Starting phenix.real_space_refine on Fri Jun 20 19:16:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9l_34572/06_2025/8h9l_34572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9l_34572/06_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_34572/06_2025/8h9l_34572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9l_34572/06_2025/8h9l_34572.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9l_34572/06_2025/8h9l_34572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9l_34572/06_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-5710/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: 17.26, per 1000 atoms: 0.72 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: 6.30 Conformation dependent library (CDL) restraints added in 3.4 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: 2.78 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: 8.70 Time building geometry restraints manager: 7.47 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: 43.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 59.000 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.380 ------------------------------------------------------------------------------- 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 : 3.645 Fit side-chains REVERT: B 498 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7529 (tptt) REVERT: C 124 LYS cc_start: 0.7947 (mmtm) cc_final: 0.7702 (mttm) REVERT: C 386 VAL cc_start: 0.8129 (m) cc_final: 0.7800 (p) REVERT: C 457 GLU cc_start: 0.7607 (tt0) cc_final: 0.7312 (mt-10) REVERT: C 471 HIS cc_start: 0.6210 (t70) cc_final: 0.5502 (t-170) REVERT: D 390 ILE cc_start: 0.8420 (mt) cc_final: 0.8212 (mm) REVERT: D 475 LYS cc_start: 0.7664 (ttpt) cc_final: 0.7425 (tmtt) REVERT: O 107 THR cc_start: 0.8274 (t) cc_final: 0.8026 (p) REVERT: O 111 VAL cc_start: 0.7598 (p) cc_final: 0.7271 (t) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 1.9104 time to fit residues: 825.1981 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 : 3.668 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.128114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100829 restraints weight = 31361.938| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.72 r_work: 0.3092 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24307 Z= 0.116 Angle : 0.520 10.242 32878 Z= 0.269 Chirality : 0.043 0.150 3827 Planarity : 0.004 0.041 4250 Dihedral : 7.677 136.535 3506 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.81 % Favored : 98.16 % Rotamer: Outliers : 1.30 % Allowed : 10.40 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.016 0.001 PHE J 34 TYR 0.013 0.001 TYR C 397 ARG 0.005 0.000 ARG F 15 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 1135) hydrogen bonds : angle 5.05929 ( 3231) covalent geometry : bond 0.00247 (24307) covalent geometry : angle 0.52018 (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 384 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 351 time to evaluate : 4.186 Fit side-chains REVERT: A 52 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8533 (mmm) REVERT: A 477 GLN cc_start: 0.8249 (mm-40) cc_final: 0.8036 (tp-100) REVERT: B 67 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8351 (mt-10) REVERT: B 353 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8098 (mm-30) REVERT: B 373 ARG cc_start: 0.8167 (mtt90) cc_final: 0.7954 (mmt90) REVERT: B 498 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7096 (tptt) REVERT: C 124 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7495 (mttm) REVERT: C 194 ASP cc_start: 0.7636 (p0) cc_final: 0.7381 (p0) REVERT: C 471 HIS cc_start: 0.5876 (t70) cc_final: 0.5170 (t-170) REVERT: F 112 LYS cc_start: 0.8327 (mttt) cc_final: 0.7989 (mttp) REVERT: F 174 ASN cc_start: 0.8375 (t0) cc_final: 0.7809 (t0) REVERT: F 205 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7517 (mp0) REVERT: F 210 ASN cc_start: 0.8764 (t0) cc_final: 0.8386 (t0) REVERT: F 397 ASP cc_start: 0.7484 (m-30) cc_final: 0.7108 (m-30) REVERT: F 400 SER cc_start: 0.7958 (OUTLIER) cc_final: 0.7467 (p) REVERT: D 249 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: D 390 ILE cc_start: 0.8025 (mt) cc_final: 0.7798 (mm) REVERT: D 431 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7236 (tpt) REVERT: D 475 LYS cc_start: 0.7417 (ttpt) cc_final: 0.7062 (tmtt) REVERT: G 233 ASP cc_start: 0.7815 (t70) cc_final: 0.7600 (t70) REVERT: O 136 THR cc_start: 0.7342 (m) cc_final: 0.7098 (p) outliers start: 33 outliers final: 11 residues processed: 366 average time/residue: 1.6175 time to fit residues: 667.1456 Evaluate side-chains 310 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 294 time to evaluate : 2.580 ------------------------------------------------------------------------------- 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: 7.9990 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 0.0020 chunk 30 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 123 optimal weight: 0.0470 chunk 303 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.7490 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.127002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099133 restraints weight = 31220.420| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.75 r_work: 0.3076 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24307 Z= 0.109 Angle : 0.491 11.143 32878 Z= 0.251 Chirality : 0.042 0.136 3827 Planarity : 0.004 0.040 4250 Dihedral : 6.969 135.664 3506 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.45 % Favored : 98.52 % Rotamer: Outliers : 1.54 % Allowed : 12.64 % Favored : 85.82 % 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: 0.44 (0.15), residues: 3102 helix: 1.31 (0.14), residues: 1327 sheet: -0.56 (0.23), residues: 480 loop : -0.35 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 476 PHE 0.017 0.001 PHE J 34 TYR 0.010 0.001 TYR O 170 ARG 0.007 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 1135) hydrogen bonds : angle 4.71729 ( 3231) covalent geometry : bond 0.00240 (24307) covalent geometry : angle 0.49103 (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 365 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 326 time to evaluate : 3.046 Fit side-chains REVERT: A 52 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8677 (mmm) REVERT: A 355 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7930 (tt0) REVERT: A 477 GLN cc_start: 0.8236 (mm-40) cc_final: 0.8027 (tp-100) REVERT: B 353 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8024 (mm-30) REVERT: B 454 ASP cc_start: 0.7911 (m-30) cc_final: 0.7675 (m-30) REVERT: B 498 LYS cc_start: 0.7750 (ttmt) cc_final: 0.7127 (tptt) REVERT: C 124 LYS cc_start: 0.7712 (mmtm) cc_final: 0.7388 (mttm) REVERT: C 224 ASP cc_start: 0.8282 (t0) cc_final: 0.7618 (t0) REVERT: C 426 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: C 471 HIS cc_start: 0.5837 (t70) cc_final: 0.5142 (t-170) REVERT: F 112 LYS cc_start: 0.8299 (mttt) cc_final: 0.7999 (mttp) REVERT: F 174 ASN cc_start: 0.8307 (t0) cc_final: 0.7820 (t0) REVERT: F 205 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7428 (mp0) REVERT: F 210 ASN cc_start: 0.8686 (t0) cc_final: 0.8285 (t0) REVERT: F 400 SER cc_start: 0.7880 (OUTLIER) cc_final: 0.7465 (p) REVERT: F 451 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: D 475 LYS cc_start: 0.7360 (ttpt) cc_final: 0.7007 (tmtt) REVERT: G 233 ASP cc_start: 0.7859 (t70) cc_final: 0.7636 (t70) REVERT: O 15 GLU cc_start: 0.7117 (mp0) cc_final: 0.6738 (mp0) REVERT: O 136 THR cc_start: 0.7154 (m) cc_final: 0.6922 (p) outliers start: 39 outliers final: 11 residues processed: 348 average time/residue: 1.7939 time to fit residues: 706.7215 Evaluate side-chains 313 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 298 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain 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 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU 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: 5.9990 chunk 96 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 304 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 349 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 430 HIS F 458 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.093139 restraints weight = 31956.501| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.72 r_work: 0.2944 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 24307 Z= 0.272 Angle : 0.610 11.708 32878 Z= 0.313 Chirality : 0.047 0.190 3827 Planarity : 0.004 0.045 4250 Dihedral : 7.928 143.745 3506 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Rotamer: Outliers : 2.32 % Allowed : 13.19 % Favored : 84.48 % 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: 0.29 (0.15), residues: 3102 helix: 1.13 (0.14), residues: 1328 sheet: -0.55 (0.23), residues: 500 loop : -0.37 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 370 PHE 0.020 0.002 PHE J 34 TYR 0.017 0.002 TYR B 446 ARG 0.007 0.001 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.05332 ( 1135) hydrogen bonds : angle 5.00328 ( 3231) covalent geometry : bond 0.00664 (24307) covalent geometry : angle 0.60989 (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 358 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 299 time to evaluate : 3.132 Fit side-chains REVERT: A 52 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8497 (mmm) REVERT: A 355 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7899 (tt0) REVERT: B 67 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8301 (mt-10) REVERT: B 353 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8038 (mm-30) REVERT: B 498 LYS cc_start: 0.7665 (ttmt) cc_final: 0.7052 (tptt) REVERT: C 124 LYS cc_start: 0.7787 (mmtm) cc_final: 0.7433 (mttm) REVERT: C 215 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8058 (mm110) REVERT: C 224 ASP cc_start: 0.8343 (t0) cc_final: 0.7600 (t0) REVERT: C 471 HIS cc_start: 0.5824 (t70) cc_final: 0.5117 (t-170) REVERT: E 29 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6748 (p0) REVERT: F 112 LYS cc_start: 0.8258 (mttt) cc_final: 0.7945 (mttp) REVERT: F 205 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7511 (mp0) REVERT: D 249 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7554 (mp10) REVERT: D 475 LYS cc_start: 0.7280 (ttpt) cc_final: 0.6921 (tmtt) REVERT: G 233 ASP cc_start: 0.7811 (t70) cc_final: 0.7569 (t70) REVERT: O 15 GLU cc_start: 0.7109 (mp0) cc_final: 0.6658 (mp0) REVERT: O 136 THR cc_start: 0.7342 (m) cc_final: 0.7125 (p) REVERT: O 168 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6782 (mt-10) outliers start: 59 outliers final: 31 residues processed: 333 average time/residue: 2.0146 time to fit residues: 756.1459 Evaluate side-chains 321 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 286 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 290 THR 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 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 184 SER 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 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: 4.9990 chunk 125 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.124961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.096910 restraints weight = 31749.008| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.76 r_work: 0.3036 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24307 Z= 0.142 Angle : 0.514 10.208 32878 Z= 0.263 Chirality : 0.043 0.155 3827 Planarity : 0.004 0.042 4250 Dihedral : 7.282 141.196 3506 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % Rotamer: Outliers : 1.77 % Allowed : 14.42 % Favored : 83.81 % 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: 0.62 (0.15), residues: 3102 helix: 1.46 (0.14), residues: 1325 sheet: -0.39 (0.24), residues: 465 loop : -0.27 (0.17), residues: 1312 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 0.011 0.001 TYR O 170 ARG 0.006 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 1135) hydrogen bonds : angle 4.78035 ( 3231) covalent geometry : bond 0.00329 (24307) covalent geometry : angle 0.51384 (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 352 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 307 time to evaluate : 2.765 Fit side-chains REVERT: A 355 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7952 (tt0) REVERT: B 353 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8060 (mm-30) REVERT: B 454 ASP cc_start: 0.7951 (m-30) cc_final: 0.7670 (m-30) REVERT: B 498 LYS cc_start: 0.7793 (ttmt) cc_final: 0.7166 (tptt) REVERT: C 124 LYS cc_start: 0.7813 (mmtm) cc_final: 0.7468 (mttm) REVERT: C 215 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8145 (mm110) REVERT: C 224 ASP cc_start: 0.8334 (t0) cc_final: 0.7676 (t0) REVERT: C 426 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: C 471 HIS cc_start: 0.5794 (t70) cc_final: 0.5058 (t-170) REVERT: E 29 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6736 (p0) REVERT: E 340 ARG cc_start: 0.8298 (mtp-110) cc_final: 0.8037 (mtt-85) REVERT: F 112 LYS cc_start: 0.8284 (mttt) cc_final: 0.7971 (mttp) REVERT: F 174 ASN cc_start: 0.8387 (t0) cc_final: 0.7804 (t0) REVERT: F 205 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7435 (mp0) REVERT: F 210 ASN cc_start: 0.8738 (t0) cc_final: 0.8328 (t0) REVERT: F 400 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7411 (p) REVERT: D 205 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7292 (tp30) REVERT: D 249 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7562 (mp10) REVERT: D 475 LYS cc_start: 0.7407 (ttpt) cc_final: 0.7064 (tmtt) REVERT: G 233 ASP cc_start: 0.7878 (t70) cc_final: 0.7666 (t70) REVERT: O 15 GLU cc_start: 0.7069 (mp0) cc_final: 0.6657 (mp0) REVERT: O 136 THR cc_start: 0.7307 (m) cc_final: 0.7070 (p) REVERT: O 168 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6799 (tt0) outliers start: 45 outliers final: 25 residues processed: 335 average time/residue: 1.6275 time to fit residues: 615.9086 Evaluate side-chains 325 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 295 time to evaluate : 2.694 ------------------------------------------------------------------------------- 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 54 GLU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 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 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 290 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 31 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 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 = 0.3495 r_free = 0.3495 target = 0.125436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.097311 restraints weight = 31254.345| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.75 r_work: 0.3013 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24307 Z= 0.164 Angle : 0.533 11.888 32878 Z= 0.273 Chirality : 0.044 0.150 3827 Planarity : 0.004 0.043 4250 Dihedral : 7.345 143.538 3506 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Rotamer: Outliers : 1.89 % Allowed : 14.73 % 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: 0.68 (0.15), residues: 3102 helix: 1.51 (0.14), residues: 1323 sheet: -0.49 (0.23), residues: 494 loop : -0.16 (0.18), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 476 PHE 0.018 0.001 PHE C 468 TYR 0.020 0.001 TYR B 446 ARG 0.006 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 1135) hydrogen bonds : angle 4.77907 ( 3231) covalent geometry : bond 0.00389 (24307) covalent geometry : angle 0.53272 (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 346 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 298 time to evaluate : 2.640 Fit side-chains REVERT: A 355 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7941 (tt0) REVERT: B 67 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: B 353 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8035 (mm-30) REVERT: B 454 ASP cc_start: 0.7956 (m-30) cc_final: 0.7668 (m-30) REVERT: B 498 LYS cc_start: 0.7782 (ttmt) cc_final: 0.7044 (tptt) REVERT: C 124 LYS cc_start: 0.7817 (mmtm) cc_final: 0.7471 (mttm) REVERT: C 224 ASP cc_start: 0.8343 (t0) cc_final: 0.7675 (t0) REVERT: C 301 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8961 (tp) REVERT: C 426 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: C 471 HIS cc_start: 0.5822 (t70) cc_final: 0.5087 (t-170) REVERT: E 29 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6749 (p0) REVERT: E 340 ARG cc_start: 0.8316 (mtp-110) cc_final: 0.8062 (mtt-85) REVERT: F 112 LYS cc_start: 0.8264 (mttt) cc_final: 0.7967 (mttp) REVERT: F 174 ASN cc_start: 0.8396 (t0) cc_final: 0.7805 (t0) REVERT: F 205 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7458 (mp0) REVERT: F 210 ASN cc_start: 0.8729 (t0) cc_final: 0.8301 (t0) REVERT: F 400 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7335 (p) REVERT: F 451 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: D 205 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7245 (tp30) REVERT: D 249 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7568 (mp10) REVERT: D 475 LYS cc_start: 0.7413 (ttpt) cc_final: 0.7059 (tmtt) REVERT: G 233 ASP cc_start: 0.7878 (t70) cc_final: 0.7660 (t70) REVERT: O 15 GLU cc_start: 0.7012 (mp0) cc_final: 0.6583 (pt0) REVERT: O 136 THR cc_start: 0.7294 (m) cc_final: 0.7075 (p) outliers start: 48 outliers final: 27 residues processed: 327 average time/residue: 1.5704 time to fit residues: 580.1253 Evaluate side-chains 319 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 2.576 ------------------------------------------------------------------------------- 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 54 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 169 optimal weight: 0.8980 chunk 228 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 243 optimal weight: 7.9990 chunk 300 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097830 restraints weight = 31602.564| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.76 r_work: 0.3049 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24307 Z= 0.126 Angle : 0.504 11.127 32878 Z= 0.257 Chirality : 0.043 0.144 3827 Planarity : 0.004 0.042 4250 Dihedral : 7.082 147.283 3506 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.93 % Favored : 98.03 % Rotamer: Outliers : 1.93 % Allowed : 15.12 % Favored : 82.95 % 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: 0.86 (0.15), residues: 3102 helix: 1.68 (0.14), residues: 1325 sheet: -0.34 (0.24), residues: 467 loop : -0.14 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 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 B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 1135) hydrogen bonds : angle 4.69080 ( 3231) covalent geometry : bond 0.00290 (24307) covalent geometry : angle 0.50361 (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 358 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 309 time to evaluate : 3.009 Fit side-chains REVERT: A 355 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7933 (tt0) REVERT: B 67 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: B 353 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8060 (mm-30) REVERT: B 415 GLN cc_start: 0.6664 (mt0) cc_final: 0.5962 (mt0) REVERT: B 454 ASP cc_start: 0.7896 (m-30) cc_final: 0.7535 (m-30) REVERT: B 498 LYS cc_start: 0.7781 (ttmt) cc_final: 0.7158 (tptt) REVERT: C 124 LYS cc_start: 0.7799 (mmtm) cc_final: 0.7463 (mttm) REVERT: C 224 ASP cc_start: 0.8343 (t0) cc_final: 0.7705 (t0) REVERT: C 301 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8928 (tp) REVERT: C 426 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: C 471 HIS cc_start: 0.5863 (t70) cc_final: 0.5156 (t-170) REVERT: E 29 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.6773 (p0) REVERT: E 340 ARG cc_start: 0.8314 (mtp-110) cc_final: 0.8064 (mtt-85) REVERT: F 112 LYS cc_start: 0.8283 (mttt) cc_final: 0.7980 (mttp) REVERT: F 174 ASN cc_start: 0.8355 (t0) cc_final: 0.7808 (t0) REVERT: F 205 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7425 (mp0) REVERT: F 217 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8155 (mptm) REVERT: F 400 SER cc_start: 0.7858 (OUTLIER) cc_final: 0.7389 (p) REVERT: F 451 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: D 249 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: D 475 LYS cc_start: 0.7405 (ttpt) cc_final: 0.7053 (tmtt) REVERT: G 233 ASP cc_start: 0.7888 (t70) cc_final: 0.7669 (t70) REVERT: O 15 GLU cc_start: 0.7037 (mp0) cc_final: 0.6591 (pt0) REVERT: O 103 SER cc_start: 0.7230 (t) cc_final: 0.6793 (p) REVERT: O 136 THR cc_start: 0.7276 (m) cc_final: 0.7051 (p) REVERT: O 168 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6534 (tt0) outliers start: 49 outliers final: 26 residues processed: 340 average time/residue: 1.5485 time to fit residues: 596.6621 Evaluate side-chains 330 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 296 time to evaluate : 2.656 ------------------------------------------------------------------------------- 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 54 GLU 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 301 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 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 217 LYS Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 262 LEU 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: 0.9990 chunk 167 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 274 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 27 GLN F 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093647 restraints weight = 31527.123| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.75 r_work: 0.2983 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1698 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= 0.244 Angle : 0.590 12.265 32878 Z= 0.302 Chirality : 0.047 0.173 3827 Planarity : 0.004 0.044 4250 Dihedral : 7.725 154.776 3506 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.52 % Rotamer: Outliers : 2.01 % Allowed : 15.36 % Favored : 82.63 % 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: 0.62 (0.15), residues: 3102 helix: 1.38 (0.14), residues: 1334 sheet: -0.40 (0.23), residues: 501 loop : -0.17 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS B 476 PHE 0.023 0.002 PHE C 468 TYR 0.019 0.002 TYR B 446 ARG 0.005 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.05032 ( 1135) hydrogen bonds : angle 4.90472 ( 3231) covalent geometry : bond 0.00592 (24307) covalent geometry : angle 0.59033 (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 334 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 283 time to evaluate : 2.603 Fit side-chains REVERT: A 355 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7915 (tt0) REVERT: B 67 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8307 (mt-10) REVERT: B 353 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8093 (mm-30) REVERT: B 498 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7066 (tptt) REVERT: C 124 LYS cc_start: 0.7789 (mmtm) cc_final: 0.7460 (mttm) REVERT: C 224 ASP cc_start: 0.8364 (t0) cc_final: 0.7661 (t0) REVERT: C 426 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: C 471 HIS cc_start: 0.5960 (t70) cc_final: 0.5228 (t-170) REVERT: E 29 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.6864 (p0) REVERT: E 128 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: E 340 ARG cc_start: 0.8341 (mtp-110) cc_final: 0.8117 (mtt-85) REVERT: F 112 LYS cc_start: 0.8316 (mttt) cc_final: 0.8011 (mttp) REVERT: F 205 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7529 (mp0) REVERT: F 217 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8195 (mptm) REVERT: D 205 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7246 (tp30) REVERT: D 249 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: D 475 LYS cc_start: 0.7395 (ttpt) cc_final: 0.7044 (tmtt) REVERT: G 233 ASP cc_start: 0.7881 (t70) cc_final: 0.7634 (t70) REVERT: O 15 GLU cc_start: 0.7085 (mp0) cc_final: 0.6631 (pt0) REVERT: O 136 THR cc_start: 0.7313 (m) cc_final: 0.7092 (p) outliers start: 51 outliers final: 31 residues processed: 315 average time/residue: 1.6147 time to fit residues: 578.0949 Evaluate side-chains 310 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 2.849 ------------------------------------------------------------------------------- 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 54 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain 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 217 LYS Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 299 optimal weight: 8.9990 chunk 275 optimal weight: 7.9990 chunk 294 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 209 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.098287 restraints weight = 31373.322| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.76 r_work: 0.3040 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1926 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= 0.141 Angle : 0.524 12.050 32878 Z= 0.267 Chirality : 0.043 0.163 3827 Planarity : 0.004 0.043 4250 Dihedral : 7.276 154.437 3506 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.97 % Favored : 98.00 % Rotamer: Outliers : 1.58 % Allowed : 15.68 % Favored : 82.75 % 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: 1.62 (0.14), residues: 1326 sheet: -0.29 (0.24), residues: 467 loop : -0.15 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS B 476 PHE 0.017 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 0.04213 ( 1135) hydrogen bonds : angle 4.75319 ( 3231) covalent geometry : bond 0.00328 (24307) covalent geometry : angle 0.52357 (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 330 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 290 time to evaluate : 2.799 Fit side-chains REVERT: A 355 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7935 (tt0) REVERT: B 67 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: B 353 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8046 (mm-30) REVERT: B 415 GLN cc_start: 0.6672 (mt0) cc_final: 0.5951 (mt0) REVERT: B 454 ASP cc_start: 0.7953 (m-30) cc_final: 0.7665 (m-30) REVERT: B 498 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7070 (tptt) REVERT: C 124 LYS cc_start: 0.7792 (mmtm) cc_final: 0.7459 (mttm) REVERT: C 224 ASP cc_start: 0.8365 (t0) cc_final: 0.7682 (t0) REVERT: C 426 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: C 471 HIS cc_start: 0.5912 (t70) cc_final: 0.5200 (t-170) REVERT: E 29 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6774 (p0) REVERT: E 340 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.8102 (mtt-85) REVERT: F 112 LYS cc_start: 0.8272 (mttt) cc_final: 0.7973 (mttp) REVERT: F 174 ASN cc_start: 0.8380 (t0) cc_final: 0.7795 (t0) REVERT: F 205 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7427 (mp0) REVERT: F 210 ASN cc_start: 0.8655 (t0) cc_final: 0.8357 (t0) REVERT: F 217 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8138 (mptm) REVERT: F 400 SER cc_start: 0.7861 (OUTLIER) cc_final: 0.7375 (p) REVERT: D 205 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7186 (tp30) REVERT: D 249 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: D 475 LYS cc_start: 0.7373 (ttpt) cc_final: 0.7021 (tmtt) REVERT: G 233 ASP cc_start: 0.7888 (t70) cc_final: 0.7653 (t70) REVERT: O 15 GLU cc_start: 0.7054 (mp0) cc_final: 0.6673 (pt0) REVERT: O 103 SER cc_start: 0.7253 (t) cc_final: 0.6808 (p) REVERT: O 136 THR cc_start: 0.7315 (m) cc_final: 0.7088 (p) outliers start: 40 outliers final: 29 residues processed: 314 average time/residue: 1.5783 time to fit residues: 560.8126 Evaluate side-chains 323 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 2.862 ------------------------------------------------------------------------------- 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 54 GLU 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 27 GLN Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 136 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 265 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 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 = 0.3484 r_free = 0.3484 target = 0.124382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.096146 restraints weight = 31597.197| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.75 r_work: 0.3026 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24307 Z= 0.172 Angle : 0.547 11.822 32878 Z= 0.279 Chirality : 0.044 0.161 3827 Planarity : 0.004 0.043 4250 Dihedral : 7.421 156.977 3506 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.13 % Favored : 97.84 % Rotamer: Outliers : 1.46 % Allowed : 15.95 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.15), residues: 3102 helix: 1.55 (0.14), residues: 1331 sheet: -0.38 (0.23), residues: 497 loop : -0.10 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.001 HIS B 476 PHE 0.032 0.001 PHE C 468 TYR 0.021 0.001 TYR B 433 ARG 0.009 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 1135) hydrogen bonds : angle 4.78783 ( 3231) covalent geometry : bond 0.00410 (24307) covalent geometry : angle 0.54714 (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 320 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 283 time to evaluate : 5.250 Fit side-chains REVERT: A 355 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7921 (tt0) REVERT: B 67 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: B 353 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8049 (mm-30) REVERT: B 454 ASP cc_start: 0.7983 (m-30) cc_final: 0.7692 (m-30) REVERT: B 498 LYS cc_start: 0.7757 (ttmt) cc_final: 0.7037 (tptt) REVERT: C 124 LYS cc_start: 0.7791 (mmtm) cc_final: 0.7450 (mttm) REVERT: C 224 ASP cc_start: 0.8366 (t0) cc_final: 0.7683 (t0) REVERT: C 426 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: C 471 HIS cc_start: 0.5947 (t70) cc_final: 0.5237 (t-170) REVERT: E 29 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.6782 (p0) REVERT: E 340 ARG cc_start: 0.8314 (mtp-110) cc_final: 0.8098 (mtt-85) REVERT: F 112 LYS cc_start: 0.8276 (mttt) cc_final: 0.7984 (mttp) REVERT: F 174 ASN cc_start: 0.8415 (t0) cc_final: 0.7815 (t0) REVERT: F 205 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7437 (mp0) REVERT: F 210 ASN cc_start: 0.8631 (t0) cc_final: 0.8312 (t0) REVERT: F 217 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8133 (mptm) REVERT: F 400 SER cc_start: 0.7873 (OUTLIER) cc_final: 0.7345 (p) REVERT: D 205 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7193 (tp30) REVERT: D 249 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: D 475 LYS cc_start: 0.7368 (ttpt) cc_final: 0.7033 (tmtt) REVERT: G 233 ASP cc_start: 0.7894 (t70) cc_final: 0.7669 (t70) REVERT: O 15 GLU cc_start: 0.7067 (mp0) cc_final: 0.6693 (pt0) REVERT: O 136 THR cc_start: 0.7330 (m) cc_final: 0.7110 (p) outliers start: 37 outliers final: 28 residues processed: 305 average time/residue: 1.9346 time to fit residues: 668.6180 Evaluate side-chains 315 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 2.909 ------------------------------------------------------------------------------- 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 54 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 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 217 LYS Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 36 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3478 r_free = 0.3478 target = 0.124342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.097075 restraints weight = 31360.338| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.69 r_work: 0.2996 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24307 Z= 0.186 Angle : 0.557 11.704 32878 Z= 0.285 Chirality : 0.045 0.162 3827 Planarity : 0.004 0.043 4250 Dihedral : 7.526 160.039 3506 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.06 % Favored : 97.90 % Rotamer: Outliers : 1.69 % Allowed : 15.71 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3102 helix: 1.51 (0.14), residues: 1330 sheet: -0.38 (0.23), residues: 497 loop : -0.13 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.001 HIS B 476 PHE 0.018 0.001 PHE J 34 TYR 0.025 0.002 TYR B 433 ARG 0.007 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 1135) hydrogen bonds : angle 4.83265 ( 3231) covalent geometry : bond 0.00447 (24307) covalent geometry : angle 0.55717 (32878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20150.86 seconds wall clock time: 352 minutes 17.39 seconds (21137.39 seconds total)