Starting phenix.real_space_refine on Fri May 23 09:49:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9l_34572/05_2025/8h9l_34572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9l_34572/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h9l_34572/05_2025/8h9l_34572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9l_34572/05_2025/8h9l_34572.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9l_34572/05_2025/8h9l_34572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9l_34572/05_2025/8h9l_34572.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.17, per 1000 atoms: 0.22 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: 5.52 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 2.89 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: 9.15 Time building geometry restraints manager: 6.58 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: 32.300 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 56.580 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.120 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.980 ------------------------------------------------------------------------------- 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 : 7.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.005 0.001 HIS F 201 PHE 0.025 0.002 PHE J 34 TYR 0.015 0.002 TYR A 452 ARG 0.009 0.001 ARG F 277 Details of bonding type rmsd hydrogen bonds : bond 0.14764 ( 1135) hydrogen bonds : angle 6.91264 ( 3231) covalent geometry : bond 0.01091 (24307) covalent geometry : angle 0.87373 (32878) *********************** 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 : 2.790 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: 0.5501 (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: 1.7495 time to fit residues: 755.9107 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 : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.5980 chunk 234 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 242 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 180 optimal weight: 6.9990 chunk 280 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100905 restraints weight = 31371.039| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.72 r_work: 0.3091 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24307 Z= 0.116 Angle : 0.520 10.280 32878 Z= 0.269 Chirality : 0.043 0.150 3827 Planarity : 0.004 0.041 4250 Dihedral : 7.636 136.450 3506 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % Rotamer: Outliers : 1.34 % Allowed : 10.28 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3102 helix: 0.53 (0.14), residues: 1326 sheet: -0.73 (0.22), residues: 489 loop : -0.70 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 476 PHE 0.017 0.001 PHE C 468 TYR 0.012 0.001 TYR C 397 ARG 0.006 0.000 ARG F 15 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 1135) hydrogen bonds : angle 5.05566 ( 3231) covalent geometry : bond 0.00250 (24307) covalent geometry : angle 0.51957 (32878) *********************** 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 : 2.866 Fit side-chains REVERT: A 52 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8538 (mmm) REVERT: B 67 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: B 353 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8097 (mm-30) REVERT: B 498 LYS cc_start: 0.7727 (ttmt) cc_final: 0.7090 (tptt) REVERT: C 124 LYS cc_start: 0.7803 (mmtm) cc_final: 0.7497 (mttm) REVERT: C 194 ASP cc_start: 0.7632 (p0) cc_final: 0.7378 (p0) REVERT: C 471 HIS cc_start: 0.5844 (t70) cc_final: 0.5142 (t-170) REVERT: F 112 LYS cc_start: 0.8325 (mttt) cc_final: 0.7985 (mttp) REVERT: F 174 ASN cc_start: 0.8372 (t0) cc_final: 0.7812 (t0) REVERT: F 205 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7514 (mp0) REVERT: F 210 ASN cc_start: 0.8761 (t0) cc_final: 0.8385 (t0) REVERT: F 397 ASP cc_start: 0.7496 (m-30) cc_final: 0.7123 (m-30) REVERT: F 400 SER cc_start: 0.7950 (OUTLIER) cc_final: 0.7468 (p) REVERT: D 249 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: D 390 ILE cc_start: 0.8032 (mt) cc_final: 0.7798 (mm) REVERT: D 431 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7240 (tpt) REVERT: D 475 LYS cc_start: 0.7420 (ttpt) cc_final: 0.7065 (tmtt) REVERT: G 233 ASP cc_start: 0.7808 (t70) cc_final: 0.7595 (t70) REVERT: O 136 THR cc_start: 0.7339 (m) cc_final: 0.7097 (p) outliers start: 34 outliers final: 11 residues processed: 367 average time/residue: 1.5392 time to fit residues: 638.2117 Evaluate side-chains 317 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 301 time to evaluate : 2.502 ------------------------------------------------------------------------------- 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 192 optimal weight: 6.9990 chunk 293 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 123 optimal weight: 0.0270 chunk 303 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.097382 restraints weight = 31253.802| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.75 r_work: 0.3049 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1689 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= 0.133 Angle : 0.512 11.078 32878 Z= 0.263 Chirality : 0.043 0.138 3827 Planarity : 0.004 0.041 4250 Dihedral : 7.169 137.494 3506 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.64 % Favored : 98.32 % Rotamer: Outliers : 1.77 % Allowed : 12.33 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3102 helix: 1.20 (0.14), residues: 1327 sheet: -0.57 (0.23), residues: 480 loop : -0.38 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 476 PHE 0.018 0.001 PHE J 34 TYR 0.011 0.001 TYR O 170 ARG 0.007 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 1135) hydrogen bonds : angle 4.79764 ( 3231) covalent geometry : bond 0.00305 (24307) covalent geometry : angle 0.51204 (32878) *********************** 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 367 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 322 time to evaluate : 2.704 Fit side-chains REVERT: A 355 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7947 (tt0) REVERT: B 67 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: B 353 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8067 (mm-30) REVERT: B 475 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7021 (mp10) REVERT: B 498 LYS cc_start: 0.7773 (ttmt) cc_final: 0.7145 (tptt) REVERT: C 124 LYS cc_start: 0.7781 (mmtm) cc_final: 0.7444 (mttm) REVERT: C 224 ASP cc_start: 0.8332 (t0) cc_final: 0.7693 (t0) REVERT: C 471 HIS cc_start: 0.5795 (t70) cc_final: 0.5096 (t-170) REVERT: F 112 LYS cc_start: 0.8299 (mttt) cc_final: 0.7986 (mttp) REVERT: F 174 ASN cc_start: 0.8350 (t0) cc_final: 0.7838 (t0) REVERT: F 205 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7459 (mp0) REVERT: F 210 ASN cc_start: 0.8711 (t0) cc_final: 0.8302 (t0) REVERT: F 400 SER cc_start: 0.7907 (OUTLIER) cc_final: 0.7419 (p) REVERT: F 451 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: D 475 LYS cc_start: 0.7381 (ttpt) cc_final: 0.7024 (tmtt) REVERT: O 15 GLU cc_start: 0.7156 (mp0) cc_final: 0.6776 (mp0) REVERT: O 136 THR cc_start: 0.7256 (m) cc_final: 0.7003 (p) outliers start: 45 outliers final: 19 residues processed: 344 average time/residue: 1.5720 time to fit residues: 612.6243 Evaluate side-chains 326 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 303 time to evaluate : 2.841 ------------------------------------------------------------------------------- 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 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 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 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 184 SER Chi-restraints excluded: chain D residue 212 LYS 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 201 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 304 optimal weight: 8.9990 chunk 256 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN C 78 ASN E 388 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 42 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 = 0.3446 r_free = 0.3446 target = 0.122275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.094535 restraints weight = 31638.580| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.72 r_work: 0.2951 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 24307 Z= 0.239 Angle : 0.586 11.594 32878 Z= 0.300 Chirality : 0.046 0.158 3827 Planarity : 0.004 0.045 4250 Dihedral : 7.807 143.642 3506 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 2.28 % Allowed : 13.00 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3102 helix: 1.15 (0.14), residues: 1328 sheet: -0.56 (0.23), residues: 499 loop : -0.35 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 454 PHE 0.019 0.002 PHE J 34 TYR 0.011 0.002 TYR O 170 ARG 0.005 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.05119 ( 1135) hydrogen bonds : angle 4.96581 ( 3231) covalent geometry : bond 0.00580 (24307) covalent geometry : angle 0.58619 (32878) *********************** 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 360 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 302 time to evaluate : 2.604 Fit side-chains REVERT: A 355 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7882 (tt0) REVERT: B 67 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8299 (mt-10) REVERT: B 353 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8056 (mm-30) REVERT: B 475 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.6945 (mp10) REVERT: B 498 LYS cc_start: 0.7660 (ttmt) cc_final: 0.7028 (tptt) REVERT: C 124 LYS cc_start: 0.7809 (mmtm) cc_final: 0.7457 (mttm) REVERT: C 224 ASP cc_start: 0.8341 (t0) cc_final: 0.7613 (t0) REVERT: C 426 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: C 471 HIS cc_start: 0.5789 (t70) cc_final: 0.5086 (t-170) REVERT: E 29 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6703 (p0) REVERT: F 112 LYS cc_start: 0.8223 (mttt) cc_final: 0.7899 (mttp) REVERT: F 205 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7467 (mp0) REVERT: D 249 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: D 431 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7055 (tpt) REVERT: D 475 LYS cc_start: 0.7253 (ttpt) cc_final: 0.6896 (tmtt) REVERT: O 15 GLU cc_start: 0.7088 (mp0) cc_final: 0.6642 (mp0) REVERT: O 136 THR cc_start: 0.7354 (m) cc_final: 0.7133 (p) outliers start: 58 outliers final: 30 residues processed: 337 average time/residue: 1.5943 time to fit residues: 606.3052 Evaluate side-chains 324 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 2.468 ------------------------------------------------------------------------------- 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 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 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 E residue 438 LYS 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 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 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 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 84 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 254 optimal weight: 0.9980 chunk 233 optimal weight: 0.0470 chunk 98 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099740 restraints weight = 31525.545| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.78 r_work: 0.3066 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24307 Z= 0.106 Angle : 0.489 12.015 32878 Z= 0.249 Chirality : 0.042 0.151 3827 Planarity : 0.003 0.041 4250 Dihedral : 6.975 139.997 3506 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.64 % Favored : 98.32 % Rotamer: Outliers : 1.54 % Allowed : 14.53 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 3102 helix: 1.64 (0.14), residues: 1325 sheet: -0.17 (0.24), residues: 467 loop : -0.22 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 454 PHE 0.017 0.001 PHE J 34 TYR 0.021 0.001 TYR B 446 ARG 0.005 0.000 ARG E 340 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 1135) hydrogen bonds : angle 4.67991 ( 3231) covalent geometry : bond 0.00229 (24307) covalent geometry : angle 0.48855 (32878) *********************** 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 364 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 325 time to evaluate : 2.975 Fit side-chains REVERT: A 355 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7933 (tt0) REVERT: A 403 PHE cc_start: 0.7172 (m-80) cc_final: 0.6963 (m-80) REVERT: B 353 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8025 (mm-30) REVERT: B 415 GLN cc_start: 0.6670 (mt0) cc_final: 0.5947 (mt0) REVERT: B 454 ASP cc_start: 0.7886 (m-30) cc_final: 0.7522 (m-30) REVERT: B 498 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7132 (tptt) REVERT: C 124 LYS cc_start: 0.7760 (mmtm) cc_final: 0.7417 (mttm) REVERT: C 224 ASP cc_start: 0.8308 (t0) cc_final: 0.7645 (t0) REVERT: C 426 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: C 471 HIS cc_start: 0.5785 (t70) cc_final: 0.5050 (t-170) REVERT: E 340 ARG cc_start: 0.8285 (mtp-110) cc_final: 0.8060 (mtt-85) REVERT: F 112 LYS cc_start: 0.8287 (mttt) cc_final: 0.7970 (mttp) REVERT: F 174 ASN cc_start: 0.8323 (t0) cc_final: 0.7779 (t0) REVERT: F 205 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7410 (mp0) REVERT: F 210 ASN cc_start: 0.8670 (t0) cc_final: 0.8299 (t0) REVERT: F 400 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7446 (p) REVERT: F 405 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7987 (tp) REVERT: F 408 SER cc_start: 0.8552 (t) cc_final: 0.8331 (p) REVERT: D 205 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7237 (tp30) REVERT: D 249 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7551 (mp10) REVERT: D 475 LYS cc_start: 0.7382 (ttpt) cc_final: 0.7034 (tmtt) REVERT: G 241 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: O 15 GLU cc_start: 0.7015 (mp0) cc_final: 0.6577 (pt0) REVERT: O 103 SER cc_start: 0.7251 (t) cc_final: 0.6816 (p) REVERT: O 136 THR cc_start: 0.7173 (m) cc_final: 0.6941 (p) outliers start: 39 outliers final: 14 residues processed: 349 average time/residue: 1.5065 time to fit residues: 594.7072 Evaluate side-chains 323 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 303 time to evaluate : 2.668 ------------------------------------------------------------------------------- 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 54 GLU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU 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 405 LEU 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 249 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 241 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 31 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 243 optimal weight: 0.2980 chunk 263 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** B 466 ASN E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.097591 restraints weight = 31341.528| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.76 r_work: 0.3046 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1942 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= 0.133 Angle : 0.506 10.738 32878 Z= 0.259 Chirality : 0.043 0.145 3827 Planarity : 0.004 0.042 4250 Dihedral : 7.015 144.059 3506 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % Rotamer: Outliers : 1.73 % Allowed : 14.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.15), residues: 3102 helix: 1.69 (0.14), residues: 1325 sheet: -0.25 (0.24), residues: 449 loop : -0.13 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 454 PHE 0.018 0.001 PHE C 468 TYR 0.020 0.001 TYR B 446 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 1135) hydrogen bonds : angle 4.67809 ( 3231) covalent geometry : bond 0.00309 (24307) covalent geometry : angle 0.50645 (32878) *********************** 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: 44 poor density : 306 time to evaluate : 2.916 Fit side-chains REVERT: A 355 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7945 (tt0) REVERT: B 353 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8060 (mm-30) REVERT: B 415 GLN cc_start: 0.6674 (mt0) cc_final: 0.5958 (mt0) REVERT: B 454 ASP cc_start: 0.7889 (m-30) cc_final: 0.7509 (m-30) REVERT: B 498 LYS cc_start: 0.7784 (ttmt) cc_final: 0.7062 (tptt) REVERT: C 124 LYS cc_start: 0.7773 (mmtm) cc_final: 0.7432 (mttm) REVERT: C 224 ASP cc_start: 0.8329 (t0) cc_final: 0.7633 (t0) REVERT: C 426 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: C 471 HIS cc_start: 0.5783 (t70) cc_final: 0.5036 (t-170) REVERT: E 29 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6764 (p0) REVERT: E 340 ARG cc_start: 0.8330 (mtp-110) cc_final: 0.8056 (mtt-85) REVERT: F 112 LYS cc_start: 0.8271 (mttt) cc_final: 0.7977 (mttp) REVERT: F 174 ASN cc_start: 0.8352 (t0) cc_final: 0.7818 (t0) REVERT: F 205 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7408 (mp0) REVERT: F 400 SER cc_start: 0.7890 (OUTLIER) cc_final: 0.7414 (p) REVERT: F 451 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: D 205 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7205 (tp30) REVERT: D 249 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7517 (mp10) REVERT: D 431 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7007 (tpt) REVERT: D 475 LYS cc_start: 0.7396 (ttpt) cc_final: 0.7048 (tmtt) REVERT: O 15 GLU cc_start: 0.7042 (mp0) cc_final: 0.6599 (pt0) REVERT: O 136 THR cc_start: 0.7236 (m) cc_final: 0.7007 (p) REVERT: O 168 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6848 (tt0) outliers start: 44 outliers final: 22 residues processed: 333 average time/residue: 1.5705 time to fit residues: 597.5993 Evaluate side-chains 328 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 299 time to evaluate : 2.755 ------------------------------------------------------------------------------- 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 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 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 127 MET 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 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 O residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 169 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 300 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 264 optimal weight: 0.3980 chunk 179 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 458 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099611 restraints weight = 31411.144| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.76 r_work: 0.3058 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24307 Z= 0.122 Angle : 0.499 12.285 32878 Z= 0.254 Chirality : 0.043 0.142 3827 Planarity : 0.003 0.041 4250 Dihedral : 6.934 145.306 3506 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.87 % Favored : 98.10 % Rotamer: Outliers : 1.69 % Allowed : 15.48 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.15), residues: 3102 helix: 1.78 (0.14), residues: 1325 sheet: -0.16 (0.24), residues: 458 loop : -0.07 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS B 476 PHE 0.016 0.001 PHE J 34 TYR 0.021 0.001 TYR B 446 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 1135) hydrogen bonds : angle 4.64893 ( 3231) covalent geometry : bond 0.00279 (24307) covalent geometry : angle 0.49926 (32878) *********************** 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 350 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 307 time to evaluate : 2.614 Fit side-chains revert: symmetry clash REVERT: A 355 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7932 (tt0) REVERT: B 67 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: B 353 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8075 (mm-30) REVERT: B 415 GLN cc_start: 0.6666 (mt0) cc_final: 0.5967 (mt0) REVERT: B 454 ASP cc_start: 0.7908 (m-30) cc_final: 0.7508 (m-30) REVERT: B 498 LYS cc_start: 0.7792 (ttmt) cc_final: 0.7051 (tptt) REVERT: C 124 LYS cc_start: 0.7767 (mmtm) cc_final: 0.7429 (mttm) REVERT: C 224 ASP cc_start: 0.8340 (t0) cc_final: 0.7671 (t0) REVERT: C 426 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: C 471 HIS cc_start: 0.5874 (t70) cc_final: 0.5174 (t-170) REVERT: E 29 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6788 (p0) REVERT: E 340 ARG cc_start: 0.8326 (mtp-110) cc_final: 0.8064 (mtt-85) REVERT: F 112 LYS cc_start: 0.8279 (mttt) cc_final: 0.7990 (mttp) REVERT: F 174 ASN cc_start: 0.8335 (t0) cc_final: 0.7817 (t0) REVERT: F 205 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7398 (mp0) REVERT: F 400 SER cc_start: 0.7871 (OUTLIER) cc_final: 0.7419 (p) REVERT: F 408 SER cc_start: 0.8593 (t) cc_final: 0.8359 (p) REVERT: F 451 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: D 249 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: D 431 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6990 (tpt) REVERT: D 475 LYS cc_start: 0.7381 (ttpt) cc_final: 0.7026 (tmtt) REVERT: G 25 MET cc_start: 0.8319 (mmp) cc_final: 0.8116 (mmm) REVERT: O 15 GLU cc_start: 0.7015 (mp0) cc_final: 0.6600 (pt0) REVERT: O 136 THR cc_start: 0.7267 (m) cc_final: 0.7034 (p) REVERT: O 168 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6989 (tt0) outliers start: 43 outliers final: 23 residues processed: 333 average time/residue: 1.5353 time to fit residues: 578.1144 Evaluate side-chains 334 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 304 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 67 GLU 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 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 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 D residue 467 GLU 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 227 optimal weight: 0.7980 chunk 167 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 274 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 271 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- 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 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.123775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.096501 restraints weight = 31411.580| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.68 r_work: 0.2999 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24307 Z= 0.218 Angle : 0.575 11.443 32878 Z= 0.293 Chirality : 0.046 0.167 3827 Planarity : 0.004 0.043 4250 Dihedral : 7.570 152.831 3506 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.32 % Favored : 97.65 % Rotamer: Outliers : 1.61 % Allowed : 15.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3102 helix: 1.51 (0.14), residues: 1329 sheet: -0.34 (0.24), residues: 476 loop : -0.12 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.001 HIS B 476 PHE 0.022 0.002 PHE C 468 TYR 0.020 0.002 TYR B 446 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04859 ( 1135) hydrogen bonds : angle 4.84488 ( 3231) covalent geometry : bond 0.00527 (24307) covalent geometry : angle 0.57466 (32878) *********************** 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 332 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 291 time to evaluate : 2.558 Fit side-chains REVERT: A 355 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7856 (tt0) REVERT: A 403 PHE cc_start: 0.7117 (m-80) cc_final: 0.6826 (m-80) REVERT: B 67 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: B 353 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8037 (mm-30) REVERT: B 415 GLN cc_start: 0.6559 (mt0) cc_final: 0.6206 (mt0) REVERT: B 454 ASP cc_start: 0.8052 (m-30) cc_final: 0.7773 (m-30) REVERT: B 498 LYS cc_start: 0.7708 (ttmt) cc_final: 0.6981 (tptt) REVERT: C 124 LYS cc_start: 0.7775 (mmtm) cc_final: 0.7411 (mttm) REVERT: C 224 ASP cc_start: 0.8360 (t0) cc_final: 0.7604 (t0) REVERT: C 426 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: C 471 HIS cc_start: 0.5919 (t70) cc_final: 0.5191 (t-170) REVERT: E 29 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.6831 (p0) REVERT: E 340 ARG cc_start: 0.8317 (mtp-110) cc_final: 0.8069 (mtt-85) REVERT: F 112 LYS cc_start: 0.8250 (mttt) cc_final: 0.7951 (mttp) REVERT: F 174 ASN cc_start: 0.8388 (t0) cc_final: 0.7760 (t0) REVERT: F 205 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7463 (mp0) REVERT: D 205 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7192 (tp30) REVERT: D 249 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7471 (mp10) REVERT: D 431 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.7035 (tpt) REVERT: D 475 LYS cc_start: 0.7360 (ttpt) cc_final: 0.7010 (tmtt) REVERT: O 15 GLU cc_start: 0.7058 (mp0) cc_final: 0.6599 (pt0) REVERT: O 136 THR cc_start: 0.7326 (m) cc_final: 0.7107 (p) REVERT: O 168 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6872 (tt0) outliers start: 41 outliers final: 26 residues processed: 313 average time/residue: 1.5555 time to fit residues: 557.6062 Evaluate side-chains 317 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 285 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 67 GLU 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 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 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 O residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 299 optimal weight: 5.9990 chunk 275 optimal weight: 8.9990 chunk 294 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 179 optimal weight: 0.8980 chunk 53 optimal weight: 0.0970 chunk 209 optimal weight: 0.9980 overall best weight: 0.6076 ------------------------------------------------------------------------------- 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** B 466 ASN E 224 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 = 0.3524 r_free = 0.3524 target = 0.127546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099522 restraints weight = 31366.838| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.76 r_work: 0.3074 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24307 Z= 0.102 Angle : 0.493 11.459 32878 Z= 0.251 Chirality : 0.042 0.157 3827 Planarity : 0.003 0.041 4250 Dihedral : 6.899 150.137 3506 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 1.46 % Allowed : 15.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 3102 helix: 1.86 (0.14), residues: 1320 sheet: -0.14 (0.24), residues: 458 loop : -0.05 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.001 HIS B 476 PHE 0.016 0.001 PHE J 34 TYR 0.022 0.001 TYR B 446 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 1135) hydrogen bonds : angle 4.62893 ( 3231) covalent geometry : bond 0.00223 (24307) covalent geometry : angle 0.49342 (32878) *********************** 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 350 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 313 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7914 (tt0) REVERT: A 403 PHE cc_start: 0.7193 (m-80) cc_final: 0.6937 (m-80) REVERT: A 461 ILE cc_start: 0.8615 (mm) cc_final: 0.8325 (mm) REVERT: B 353 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8052 (mm-30) REVERT: B 415 GLN cc_start: 0.6661 (mt0) cc_final: 0.5966 (mt0) REVERT: B 454 ASP cc_start: 0.7900 (m-30) cc_final: 0.7505 (m-30) REVERT: B 496 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7696 (ttmm) REVERT: B 498 LYS cc_start: 0.7763 (ttmt) cc_final: 0.7013 (tptt) REVERT: C 124 LYS cc_start: 0.7786 (mmtm) cc_final: 0.7449 (mttm) REVERT: C 224 ASP cc_start: 0.8336 (t0) cc_final: 0.7666 (t0) REVERT: C 426 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: C 471 HIS cc_start: 0.5880 (t70) cc_final: 0.5173 (t-170) REVERT: E 29 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6860 (p0) REVERT: E 340 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.8088 (mtt-85) REVERT: F 112 LYS cc_start: 0.8296 (mttt) cc_final: 0.8009 (mttp) REVERT: F 174 ASN cc_start: 0.8311 (t0) cc_final: 0.7810 (t0) REVERT: F 202 GLU cc_start: 0.8573 (tt0) cc_final: 0.8361 (pt0) REVERT: F 205 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7391 (mp0) REVERT: F 400 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7466 (p) REVERT: D 205 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7097 (tp30) REVERT: D 249 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: D 431 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6980 (tpt) REVERT: D 475 LYS cc_start: 0.7294 (ttpt) cc_final: 0.6941 (tmtt) REVERT: O 15 GLU cc_start: 0.7026 (mp0) cc_final: 0.6671 (pt0) REVERT: O 136 THR cc_start: 0.7269 (m) cc_final: 0.6900 (p) REVERT: O 139 LYS cc_start: 0.6709 (ptmm) cc_final: 0.6064 (tptp) REVERT: O 165 ARG cc_start: 0.6699 (ttt-90) cc_final: 0.6083 (tpt-90) REVERT: O 168 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6989 (tt0) outliers start: 37 outliers final: 18 residues processed: 335 average time/residue: 1.5239 time to fit residues: 577.0893 Evaluate side-chains 332 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 307 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LYS 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 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 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 205 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 136 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 68 optimal weight: 0.0470 chunk 166 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- 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** E 210 ASN E 224 GLN F 458 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101944 restraints weight = 31263.042| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.70 r_work: 0.3080 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24307 Z= 0.110 Angle : 0.496 11.319 32878 Z= 0.252 Chirality : 0.042 0.151 3827 Planarity : 0.003 0.041 4250 Dihedral : 6.832 150.629 3506 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.61 % Favored : 98.36 % Rotamer: Outliers : 1.14 % Allowed : 16.35 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 3102 helix: 1.93 (0.14), residues: 1320 sheet: -0.14 (0.24), residues: 461 loop : 0.03 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.001 HIS B 476 PHE 0.029 0.001 PHE C 468 TYR 0.022 0.001 TYR B 446 ARG 0.007 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 1135) hydrogen bonds : angle 4.57481 ( 3231) covalent geometry : bond 0.00249 (24307) covalent geometry : angle 0.49582 (32878) ********************** 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 337 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 308 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ILE cc_start: 0.8813 (tp) cc_final: 0.8555 (tt) REVERT: A 355 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7894 (tt0) REVERT: B 415 GLN cc_start: 0.6608 (mt0) cc_final: 0.6332 (mt0) REVERT: B 454 ASP cc_start: 0.7839 (m-30) cc_final: 0.7523 (m-30) REVERT: B 496 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7670 (ttmm) REVERT: B 498 LYS cc_start: 0.7744 (ttmt) cc_final: 0.7076 (tptt) REVERT: C 124 LYS cc_start: 0.7775 (mmtm) cc_final: 0.7457 (mttm) REVERT: C 224 ASP cc_start: 0.8307 (t0) cc_final: 0.7665 (t0) REVERT: C 426 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: C 471 HIS cc_start: 0.5873 (t70) cc_final: 0.5168 (t-170) REVERT: E 29 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6834 (p0) REVERT: E 340 ARG cc_start: 0.8326 (mtp-110) cc_final: 0.8091 (mtt-85) REVERT: F 112 LYS cc_start: 0.8288 (mttt) cc_final: 0.8021 (mttp) REVERT: F 174 ASN cc_start: 0.8273 (t0) cc_final: 0.7788 (t0) REVERT: F 202 GLU cc_start: 0.8549 (tt0) cc_final: 0.8329 (pt0) REVERT: F 205 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7360 (mp0) REVERT: F 400 SER cc_start: 0.7813 (OUTLIER) cc_final: 0.7431 (p) REVERT: D 205 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7041 (tp30) REVERT: D 249 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7518 (mp10) REVERT: D 431 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.6999 (tpt) REVERT: D 453 ASP cc_start: 0.7924 (m-30) cc_final: 0.7473 (m-30) REVERT: D 475 LYS cc_start: 0.7258 (ttpt) cc_final: 0.6907 (tmtt) REVERT: O 15 GLU cc_start: 0.7022 (mp0) cc_final: 0.6657 (pt0) REVERT: O 103 SER cc_start: 0.7217 (t) cc_final: 0.6813 (p) REVERT: O 136 THR cc_start: 0.7264 (m) cc_final: 0.6891 (p) REVERT: O 139 LYS cc_start: 0.6697 (ptmm) cc_final: 0.5932 (tptp) outliers start: 29 outliers final: 18 residues processed: 324 average time/residue: 1.5291 time to fit residues: 561.5179 Evaluate side-chains 329 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 304 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LYS 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 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 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 205 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 36 optimal weight: 0.6980 chunk 269 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 87 optimal weight: 0.3980 chunk 261 optimal weight: 2.9990 chunk 183 optimal weight: 0.1980 chunk 293 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.100379 restraints weight = 31209.593| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.75 r_work: 0.3069 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24307 Z= 0.122 Angle : 0.506 11.259 32878 Z= 0.257 Chirality : 0.043 0.152 3827 Planarity : 0.003 0.041 4250 Dihedral : 6.910 151.465 3506 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.93 % Favored : 98.03 % Rotamer: Outliers : 1.14 % Allowed : 16.35 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3102 helix: 1.91 (0.14), residues: 1325 sheet: -0.23 (0.24), residues: 476 loop : 0.07 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.001 HIS B 476 PHE 0.016 0.001 PHE J 34 TYR 0.023 0.001 TYR B 446 ARG 0.006 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1135) hydrogen bonds : angle 4.60524 ( 3231) covalent geometry : bond 0.00280 (24307) covalent geometry : angle 0.50641 (32878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18569.83 seconds wall clock time: 321 minutes 29.21 seconds (19289.21 seconds total)