 13 15.00 Mg 5 11.99 O 4609 8.00 N 4170 7.00 C 15081 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5678 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 16 sheets defined 51.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.646A 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: 3.802A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.566A pdb=" N GLY A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.725A pdb=" N LYS A 198 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.995A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.619A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.780A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 401 removed outlier: 3.946A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.646A pdb=" N LYS A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 490 through 507 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.615A 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 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 239 through 259 Proline residue: B 247 - end of helix removed outlier: 4.058A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.602A pdb=" N GLN B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 295 through 296 No H-bonds generated for 'chain 'B' and resid 295 through 296' Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.833A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.522A pdb=" N GLY B 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.545A pdb=" N GLN B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 401 removed outlier: 4.627A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 429 removed outlier: 3.639A pdb=" N LYS B 429 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 460 through 475 Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.520A pdb=" N LEU B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 507 removed outlier: 3.657A pdb=" N GLY B 507 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.573A pdb=" N LEU C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.740A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 239 through 259 Proline residue: C 247 - end of helix removed outlier: 4.020A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.540A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 297 through 307 removed outlier: 4.057A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.576A pdb=" N GLY C 317 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.737A pdb=" N ALA C 377 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 379 " --> pdb=" O SER C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 removed outlier: 3.594A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 429 removed outlier: 3.592A 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 457 through 476 removed outlier: 4.398A pdb=" N THR C 462 " --> pdb=" O PRO C 458 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 508 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.611A pdb=" N MET E 129 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 164 through 180 Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 228 through 249 removed outlier: 4.976A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.538A pdb=" N PHE E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 322 through 329 Processing helix chain 'E' and resid 339 through 345 removed outlier: 3.531A pdb=" N LEU E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 367 through 391 removed outlier: 4.167A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.796A pdb=" N SER E 418 " --> pdb=" O GLN E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 423 No H-bonds generated for 'chain 'E' and resid 421 through 423' Processing helix chain 'E' and resid 424 through 429 Processing helix chain 'E' and resid 436 through 449 Processing helix chain 'E' and resid 456 through 460 removed outlier: 3.515A pdb=" N PHE E 460 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 475 removed outlier: 3.656A pdb=" N ALA E 469 " --> pdb=" O PRO E 465 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS E 475 " --> pdb=" O ALA E 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.601A pdb=" N MET F 129 " --> pdb=" O PHE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 164 through 176 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 228 through 249 removed outlier: 4.897A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 275 removed outlier: 4.178A pdb=" N PHE F 264 " --> pdb=" O ASN F 260 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 287 through 297 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 322 through 329 Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 339 through 345 removed outlier: 3.507A pdb=" N LEU F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 367 through 395 removed outlier: 4.843A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 399 removed outlier: 3.589A pdb=" N LEU F 399 " --> pdb=" O MET F 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 396 through 399' Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.741A pdb=" N SER F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 428 removed outlier: 3.826A pdb=" N GLU F 425 " --> pdb=" O GLN F 422 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL F 426 " --> pdb=" O VAL F 423 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE F 427 " --> pdb=" O ALA F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 450 Processing helix chain 'F' and resid 456 through 460 Processing helix chain 'F' and resid 465 through 477 removed outlier: 3.517A pdb=" N ALA F 469 " --> pdb=" O PRO F 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 164 through 180 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 228 through 249 removed outlier: 4.957A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 removed outlier: 4.165A pdb=" N PHE D 264 " --> pdb=" O ASN D 260 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.772A pdb=" N GLY D 283 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 339 through 344 Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 367 through 395 removed outlier: 4.013A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 418 removed outlier: 3.673A pdb=" N SER D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 429 Processing helix chain 'D' and resid 436 through 450 Processing helix chain 'D' and resid 465 through 480 removed outlier: 3.570A pdb=" N ALA D 469 " --> pdb=" O PRO D 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 31 Processing helix chain 'G' and resid 224 through 271 Processing helix chain 'J' and resid 13 through 18 Processing helix chain 'J' and resid 20 through 43 removed outlier: 3.721A pdb=" N GLU J 26 " --> pdb=" O PHE J 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 30 removed outlier: 3.735A pdb=" N GLN O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 47 Processing helix chain 'O' and resid 48 through 56 Processing helix chain 'O' and resid 61 through 75 Processing helix chain 'O' and resid 79 through 93 Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'O' and resid 97 through 113 Processing helix chain 'O' and resid 127 through 139 Processing helix chain 'O' and resid 140 through 142 No H-bonds generated for 'chain 'O' and resid 140 through 142' Processing helix chain 'O' and resid 156 through 159 Processing helix chain 'O' and resid 174 through 188 removed outlier: 3.540A pdb=" N LYS O 178 " --> pdb=" O SER O 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 35 removed outlier: 6.561A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.560A 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: 5.665A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.786A 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 'B' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 43 current: chain 'B' and resid 60 through 66 removed outlier: 5.727A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' 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: 5.666A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 75 current: chain 'E' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 23 through 28 current: chain 'E' and resid 49 through 57 removed outlier: 6.710A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 60 through 65 current: chain 'F' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 23 through 28 current: chain 'F' and resid 49 through 57 removed outlier: 6.618A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 60 through 65 current: chain 'D' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 23 through 28 current: chain 'D' and resid 49 through 57 removed outlier: 6.675A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 60 through 65 current: chain 'O' and resid 147 through 150 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 147 through 150 current: chain 'O' and resid 169 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.073A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.311A pdb=" N VAL A 108 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR A 200 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE A 267 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 202 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASP A 269 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 204 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA A 264 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU A 324 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 266 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL A 326 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR A 268 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLU A 328 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.134A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.667A pdb=" N ALA B 264 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU B 324 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE B 266 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL B 326 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR B 268 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLU B 328 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.248A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.403A pdb=" N VAL C 108 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU C 352 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.243A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.161A pdb=" N MET E 98 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLN E 224 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER E 184 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL E 221 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE E 186 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY E 223 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY E 188 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL E 254 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL E 310 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU E 256 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA E 312 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE E 258 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE E 155 " --> pdb=" O GLN E 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 135 through 136 removed outlier: 4.228A pdb=" N TYR E 149 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.186A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 97 through 98 removed outlier: 6.461A pdb=" N VAL F 254 " --> pdb=" O THR F 308 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL F 310 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU F 256 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA F 312 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE F 258 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N TYR F 314 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS F 154 " --> pdb=" O ALA F 334 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N THR F 336 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY F 156 " --> pdb=" O THR F 336 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.154A pdb=" N TYR F 149 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 86 through 89 removed outlier: 4.202A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.314A pdb=" N MET D 98 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL D 254 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL D 310 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU D 256 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA D 312 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE D 258 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR D 314 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU D 157 " --> pdb=" O ILE D 313 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.162A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) 1135 hydrogen bonds defined for protein. 3231 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: 3.87 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4574 1.32 - 1.44: 5299 1.44 - 1.56: 14250 1.56 - 1.69: 21 1.69 - 1.81: 163 Bond restraints: 24307 Sorted by residual: bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.458 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.454 -0.117 1.10e-02 8.26e+03 1.12e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.453 -0.116 1.10e-02 8.26e+03 1.12e+02 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.282 0.092 1.00e-02 1.00e+04 8.51e+01 bond pdb=" C4 ATP A 601 " pdb=" N9 ATP A 601 " ideal model delta sigma weight residual 1.374 1.283 0.091 1.00e-02 1.00e+04 8.34e+01 ... (remaining 24302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 32600 3.41 - 6.81: 236 6.81 - 10.22: 31 10.22 - 13.63: 8 13.63 - 17.03: 3 Bond angle restraints: 32878 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 122.84 17.03 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 124.23 15.64 1.00e+00 1.00e+00 2.45e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 125.77 14.10 1.00e+00 1.00e+00 1.99e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 124.91 11.92 1.00e+00 1.00e+00 1.42e+02 angle pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " pdb=" C8 ATP B 601 " ideal model delta sigma weight residual 105.72 115.08 -9.36 1.00e+00 1.00e+00 8.77e+01 ... (remaining 32873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.36: 14381 29.36 - 58.71: 470 58.71 - 88.07: 61 88.07 - 117.43: 5 117.43 - 146.78: 2 Dihedral angle restraints: 14919 sinusoidal: 6035 harmonic: 8884 Sorted by residual: dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 86.78 -146.78 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 171.03 128.97 1 2.00e+01 2.50e-03 3.91e+01 dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 48.07 -108.07 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 14916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2486 0.049 - 0.099: 1078 0.099 - 0.148: 248 0.148 - 0.197: 11 0.197 - 0.247: 4 Chirality restraints: 3827 Sorted by residual: chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.43 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE C 121 " pdb=" N ILE C 121 " pdb=" C ILE C 121 " pdb=" CB ILE C 121 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.45 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 3824 not shown) Planarity restraints: 4250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 16 " -0.712 9.50e-02 1.11e+02 3.19e-01 6.21e+01 pdb=" NE ARG J 16 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG J 16 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 16 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG J 16 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 174 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.73e+00 pdb=" C ASN D 174 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN D 174 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN D 175 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 279 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C PRO D 279 " -0.036 2.00e-02 2.50e+03 pdb=" O PRO D 279 " 0.014 2.00e-02 2.50e+03 pdb=" N SER D 280 " 0.012 2.00e-02 2.50e+03 ... (remaining 4247 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 73 2.41 - 3.03: 14523 3.03 - 3.65: 35589 3.65 - 4.28: 59991 4.28 - 4.90: 97409 Nonbonded interactions: 207585 Sorted by model distance: nonbonded pdb=" OG1 THR D 166 " pdb="MG MG D 502 " model vdw 1.782 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 1.890 2.170 nonbonded pdb=" O3G ATP A 601 " pdb="MG MG A 602 " model vdw 1.975 2.170 nonbonded pdb=" OG1 THR F 166 " pdb="MG MG F 502 " model vdw 2.052 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 2.082 2.170 ... (remaining 207580 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 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 12 through 391 or resid 400 through 475)) selection = chain 'E' selection = (chain 'F' and (resid 12 through 391 or resid 400 through 475)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.270 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.820 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 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:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 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 : 0.011 0.144 24307 Z= 0.526 Angle : 0.874 17.033 32878 Z= 0.538 Chirality : 0.054 0.247 3827 Planarity : 0.007 0.319 4250 Dihedral : 14.631 146.783 9241 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 aren not related in a simple way. whole: -2.29 (0.13), residues: 3102 helix: -1.50 (0.12), residues: 1333 sheet: -1.23 (0.22), residues: 479 loop : -1.46 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 277 TYR 0.015 0.002 TYR A 452 PHE 0.025 0.002 PHE J 34 HIS 0.005 0.001 HIS F 201 Details of bonding type rmsd covalent geometry : bond 0.01091 (24307) covalent geometry : angle 0.87373 (32878) hydrogen bonds : bond 0.14764 ( 1135) hydrogen bonds : angle 6.91264 ( 3231) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.747 Fit side-chains REVERT: B 498 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7529 (tptt) REVERT: C 124 LYS cc_start: 0.7947 (mmtm) cc_final: 0.7702 (mttm) REVERT: C 386 VAL cc_start: 0.8129 (m) cc_final: 0.7800 (p) REVERT: C 457 GLU cc_start: 0.7607 (tt0) cc_final: 0.7312 (mt-10) REVERT: C 471 HIS cc_start: 0.6210 (t70) cc_final: 0.5502 (t-170) REVERT: D 390 ILE cc_start: 0.8420 (mt) cc_final: 0.8212 (mm) REVERT: D 475 LYS cc_start: 0.7664 (ttpt) cc_final: 0.7425 (tmtt) REVERT: O 107 THR cc_start: 0.8274 (t) cc_final: 0.8026 (p) REVERT: O 111 VAL cc_start: 0.7598 (p) cc_final: 0.7271 (t) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.7636 time to fit residues: 328.0444 Evaluate side-chains 289 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS A 385 GLN A 396 GLN A 475 GLN A 477 GLN A 503 ASN B 48 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 GLN C 215 GLN ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 HIS F 27 GLN F 174 ASN F 180 HIS F 197 ASN F 296 GLN F 331 HIS F 458 GLN D 180 HIS D 266 GLN O 87 ASN O 92 ASN O 97 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100605 restraints weight = 31560.642| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.72 r_work: 0.3087 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24307 Z= 0.120 Angle : 0.523 10.321 32878 Z= 0.270 Chirality : 0.043 0.151 3827 Planarity : 0.004 0.041 4250 Dihedral : 7.696 136.735 3506 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % Rotamer: Outliers : 1.34 % Allowed : 10.36 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 aren not related in a simple way. whole: -0.37 (0.15), residues: 3102 helix: 0.50 (0.14), residues: 1326 sheet: -0.74 (0.22), residues: 489 loop : -0.71 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 15 TYR 0.013 0.001 TYR C 397 PHE 0.017 0.001 PHE J 34 HIS 0.007 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00260 (24307) covalent geometry : angle 0.52274 (32878) hydrogen bonds : bond 0.04370 ( 1135) hydrogen bonds : angle 5.07193 ( 3231) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 351 time to evaluate : 0.680 Fit side-chains REVERT: A 52 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8595 (mmm) REVERT: A 477 GLN cc_start: 0.8245 (mm-40) cc_final: 0.8029 (tp-100) REVERT: B 67 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8350 (mt-10) REVERT: B 353 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8091 (mm-30) REVERT: B 373 ARG cc_start: 0.8162 (mtt90) cc_final: 0.7947 (mmt90) REVERT: B 498 LYS cc_start: 0.7738 (ttmt) cc_final: 0.7102 (tptt) REVERT: C 124 LYS cc_start: 0.7806 (mmtm) cc_final: 0.7498 (mttm) REVERT: C 471 HIS cc_start: 0.5891 (t70) cc_final: 0.5155 (t-170) REVERT: F 112 LYS cc_start: 0.8327 (mttt) cc_final: 0.7991 (mttp) REVERT: F 205 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7527 (mp0) REVERT: F 210 ASN cc_start: 0.8775 (t0) cc_final: 0.8396 (t0) REVERT: F 397 ASP cc_start: 0.7493 (m-30) cc_final: 0.7120 (m-30) REVERT: F 400 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7482 (p) REVERT: D 249 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: D 390 ILE cc_start: 0.8046 (mt) cc_final: 0.7812 (mm) REVERT: D 431 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7244 (tpt) REVERT: D 475 LYS cc_start: 0.7435 (ttpt) cc_final: 0.7080 (tmtt) REVERT: G 233 ASP cc_start: 0.7835 (t70) cc_final: 0.7623 (t70) REVERT: O 136 THR cc_start: 0.7349 (m) cc_final: 0.7107 (p) outliers start: 34 outliers final: 11 residues processed: 367 average time/residue: 0.6842 time to fit residues: 282.6186 Evaluate side-chains 307 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 291 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 434 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 92 optimal weight: 7.9990 chunk 290 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 287 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 302 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 405 GLN A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN F 27 GLN F 458 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097440 restraints weight = 31664.330| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.74 r_work: 0.3045 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24307 Z= 0.196 Angle : 0.561 10.803 32878 Z= 0.288 Chirality : 0.045 0.143 3827 Planarity : 0.004 0.044 4250 Dihedral : 7.713 140.541 3506 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.13 % Favored : 97.84 % Rotamer: Outliers : 2.01 % Allowed : 12.45 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 aren not related in a simple way. whole: 0.10 (0.15), residues: 3102 helix: 0.96 (0.14), residues: 1331 sheet: -0.63 (0.23), residues: 498 loop : -0.47 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 30 TYR 0.011 0.001 TYR O 170 PHE 0.019 0.001 PHE J 34 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00471 (24307) covalent geometry : angle 0.56105 (32878) hydrogen bonds : bond 0.04891 ( 1135) hydrogen bonds : angle 4.97123 ( 3231) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 299 time to evaluate : 0.967 Fit side-chains REVERT: A 355 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7942 (tt0) REVERT: A 477 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7965 (mm110) REVERT: B 67 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8324 (mt-10) REVERT: B 353 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8075 (mm-30) REVERT: B 466 ASN cc_start: 0.8121 (m-40) cc_final: 0.7908 (m110) REVERT: B 475 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: B 498 LYS cc_start: 0.7746 (ttmt) cc_final: 0.7128 (tptt) REVERT: C 124 LYS cc_start: 0.7860 (mmtm) cc_final: 0.7518 (mttm) REVERT: C 224 ASP cc_start: 0.8294 (t0) cc_final: 0.7674 (t0) REVERT: C 471 HIS cc_start: 0.5793 (t70) cc_final: 0.5090 (t-170) REVERT: F 112 LYS cc_start: 0.8285 (mttt) cc_final: 0.7961 (mttp) REVERT: F 174 ASN cc_start: 0.8412 (t0) cc_final: 0.7814 (t0) REVERT: F 205 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7519 (mp0) REVERT: F 397 ASP cc_start: 0.7533 (m-30) cc_final: 0.7175 (m-30) REVERT: F 451 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: D 249 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7702 (mp10) REVERT: D 390 ILE cc_start: 0.8069 (mt) cc_final: 0.7834 (mm) REVERT: D 475 LYS cc_start: 0.7364 (ttpt) cc_final: 0.7009 (tmtt) REVERT: G 233 ASP cc_start: 0.7885 (t70) cc_final: 0.7671 (t70) REVERT: O 15 GLU cc_start: 0.7180 (mp0) cc_final: 0.6852 (mp0) REVERT: O 136 THR cc_start: 0.7341 (m) cc_final: 0.7103 (p) outliers start: 51 outliers final: 27 residues processed: 328 average time/residue: 0.7731 time to fit residues: 283.8104 Evaluate side-chains 317 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 262 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 253 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 292 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN F 27 GLN F 42 GLN F 458 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096906 restraints weight = 31479.082| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.76 r_work: 0.3041 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24307 Z= 0.141 Angle : 0.513 11.222 32878 Z= 0.263 Chirality : 0.043 0.157 3827 Planarity : 0.004 0.042 4250 Dihedral : 7.275 140.037 3506 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.87 % Favored : 98.10 % Rotamer: Outliers : 1.81 % Allowed : 13.19 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 aren not related in a simple way. whole: 0.48 (0.15), residues: 3102 helix: 1.33 (0.14), residues: 1326 sheet: -0.45 (0.24), residues: 465 loop : -0.34 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 373 TYR 0.011 0.001 TYR O 170 PHE 0.018 0.001 PHE J 34 HIS 0.003 0.001 HIS D 370 Details of bonding type rmsd covalent geometry : bond 0.00326 (24307) covalent geometry : angle 0.51324 (32878) hydrogen bonds : bond 0.04291 ( 1135) hydrogen bonds : angle 4.80732 ( 3231) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 325 time to evaluate : 0.855 Fit side-chains REVERT: A 355 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7950 (tt0) REVERT: B 67 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8285 (mt-10) REVERT: B 124 LYS cc_start: 0.8529 (mtmm) cc_final: 0.8326 (mppt) REVERT: B 353 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8045 (mm-30) REVERT: B 466 ASN cc_start: 0.8123 (m-40) cc_final: 0.7907 (m110) REVERT: B 475 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.6867 (mp10) REVERT: B 498 LYS cc_start: 0.7785 (ttmt) cc_final: 0.7163 (tptt) REVERT: C 124 LYS cc_start: 0.7809 (mmtm) cc_final: 0.7459 (mttm) REVERT: C 215 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8092 (mm110) REVERT: C 224 ASP cc_start: 0.8344 (t0) cc_final: 0.7620 (t0) REVERT: C 426 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: C 433 TYR cc_start: 0.8170 (m-80) cc_final: 0.7938 (m-80) REVERT: C 471 HIS cc_start: 0.5881 (t70) cc_final: 0.5156 (t-170) REVERT: F 112 LYS cc_start: 0.8275 (mttt) cc_final: 0.7953 (mttp) REVERT: F 174 ASN cc_start: 0.8375 (t0) cc_final: 0.7790 (t0) REVERT: F 205 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7437 (mp0) REVERT: F 210 ASN cc_start: 0.8707 (t0) cc_final: 0.8357 (t0) REVERT: F 400 SER cc_start: 0.7909 (OUTLIER) cc_final: 0.7404 (p) REVERT: F 451 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: D 205 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7265 (tp30) REVERT: D 431 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7128 (tpt) REVERT: D 475 LYS cc_start: 0.7411 (ttpt) cc_final: 0.7065 (tmtt) REVERT: G 233 ASP cc_start: 0.7885 (t70) cc_final: 0.7680 (t70) REVERT: O 15 GLU cc_start: 0.7126 (mp0) cc_final: 0.6726 (mp0) REVERT: O 136 THR cc_start: 0.7322 (m) cc_final: 0.7079 (p) outliers start: 46 outliers final: 24 residues processed: 352 average time/residue: 0.7566 time to fit residues: 300.1830 Evaluate side-chains 332 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 301 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 287 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 28 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN E 224 GLN E 388 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096578 restraints weight = 31401.844| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.71 r_work: 0.3001 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24307 Z= 0.190 Angle : 0.550 11.720 32878 Z= 0.281 Chirality : 0.045 0.162 3827 Planarity : 0.004 0.044 4250 Dihedral : 7.500 144.166 3506 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Rotamer: Outliers : 2.09 % Allowed : 14.02 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 aren not related in a simple way. whole: 0.53 (0.15), residues: 3102 helix: 1.34 (0.14), residues: 1330 sheet: -0.47 (0.23), residues: 498 loop : -0.24 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 373 TYR 0.019 0.001 TYR B 446 PHE 0.019 0.001 PHE J 34 HIS 0.005 0.001 HIS E 454 Details of bonding type rmsd covalent geometry : bond 0.00454 (24307) covalent geometry : angle 0.54955 (32878) hydrogen bonds : bond 0.04692 ( 1135) hydrogen bonds : angle 4.85231 ( 3231) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 295 time to evaluate : 0.789 Fit side-chains REVERT: A 355 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7936 (tt0) REVERT: B 67 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: B 353 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8057 (mm-30) REVERT: B 466 ASN cc_start: 0.8107 (m-40) cc_final: 0.7885 (m110) REVERT: B 475 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: B 498 LYS cc_start: 0.7745 (ttmt) cc_final: 0.7104 (tptt) REVERT: C 124 LYS cc_start: 0.7864 (mmtm) cc_final: 0.7502 (mttm) REVERT: C 215 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8138 (mm110) REVERT: C 224 ASP cc_start: 0.8339 (t0) cc_final: 0.7612 (t0) REVERT: C 301 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8975 (tp) REVERT: C 426 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: C 471 HIS cc_start: 0.5775 (t70) cc_final: 0.5054 (t-170) REVERT: E 29 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.6760 (p0) REVERT: F 112 LYS cc_start: 0.8281 (mttt) cc_final: 0.7956 (mttp) REVERT: F 174 ASN cc_start: 0.8413 (t0) cc_final: 0.7819 (t0) REVERT: F 205 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7486 (mp0) REVERT: F 210 ASN cc_start: 0.8734 (t0) cc_final: 0.8349 (t0) REVERT: F 217 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8210 (mptm) REVERT: F 400 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7330 (p) REVERT: F 451 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: D 205 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: D 249 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: D 431 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7051 (tpt) REVERT: D 475 LYS cc_start: 0.7395 (ttpt) cc_final: 0.7047 (tmtt) REVERT: G 233 ASP cc_start: 0.7883 (t70) cc_final: 0.7666 (t70) REVERT: O 15 GLU cc_start: 0.7090 (mp0) cc_final: 0.6705 (mp0) REVERT: O 136 THR cc_start: 0.7319 (m) cc_final: 0.7081 (p) outliers start: 53 outliers final: 27 residues processed: 324 average time/residue: 0.6757 time to fit residues: 246.3259 Evaluate side-chains 326 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 288 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 135 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 271 optimal weight: 0.3980 chunk 147 optimal weight: 6.9990 chunk 173 optimal weight: 0.5980 chunk 207 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.121806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.094093 restraints weight = 31633.743| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.71 r_work: 0.2959 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24307 Z= 0.214 Angle : 0.570 10.484 32878 Z= 0.292 Chirality : 0.046 0.166 3827 Planarity : 0.004 0.045 4250 Dihedral : 7.717 152.462 3506 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.19 % Favored : 97.78 % Rotamer: Outliers : 2.28 % Allowed : 14.34 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 aren not related in a simple way. whole: 0.48 (0.15), residues: 3102 helix: 1.26 (0.14), residues: 1334 sheet: -0.47 (0.23), residues: 499 loop : -0.25 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 340 TYR 0.019 0.002 TYR B 446 PHE 0.019 0.002 PHE C 468 HIS 0.005 0.001 HIS E 454 Details of bonding type rmsd covalent geometry : bond 0.00515 (24307) covalent geometry : angle 0.56977 (32878) hydrogen bonds : bond 0.04903 ( 1135) hydrogen bonds : angle 4.91271 ( 3231) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 292 time to evaluate : 0.935 Fit side-chains REVERT: A 355 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7870 (tt0) REVERT: B 67 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8260 (mt-10) REVERT: B 353 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8016 (mm-30) REVERT: B 466 ASN cc_start: 0.8012 (m-40) cc_final: 0.7768 (m110) REVERT: B 498 LYS cc_start: 0.7698 (ttmt) cc_final: 0.6980 (tptt) REVERT: C 124 LYS cc_start: 0.7793 (mmtm) cc_final: 0.7439 (mttm) REVERT: C 215 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8016 (mm110) REVERT: C 224 ASP cc_start: 0.8337 (t0) cc_final: 0.7639 (t0) REVERT: C 426 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: C 471 HIS cc_start: 0.5790 (t70) cc_final: 0.5089 (t-170) REVERT: E 29 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6745 (p0) REVERT: E 128 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7434 (mm-30) REVERT: E 340 ARG cc_start: 0.8222 (mtp-110) cc_final: 0.7983 (mtt-85) REVERT: E 439 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: F 112 LYS cc_start: 0.8244 (mttt) cc_final: 0.7923 (mttp) REVERT: F 174 ASN cc_start: 0.8358 (t0) cc_final: 0.7698 (t0) REVERT: F 205 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7439 (mp0) REVERT: F 217 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8142 (mptm) REVERT: F 400 SER cc_start: 0.7702 (OUTLIER) cc_final: 0.7106 (p) REVERT: D 205 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7251 (tp30) REVERT: D 249 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7547 (mp10) REVERT: D 431 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6999 (tpt) REVERT: D 475 LYS cc_start: 0.7319 (ttpt) cc_final: 0.6964 (tmtt) REVERT: G 233 ASP cc_start: 0.7781 (t70) cc_final: 0.7535 (t70) REVERT: O 15 GLU cc_start: 0.7015 (mp0) cc_final: 0.6590 (mp0) REVERT: O 136 THR cc_start: 0.7311 (m) cc_final: 0.7094 (p) outliers start: 58 outliers final: 30 residues processed: 327 average time/residue: 0.7207 time to fit residues: 265.6705 Evaluate side-chains 323 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 283 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 439 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 206 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098474 restraints weight = 31489.694| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.76 r_work: 0.3062 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24307 Z= 0.116 Angle : 0.497 12.037 32878 Z= 0.253 Chirality : 0.042 0.146 3827 Planarity : 0.003 0.042 4250 Dihedral : 7.053 150.681 3506 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % Rotamer: Outliers : 1.81 % Allowed : 15.48 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 aren not related in a simple way. whole: 0.86 (0.15), residues: 3102 helix: 1.65 (0.14), residues: 1326 sheet: -0.26 (0.24), residues: 476 loop : -0.13 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 340 TYR 0.022 0.001 TYR B 446 PHE 0.017 0.001 PHE J 34 HIS 0.015 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00262 (24307) covalent geometry : angle 0.49707 (32878) hydrogen bonds : bond 0.03879 ( 1135) hydrogen bonds : angle 4.68444 ( 3231) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 312 time to evaluate : 0.760 Fit side-chains REVERT: A 355 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7881 (tt0) REVERT: B 353 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8041 (mm-30) REVERT: B 415 GLN cc_start: 0.6639 (mt0) cc_final: 0.5933 (mt0) REVERT: B 466 ASN cc_start: 0.8139 (m-40) cc_final: 0.7929 (m110) REVERT: B 498 LYS cc_start: 0.7756 (ttmt) cc_final: 0.7019 (tptt) REVERT: C 124 LYS cc_start: 0.7786 (mmtm) cc_final: 0.7446 (mttm) REVERT: C 215 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8099 (mm110) REVERT: C 224 ASP cc_start: 0.8321 (t0) cc_final: 0.7681 (t0) REVERT: C 426 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: C 471 HIS cc_start: 0.5819 (t70) cc_final: 0.5131 (t-170) REVERT: E 29 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6740 (p0) REVERT: E 340 ARG cc_start: 0.8275 (mtp-110) cc_final: 0.8067 (mtt-85) REVERT: F 112 LYS cc_start: 0.8282 (mttt) cc_final: 0.7969 (mttp) REVERT: F 174 ASN cc_start: 0.8361 (t0) cc_final: 0.7770 (t0) REVERT: F 202 GLU cc_start: 0.8546 (tt0) cc_final: 0.8296 (pt0) REVERT: F 205 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7389 (mp0) REVERT: F 210 ASN cc_start: 0.8640 (t0) cc_final: 0.8364 (t0) REVERT: F 400 SER cc_start: 0.7850 (OUTLIER) cc_final: 0.7439 (p) REVERT: F 451 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8114 (mt-10) REVERT: D 249 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: D 475 LYS cc_start: 0.7356 (ttpt) cc_final: 0.7022 (tmtt) REVERT: G 233 ASP cc_start: 0.7864 (t70) cc_final: 0.7635 (t70) REVERT: O 15 GLU cc_start: 0.7025 (mp0) cc_final: 0.6575 (pt0) REVERT: O 136 THR cc_start: 0.7244 (m) cc_final: 0.7009 (p) outliers start: 46 outliers final: 19 residues processed: 340 average time/residue: 0.6489 time to fit residues: 250.0242 Evaluate side-chains 320 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 296 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 43 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097845 restraints weight = 31327.477| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.76 r_work: 0.3050 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24307 Z= 0.128 Angle : 0.511 11.218 32878 Z= 0.261 Chirality : 0.043 0.143 3827 Planarity : 0.004 0.042 4250 Dihedral : 7.059 152.463 3506 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.19 % Rotamer: Outliers : 1.54 % Allowed : 15.87 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 aren not related in a simple way. whole: 0.95 (0.15), residues: 3102 helix: 1.72 (0.14), residues: 1325 sheet: -0.33 (0.23), residues: 503 loop : -0.03 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 373 TYR 0.022 0.001 TYR B 446 PHE 0.026 0.001 PHE C 468 HIS 0.015 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00296 (24307) covalent geometry : angle 0.51136 (32878) hydrogen bonds : bond 0.04065 ( 1135) hydrogen bonds : angle 4.66661 ( 3231) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 299 time to evaluate : 0.672 Fit side-chains REVERT: A 355 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7919 (tt0) REVERT: B 353 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8060 (mm-30) REVERT: B 415 GLN cc_start: 0.6637 (mt0) cc_final: 0.6367 (mt0) REVERT: B 466 ASN cc_start: 0.8129 (m-40) cc_final: 0.7919 (m110) REVERT: B 498 LYS cc_start: 0.7768 (ttmt) cc_final: 0.7133 (tmtt) REVERT: C 124 LYS cc_start: 0.7798 (mmtm) cc_final: 0.7461 (mttm) REVERT: C 215 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8113 (mm110) REVERT: C 224 ASP cc_start: 0.8348 (t0) cc_final: 0.7694 (t0) REVERT: C 426 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: C 471 HIS cc_start: 0.5873 (t70) cc_final: 0.5193 (t-170) REVERT: E 29 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6785 (p0) REVERT: F 112 LYS cc_start: 0.8264 (mttt) cc_final: 0.7957 (mttp) REVERT: F 174 ASN cc_start: 0.8371 (t0) cc_final: 0.7830 (t0) REVERT: F 202 GLU cc_start: 0.8592 (tt0) cc_final: 0.8343 (pt0) REVERT: F 205 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7442 (mp0) REVERT: F 210 ASN cc_start: 0.8628 (t0) cc_final: 0.8357 (t0) REVERT: F 400 SER cc_start: 0.7852 (OUTLIER) cc_final: 0.7404 (p) REVERT: F 451 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: D 249 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: D 431 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7056 (tpt) REVERT: D 475 LYS cc_start: 0.7315 (ttpt) cc_final: 0.6959 (tmtt) REVERT: G 233 ASP cc_start: 0.7890 (t70) cc_final: 0.7666 (t70) REVERT: O 15 GLU cc_start: 0.7047 (mp0) cc_final: 0.6648 (pt0) REVERT: O 136 THR cc_start: 0.7291 (m) cc_final: 0.6935 (p) REVERT: O 139 LYS cc_start: 0.6701 (ptmm) cc_final: 0.5846 (tptp) outliers start: 39 outliers final: 23 residues processed: 324 average time/residue: 0.6491 time to fit residues: 237.5887 Evaluate side-chains 323 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 294 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 171 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 217 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 68 optimal weight: 0.0030 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 87 optimal weight: 0.0030 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097123 restraints weight = 31579.080| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.76 r_work: 0.3039 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24307 Z= 0.145 Angle : 0.527 10.835 32878 Z= 0.268 Chirality : 0.043 0.141 3827 Planarity : 0.004 0.043 4250 Dihedral : 7.183 155.314 3506 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer: Outliers : 1.50 % Allowed : 16.11 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 aren not related in a simple way. whole: 0.91 (0.15), residues: 3102 helix: 1.68 (0.14), residues: 1331 sheet: -0.35 (0.24), residues: 482 loop : -0.05 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 373 TYR 0.021 0.001 TYR B 446 PHE 0.017 0.001 PHE J 34 HIS 0.017 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00341 (24307) covalent geometry : angle 0.52650 (32878) hydrogen bonds : bond 0.04230 ( 1135) hydrogen bonds : angle 4.70683 ( 3231) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 293 time to evaluate : 0.698 Fit side-chains REVERT: A 52 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8625 (mmm) REVERT: A 355 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7931 (tt0) REVERT: B 353 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8063 (mm-30) REVERT: B 466 ASN cc_start: 0.8130 (m-40) cc_final: 0.7918 (m110) REVERT: B 498 LYS cc_start: 0.7770 (ttmt) cc_final: 0.7114 (tptt) REVERT: C 124 LYS cc_start: 0.7806 (mmtm) cc_final: 0.7463 (mttm) REVERT: C 215 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8122 (mm110) REVERT: C 224 ASP cc_start: 0.8370 (t0) cc_final: 0.7709 (t0) REVERT: C 426 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: C 471 HIS cc_start: 0.5889 (t70) cc_final: 0.5211 (t-170) REVERT: E 29 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.6823 (p0) REVERT: F 112 LYS cc_start: 0.8267 (mttt) cc_final: 0.7975 (mttp) REVERT: F 174 ASN cc_start: 0.8378 (t0) cc_final: 0.7836 (t0) REVERT: F 205 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7453 (mp0) REVERT: F 210 ASN cc_start: 0.8647 (t0) cc_final: 0.8361 (t0) REVERT: F 400 SER cc_start: 0.7891 (OUTLIER) cc_final: 0.7413 (p) REVERT: F 451 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: D 249 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7513 (mp10) REVERT: D 431 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7033 (tpt) REVERT: D 475 LYS cc_start: 0.7312 (ttpt) cc_final: 0.6959 (tmtt) REVERT: G 233 ASP cc_start: 0.7885 (t70) cc_final: 0.7661 (t70) REVERT: O 15 GLU cc_start: 0.7048 (mp0) cc_final: 0.6681 (pt0) REVERT: O 136 THR cc_start: 0.7325 (m) cc_final: 0.6977 (p) REVERT: O 139 LYS cc_start: 0.6739 (ptmm) cc_final: 0.5893 (tptp) outliers start: 38 outliers final: 25 residues processed: 315 average time/residue: 0.6626 time to fit residues: 235.8383 Evaluate side-chains 322 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 290 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 295 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 264 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 306 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 208 optimal weight: 0.8980 chunk 171 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098927 restraints weight = 31502.265| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.76 r_work: 0.3052 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24307 Z= 0.114 Angle : 0.503 10.779 32878 Z= 0.255 Chirality : 0.042 0.141 3827 Planarity : 0.004 0.042 4250 Dihedral : 6.942 155.264 3506 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.71 % Favored : 98.26 % Rotamer: Outliers : 1.26 % Allowed : 16.07 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 aren not related in a simple way. whole: 1.08 (0.15), residues: 3102 helix: 1.82 (0.14), residues: 1325 sheet: -0.20 (0.23), residues: 497 loop : 0.03 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 373 TYR 0.023 0.001 TYR B 446 PHE 0.030 0.001 PHE C 468 HIS 0.017 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00258 (24307) covalent geometry : angle 0.50255 (32878) hydrogen bonds : bond 0.03866 ( 1135) hydrogen bonds : angle 4.62572 ( 3231) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7902 (tt0) REVERT: B 393 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7896 (mm-30) REVERT: B 415 GLN cc_start: 0.6750 (mt0) cc_final: 0.6211 (mt0) REVERT: B 498 LYS cc_start: 0.7826 (ttmt) cc_final: 0.7089 (tptt) REVERT: C 124 LYS cc_start: 0.7798 (mmtm) cc_final: 0.7455 (mttm) REVERT: C 215 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8115 (mm110) REVERT: C 224 ASP cc_start: 0.8346 (t0) cc_final: 0.7719 (t0) REVERT: C 426 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: C 471 HIS cc_start: 0.5880 (t70) cc_final: 0.5505 (t-90) REVERT: E 29 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6815 (p0) REVERT: F 112 LYS cc_start: 0.8302 (mttt) cc_final: 0.8010 (mttp) REVERT: F 174 ASN cc_start: 0.8370 (t0) cc_final: 0.7820 (t0) REVERT: F 202 GLU cc_start: 0.8556 (tt0) cc_final: 0.8339 (pt0) REVERT: F 205 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7405 (mp0) REVERT: F 400 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7448 (p) REVERT: F 408 SER cc_start: 0.8564 (t) cc_final: 0.8349 (p) REVERT: F 451 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: D 249 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: D 431 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6988 (tpt) REVERT: D 475 LYS cc_start: 0.7298 (ttpt) cc_final: 0.6950 (tmtt) REVERT: G 233 ASP cc_start: 0.7864 (t70) cc_final: 0.7644 (t70) REVERT: O 15 GLU cc_start: 0.7074 (mp0) cc_final: 0.6713 (pt0) REVERT: O 136 THR cc_start: 0.7295 (m) cc_final: 0.6935 (p) REVERT: O 139 LYS cc_start: 0.6693 (ptmm) cc_final: 0.5930 (tptp) outliers start: 32 outliers final: 21 residues processed: 319 average time/residue: 0.6775 time to fit residues: 244.1737 Evaluate side-chains 317 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 201 optimal weight: 6.9990 chunk 252 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 304 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 147 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.100109 restraints weight = 31312.288| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.76 r_work: 0.3067 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24307 Z= 0.119 Angle : 0.511 13.355 32878 Z= 0.259 Chirality : 0.042 0.139 3827 Planarity : 0.004 0.042 4250 Dihedral : 6.951 156.513 3506 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.71 % Favored : 98.26 % Rotamer: Outliers : 1.42 % Allowed : 16.38 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 aren not related in a simple way. whole: 1.11 (0.15), residues: 3102 helix: 1.84 (0.14), residues: 1325 sheet: -0.19 (0.23), residues: 497 loop : 0.05 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.023 0.001 TYR B 446 PHE 0.016 0.001 PHE J 34 HIS 0.019 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00273 (24307) covalent geometry : angle 0.51129 (32878) hydrogen bonds : bond 0.03903 ( 1135) hydrogen bonds : angle 4.62389 ( 3231) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8369.86 seconds wall clock time: 143 minutes 4.86 seconds (8584.86 seconds total)